Contacts of the helix formed by residues 43 - 69 (chain A) in PDB entry 1S13
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 1.3 80.8 - - - +
44A ARG* 1.3 64.1 + - - +
45A ASP* 3.7 9.4 + - - +
46A GLY* 2.8 27.1 + - - -
47A PHE* 3.1 20.3 + - - +
155A LEU* 3.8 1.5 - - - +
221A LEU* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 1.3 74.3 - - - +
45A ASP* 1.3 60.9 + - - +
47A PHE* 3.3 3.1 + - - +
48A LYS* 2.9 38.6 + - + +
95A PHE* 5.9 0.4 - - - -
96A TRP* 3.8 26.1 - - + -
155A LEU* 3.6 37.8 + - + +
156A ASP* 3.6 7.3 + - - +
157A LEU* 3.2 32.9 - - - +
158A PRO* 3.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.2 8.9 + - - +
44A ARG* 1.3 81.8 - - - +
46A GLY* 1.3 60.0 + - - +
48A LYS* 3.7 21.0 + - - +
49A LEU* 3.2 28.7 + - + +
221A LEU* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.1 8.6 - - - -
42A VAL* 5.0 2.9 - - - -
43A THR* 2.8 21.3 + - - -
45A ASP* 1.3 74.7 - - - +
47A PHE* 1.3 64.1 + - - +
49A LEU* 3.3 5.7 + - - +
50A VAL* 3.2 26.2 + - - +
221A LEU* 3.5 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 28.0 - + - -
42A VAL* 4.5 5.9 - - + +
43A THR 3.1 13.4 + - - +
44A ARG 3.3 7.4 + - - +
46A GLY* 1.3 74.3 - - - +
48A LYS* 1.3 64.6 + - - +
50A VAL* 2.9 30.4 - - + +
51A MET* 3.1 44.3 + - + +
96A TRP* 3.6 35.9 - + + -
147A LEU* 5.1 0.9 - - + -
151A ALA* 3.7 21.1 - - + -
155A LEU* 3.8 16.4 - - + -
164A LEU* 3.8 12.6 - - + -
167A PHE* 3.8 26.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.9 34.3 + - + +
45A ASP* 3.7 20.5 + - - +
46A GLY 3.2 0.2 - - - -
47A PHE* 1.3 78.9 - - - +
49A LEU* 1.3 56.9 + - - +
51A MET* 3.2 6.9 + - - +
52A ALA* 2.9 25.1 + - - +
96A TRP* 3.2 50.5 - - + +
97A TYR* 3.0 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 3.2 9.3 + - + +
46A GLY 3.5 8.1 - - - +
47A PHE 3.2 0.2 - - - -
48A LYS* 1.3 78.8 - - - +
50A VAL* 1.3 52.2 + - - +
52A ALA* 3.6 3.5 + - - +
53A SER* 2.6 36.9 + - - -
97A TYR* 4.6 2.5 - - - +
106A PRO* 3.5 31.9 - - + -
108A THR* 5.7 0.2 - - + -
111A MET* 3.9 9.7 - - + +
217A LEU* 4.1 27.6 - - + +
220A LEU* 4.6 16.2 - - + -
221A LEU* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.4 39.9 - - + -
34A MET* 5.6 2.2 - - + -
37A PHE* 5.1 6.5 - - + -
46A GLY 3.2 3.5 + - - +
47A PHE* 2.9 46.2 - - + +
49A LEU* 1.3 74.3 - - - +
51A MET* 1.3 66.1 + - + +
53A SER* 3.3 7.7 + - - -
54A LEU* 2.8 41.3 + - + +
167A PHE* 6.3 0.2 - - + -
214A PHE* 5.3 6.1 - - + -
217A LEU* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.1 52.9 + - + +
48A LYS* 3.6 6.5 - - - +
50A VAL* 1.3 78.7 - - - +
52A ALA* 1.3 61.8 + - - +
54A LEU* 3.5 13.9 + - - +
55A TYR* 3.1 22.0 + - - +
89A LEU* 3.6 26.0 - - + +
92A ASP* 3.6 33.9 - - + +
93A LEU* 3.7 18.3 - - + +
96A TRP* 4.3 10.5 - - + +
97A TYR* 5.6 0.2 - - + -
163A GLY 4.4 3.6 - - - +
166A PHE* 3.9 9.4 - - + -
