Contacts of the helix formed by residues 60 - 80 (chain A) in PDB entry 3DC5
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 LEU 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.0 12.1 - - + +
44A LYS* 3.6 48.5 - - + +
45A LEU* 3.6 28.0 - - + +
48A ALA* 4.2 8.3 - - + -
56A GLU* 3.0 36.1 + - + +
57A ALA 4.0 0.4 - - - -
58A ILE 3.1 1.0 - - - -
59A ALA* 1.3 76.9 - - - +
61A GLN* 1.3 63.6 + - - +
62A PRO 3.5 0.4 - - - -
63A ALA* 3.2 13.5 + - + +
64A LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.6 2.0 - - + -
57A ALA 3.6 9.4 - - - +
58A ILE* 3.1 22.6 + - - +
60A LEU* 1.3 75.3 - - - +
62A PRO* 1.3 72.3 - - + +
64A LEU* 3.1 1.6 + - - -
65A LYS* 2.9 20.1 + - - +
45C LEU* 5.2 1.8 - - - +
61C GLN* 3.1 70.5 + - + +
64C LEU* 3.4 33.1 - - - +
65C LYS* 3.6 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE 3.8 4.5 - - - +
59A ALA* 3.4 17.5 - - - +
60A LEU 3.7 0.4 - - - -
61A GLN* 1.3 93.0 - - + +
63A ALA* 1.3 55.5 + - - +
65A LYS* 3.3 16.4 + - + +
66A PHE* 2.9 31.1 + - - +
61C GLN* 5.0 0.2 - - - +
65C LYS* 6.1 2.9 - - - +
146C GLU* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.3 27.4 - - + +
59A ALA 5.1 0.8 + - - +
60A LEU* 3.2 15.8 + - + +
61A GLN 3.1 0.8 - - - -
62A PRO* 1.3 76.9 - - - +
64A LEU* 1.3 60.0 + - - +
66A PHE* 4.4 3.6 - - - -
67A ASN* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.7 27.4 - - + -
41A ILE* 3.7 17.4 - - + +
42A GLU* 3.9 17.9 - - + +
45A LEU* 4.5 21.1 - - + -
60A LEU 3.1 9.8 + - - +
61A GLN* 3.1 2.5 + - - +
63A ALA* 1.3 74.9 - - - +
65A LYS* 1.3 59.1 + - - +
68A GLY* 2.7 33.1 + - - +
45C LEU* 5.9 1.8 - - + -
49C VAL* 5.9 1.8 - - + -
54C LEU* 4.1 10.3 - - + -
57C ALA* 4.4 19.1 - - + -
58C ILE* 3.9 15.2 - - + +
61C GLN* 3.3 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN 2.9 9.8 + - - +
62A PRO* 3.8 12.8 + - - +
64A LEU* 1.3 76.7 - - - +
66A PHE* 1.3 61.4 + - - +
69A GLY* 2.7 28.4 + - - -
142A GLN 3.9 2.8 - - - +
143A ASP* 2.9 40.0 + - + +
144A PRO* 4.2 7.0 - - + -
146A GLU* 5.5 2.2 - - - +
58C ILE* 3.8 31.9 - - + +
61C GLN* 3.6 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.8 19.5 - + - -
62A PRO 2.9 17.8 + - - +
63A ALA* 3.8 5.4 - - - +
65A LYS* 1.3 79.2 - - - +
67A ASN* 1.3 74.6 + - - +
70A GLY* 2.8 22.5 + - - -
141A ASN* 4.4 11.0 - - + -
142A GLN* 3.2 29.0 - - + +
143A ASP* 6.0 0.4 - - - -
157A TRP* 3.7 39.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 5.6 0.4 - - - +
34A TYR* 3.5 42.7 - - - +
37A ASN* 3.4 26.4 + - - +
38A LEU* 3.8 12.3 - - + +
41A ILE* 2.8 27.3 - - + +
63A ALA* 2.9 19.0 + - - +
64A LEU 4.6 0.2 - - - +
66A PHE* 1.3 88.3 - - - +
68A GLY* 1.3 60.9 + - - +
70A GLY 3.2 0.3 + - - -
71A HIS* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.7 11.6 - - - +
64A LEU 2.7 22.1 + - - -
67A ASN* 1.3 72.9 - - - +
69A GLY* 1.3 56.8 + - - +
71A HIS* 3.2 3.6 + - - +
72A ILE* 2.9 32.1 + - - +
54C LEU* 3.6 23.7 - - - +
58C ILE* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 2.7 19.8 + - - -
68A GLY* 1.3 71.3 - - - +
70A GLY* 1.3 54.3 + - - -
71A HIS 3.3 0.2 + - - -
72A ILE* 3.3 3.0 + - - +
73A ASN* 2.8 35.8 + - - -
142A GLN 3.2 24.2 - - - -
144A PRO* 4.1 16.2 - - - -
58C ILE* 3.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 4.4 0.2 - - - -
34A TYR* 3.8 13.9 - - - -
66A PHE 2.8 21.2 + - - -
67A ASN 3.2 3.2 + - - -
69A GLY* 1.3 72.5 - - - +
71A HIS* 1.3 56.7 + - - +
74A HIS* 2.6 40.1 + - - +
142A GLN* 3.5 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 3.9 20.4 + + + +
3A THR 3.4 25.9 + - - -
5A PRO* 4.1 2.9 - - + -