167A PHE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS 2.9 17.5 + - - +
49A LEU 3.7 5.6 - - - +
51A MET* 1.3 74.7 - - - +
53A SER* 1.3 63.9 + - - +
55A TYR* 3.2 13.3 + - - +
56A HIS* 3.1 22.6 + - + -
93A LEU* 4.2 9.6 - - - +
97A TYR* 4.1 3.8 - - + +
105A ILE* 4.5 8.7 - - + -
106A PRO* 3.9 36.8 - - + +
111A MET* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU 2.6 22.8 + - - -
50A VAL* 3.4 9.4 - - - -
52A ALA* 1.3 78.7 - - - +
54A LEU* 1.3 62.8 + - - +
56A HIS* 3.3 2.8 + - - +
57A ILE* 3.1 30.4 + - - +
111A MET* 3.3 26.7 - - - +
213A LEU* 3.7 32.9 - - - +
217A LEU* 3.8 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.8 30.2 + - + +
51A MET* 3.7 16.2 - - - +
53A SER* 1.3 77.5 - - - +
55A TYR* 1.3 56.5 - - - +
57A ILE* 3.7 8.2 - - + +
58A TYR* 2.9 47.8 + - + +
89A LEU* 3.7 14.8 - - + -
136A ARG* 4.0 31.9 - - - +
140A ASP* 5.2 0.9 - - - +
166A PHE* 3.7 29.4 - - + -
167A PHE* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET 3.1 9.5 + - - +
52A ALA 3.2 8.0 + - - +
54A LEU* 1.3 76.6 - - - +
56A HIS* 1.3 72.9 + + - +
58A TYR* 3.8 1.4 - - - +
59A VAL* 2.9 57.8 + - + +
86A LYS* 4.5 6.7 - - + +
89A LEU* 3.8 24.1 - - + +
90A GLU* 4.0 16.6 + - + -
93A LEU* 3.4 25.1 - - + -
101A TRP* 3.6 32.5 - + - -
102A GLN* 4.4 8.1 + - - -
105A ILE* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 3.1 21.4 + - - -
53A SER 3.3 3.6 + - - +
55A TYR* 1.3 86.9 - + - +
57A ILE* 1.3 68.5 + - + +
59A VAL* 3.3 5.7 + - + +
60A ALA* 3.1 24.6 + - - +
105A ILE* 3.9 24.2 - - + +
106A PRO 3.0 28.1 + - - -
107A TYR* 3.5 38.6 - + + +
111A MET* 4.0 10.4 - - + -
115A VAL* 3.7 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.1 25.4 + - - +
54A LEU* 3.7 11.4 - - + +
56A HIS* 1.3 78.3 - - + +
58A TYR* 1.3 59.4 + - - +
60A ALA 3.3 0.3 + - - -
61A LEU* 2.9 25.6 + - + +
111A MET* 5.5 4.3 - - - +
114A TYR* 3.5 50.9 - - + -
115A VAL* 4.6 3.8 - - + -
118A LEU* 3.5 17.9 - - + +
136A ARG* 3.7 37.2 - - + +
210A ASN* 4.8 0.9 - - - +
213A LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.9 30.7 + - + +
55A TYR 4.1 0.4 - - - +
57A ILE* 1.3 75.5 - - + +
59A VAL* 1.3 65.1 + - - +
61A LEU* 4.3 14.1 - - + -
62A GLU* 2.9 53.4 + - + +
85A ARG* 3.9 9.3 - - + +
86A LYS* 4.9 4.5 - - - +
89A LEU* 3.8 23.1 - - + -
136A ARG* 3.6 29.6 + - - -
137A TYR* 3.3 34.7 + + - -
140A ASP* 2.5 35.4 + - - +
166A PHE* 3.5 20.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 2.9 55.8 + - + +
56A HIS* 3.3 7.6 + - + +
58A TYR* 1.3 76.4 - - - +
60A ALA* 1.3 65.4 + - - +
62A GLU* 4.0 1.3 - - - +
63A GLU* 3.1 44.9 + - + +
86A LYS* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS 3.1 10.5 + - - +
57A ILE 3.5 8.1 - - - +
59A VAL* 1.3 83.1 - - - +
61A LEU* 1.3 62.6 + - - +
63A GLU* 3.3 3.0 + - - +
64A GLU* 3.2 27.4 + - - +
115A VAL* 4.0 15.0 - - + -
118A LEU* 3.8 20.2 - - + -
119A HIS* 3.9 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 2.9 19.1 + - + +
58A TYR* 4.0 10.8 - - + +
60A ALA* 1.3 75.8 - - - +
62A GLU* 1.3 57.9 + - - +
64A GLU* 3.3 4.5 + - - +
65A ILE* 3.0 45.5 + - + +
118A LEU* 4.1 15.4 - - + +
129A LEU* 4.0 24.7 - - + -
132A HIS* 4.2 20.0 - - + +
133A ALA* 4.3 5.8 - - - +
136A ARG* 4.0 30.3 - - + -
137A TYR* 4.0 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 2.9 29.4 + - + +
59A VAL* 4.2 2.5 - - - +
61A LEU* 1.3 72.7 - - - +
63A GLU* 1.3 64.6 + - - +
65A ILE* 3.9 8.8 - - + +
66A GLU* 3.1 27.7 + - - +
84A HIS* 3.2 13.5 - - - +
85A ARG* 2.7 27.3 + - - -
86A LYS* 3.1 33.3 + - + +
137A TYR* 2.7 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.1 41.4 + - + +
60A ALA* 3.5 5.6 - - - +
61A LEU 3.2 0.2 - - - -
62A GLU* 1.3 77.0 - - - +
64A GLU* 1.3 66.5 + - - +
66A GLU* 3.2 8.9 + - - +
67A ARG* 3.1 27.7 + - - +
119A HIS* 3.7 23.4 + - + -
123A ARG* 5.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.2 13.5 + - - +
61A LEU* 3.8 7.4 - - - +
63A GLU* 1.3 79.7 - - - +
65A ILE* 1.3 63.6 + - - +
67A ARG* 2.8 42.1 + - - +
68A ASN* 2.9 29.8 + - - +
118A LEU* 3.5 22.0 - - + +
119A HIS* 2.6 35.9 + - - +
122A GLY* 3.2 26.8 - - - -
123A ARG* 3.7 3.0 + - - +
129A LEU* 3.8 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.0 34.7 + - + +
62A GLU* 3.9 7.6 - - - +
63A GLU 3.2 0.4 - - - -
64A GLU* 1.3 72.7 - - - +
66A GLU* 1.3 61.5 + - - +
68A ASN 3.2 1.2 + - - -
69A LYS* 2.8 27.7 + - - +
74A PHE* 3.5 38.1 - - + -
78A TYR* 3.6 23.3 - - + -
79A PHE 6.0 0.2 - - - +
129A LEU* 3.8 13.2 - - + -
133A ALA* 4.7 1.1 - - + -
137A TYR* 3.8 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU 3.1 16.9 + - - +
63A GLU* 3.2 11.4 + - - +
65A ILE* 1.3 77.8 - - - +
67A ARG* 1.3 62.2 + - - +
69A LYS* 2.7 56.6 + - - +
78A TYR* 2.6 32.7 + - - -
80A PRO* 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 3.1 18.1 + - - +
64A GLU* 2.8 35.3 + - - +
65A ILE 3.2 0.2 - - - -
66A GLU* 1.3 79.1 - - - +
68A ASN* 1.3 63.4 + - - +
69A LYS* 5.1 1.0 - - - +
70A GLU 5.2 0.7 + - - -
122A GLY 3.7 20.4 - - - -
123A ARG* 3.3 44.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 2.9 25.4 + - - +
65A ILE 3.5 2.5 - - - +
67A ARG* 1.3 84.6 + - - +
69A LYS* 1.3 66.0 + - - +
70A GLU 3.0 4.0 - - - -
71A SER* 2.8 31.2 + - - +
73A VAL* 5.4 0.2 - - + -
74A PHE* 3.8 21.3 - - + +
122A GLY* 3.1 27.8 + - - +
126A PRO* 3.6 30.6 - - + +
129A LEU* 4.4 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE 2.8 18.3 + - - +
66A GLU* 2.7 42.5 + - - +
67A ARG 5.0 1.1 - - - +
68A ASN* 1.3 71.5 - - - +
70A GLU* 1.3 77.9 + - + +
74A PHE* 4.9 2.5 - - - -
75A ALA* 3.3 22.5 - - - +
78A TYR* 3.6 48.7 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il