31A HIS* 2.9 29.9 + - - -
34A TYR* 4.1 2.2 - - + +
35A VAL* 3.5 14.1 - - + +
38A LEU* 3.9 25.6 - - + -
67A ASN 3.0 13.6 + - - +
68A GLY 3.2 6.9 + - - +
70A GLY* 1.3 74.6 - - - +
72A ILE* 1.3 64.8 + - + +
75A SER* 2.8 46.7 + - - -
54C LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 2.9 21.7 + - - +
69A GLY* 3.7 4.9 - - - +
71A HIS* 1.3 80.8 - - + +
73A ASN* 1.3 71.8 + - - +
75A SER* 3.4 4.4 + - - -
76A ILE* 3.1 41.5 + - + +
144A PRO* 4.4 13.2 - - + -
150A PRO* 6.0 0.7 - - + -
54C LEU* 4.1 13.9 - - + -
55C LYS* 3.8 43.1 - - + +
58C ILE* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 2.8 18.5 + - - +
70A GLY 4.0 0.2 - - - +
72A ILE* 1.3 79.3 - - - +
74A HIS* 1.3 58.1 + - - +
76A ILE* 3.2 4.3 + - - +
77A PHE* 2.9 28.1 + - - +
122A TRP* 3.4 34.2 - - + +
124A TRP* 3.9 21.3 - - + -
142A GLN* 3.0 45.6 + - - +
143A ASP 3.9 4.8 + - - -
144A PRO* 3.7 17.3 - - - +
145A LEU 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.3 19.6 + + - -
30A HIS* 5.2 0.2 - - - +
31A HIS* 3.5 28.3 - + + +
34A TYR* 3.3 28.6 - + - -
70A GLY* 2.6 28.6 + - - +
73A ASN* 1.3 75.7 - - - +
75A SER* 1.3 64.2 + - - +
77A PHE* 3.2 6.6 + + - +
78A TRP* 3.1 40.5 + + + -
122A TRP* 3.7 7.8 - + - -
142A GLN* 3.3 20.2 - - - -
155A ASP* 3.5 3.1 + - - -
159A HIS* 3.9 0.8 + - - -
195A MN 2.2 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.8 9.9 - - - +
31A HIS* 3.4 16.5 - - - -
71A HIS* 2.8 37.5 + - - -
72A ILE* 3.7 5.4 - - - -
73A ASN 3.2 0.2 - - - -
74A HIS* 1.3 79.9 - - - +
76A ILE* 1.3 63.3 + - - +
78A TRP* 3.6 10.3 + - - +
79A THR* 3.6 18.9 + - - +
188A ARG* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.1 32.9 + - + +
73A ASN 3.6 5.4 - - - +
74A HIS 3.2 0.2 - - - -
75A SER* 1.3 74.8 - - - +
77A PHE* 1.3 66.8 - - - +
79A THR* 2.6 21.7 + - - -
80A ASN* 3.1 24.1 + - - +
124A TRP* 3.8 22.4 - - + -
150A PRO* 3.6 32.5 - - + -
151A LEU 5.1 1.1 - - - +
188A ARG* 3.8 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 5.0 5.2 - - + -
23A MET* 6.0 0.7 - - + -
26A HIS* 4.0 16.4 - + - -
73A ASN 2.9 17.5 + - - +
74A HIS* 3.2 6.9 + + - +
76A ILE* 1.3 77.0 - - - +
78A TRP* 1.3 85.5 + + - +
80A ASN* 2.9 22.9 + - + +
81A LEU* 3.4 34.9 - - + +
122A TRP* 3.8 23.3 - + + -
124A TRP* 5.8 0.4 - - - -
153A GLY 3.3 28.3 - - - -
155A ASP* 3.8 18.4 - - + -
160A ALA* 5.4 0.4 - - + -
172A TYR* 3.7 21.8 - - - -
176A ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.3 12.3 - - + -
6A ASP 5.5 0.9 - - - +
7A LEU* 3.5 26.0 - - + -
8A PRO* 3.5 15.3 - - + +
9A PHE* 3.4 23.8 - + + -
23A MET* 3.6 31.6 - - + -
26A HIS* 3.4 48.5 - + + -
27A HIS* 3.8 22.5 + - + -
31A HIS* 2.9 33.1 + + + -
74A HIS* 3.1 29.9 + + + -
75A SER* 3.6 8.9 + - - +
76A ILE 3.2 0.4 - - - -
77A PHE* 1.3 94.1 - + - +
79A THR* 1.3 62.0 + - + +
80A ASN 3.4 0.5 + - - -
81A LEU* 3.5 9.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.3 13.9 - - + -
75A SER 3.6 13.5 - - - +
76A ILE 2.6 18.5 + - - -
78A TRP* 1.3 76.6 - - + +
80A ASN* 1.3 56.5 + - - +
81A LEU 3.3 0.7 - - - -
181A ASN* 3.1 12.9 + - - -
184A ASN* 3.0 41.4 + - - +
188A ARG* 2.8 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.1 26.0 + - - +
77A PHE* 2.9 13.7 + - - +
79A THR* 1.3 76.4 - - - +
81A LEU* 1.3 53.1 + - + +
151A LEU 3.2 18.4 + - - -
152A PHE* 3.4 28.7 - - + -
153A GLY* 2.9 29.3 + - - +
180A ALA* 3.7 1.6 - - - -
181A ASN* 2.7 32.6 + - - +
184A ASN* 2.9 22.5 + - - -
185A ILE* 4.4 2.0 - - - +
188A ARG* 3.7 5.9 - - - +
----------------------------------------------------------
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