Contacts of the helix formed by residues 72 - 94 (chain A) in PDB entry 1X3A
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 LYS 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.9 0.9 - - - -
68A PRO* 4.9 8.3 - - + -
71A VAL* 1.3 75.8 - - - +
73A GLU* 1.3 67.9 + - - +
74A GLU* 2.6 12.6 + - + +
75A VAL* 2.8 30.9 + - + +
76A PHE 2.9 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.4 7.5 - - + -
46A TYR* 3.6 28.4 - - - -
63A ARG* 3.3 27.7 + - - +
67A VAL* 3.3 23.3 - - + +
68A PRO* 5.7 0.2 - - - +
72A LYS* 1.3 70.4 - - - +
74A GLU* 1.3 62.0 + - - +
76A PHE* 3.7 3.5 + - - +
77A TRP* 3.0 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.5 4.1 - - + -
42A PHE* 3.3 53.1 - - + +
72A LYS* 2.6 13.4 + - + +
73A GLU* 1.3 73.2 - - - +
75A VAL* 1.3 72.6 + - + +
77A TRP* 2.9 15.2 + - - +
78A ARG* 3.0 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 6.0 0.9 - - - +
31A ASP* 5.7 4.9 - - + -
71A VAL* 3.8 17.5 - - + -
72A LYS* 2.8 30.5 + - + +
74A GLU* 1.3 76.9 - - + +
76A PHE* 1.3 50.5 + - - +
78A ARG* 2.6 46.4 + - - +
79A ASN* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 2.7 66.2 - + + -
59A LEU* 4.0 6.3 - - + -
63A ARG* 3.4 45.1 - - + -
66A LEU* 4.7 0.9 - - + -
67A VAL* 3.6 24.2 - - + -
71A VAL* 3.0 20.0 - - + +
72A LYS 2.9 8.8 + - - +
73A GLU* 3.8 4.7 - - - +
75A VAL* 1.3 74.1 - - - +
77A TRP* 1.3 84.5 + + - +
79A ASN* 2.4 24.8 - - - +
80A TYR* 3.0 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.5 10.9 - - + -
42A PHE* 4.0 14.8 - + + -
45A MET 4.9 3.6 - - - +
46A TYR* 4.6 8.4 + + - -
49A ALA* 3.3 37.6 - - + +
50A LEU* 6.3 0.4 - - - +
52A MET* 5.3 0.9 - - + -
53A LEU* 3.5 43.5 - - + -
59A LEU* 4.1 6.7 - - + -
63A ARG* 3.4 28.9 - - - +
73A GLU* 3.0 34.4 + - + +
74A GLU 2.9 8.4 + - - +
76A PHE* 1.3 90.4 - + - +
78A ARG* 1.3 59.7 + - - +
80A TYR* 3.8 31.4 - + - -
81A PHE* 3.0 39.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.8 13.1 - - - +
32A PRO* 4.1 32.5 + - - +
38A PHE* 4.0 16.9 + - - -
40A PHE* 3.2 40.1 - - + +
74A GLU* 3.0 7.3 + - + +
75A VAL* 2.6 40.2 + - - +
77A TRP* 1.3 70.6 - - - +
79A ASN* 1.3 64.7 + - - +
81A PHE* 3.5 2.3 + - - +
82A TYR* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN 3.7 3.4 - - - +
28A PHE* 2.9 34.6 + - - +
29A LEU 4.9 1.4 + - - -
30A ARG 3.1 24.9 + - - +
31A ASP* 4.6 5.4 - - - +
32A PRO* 4.7 1.8 - - + -
71A VAL* 4.7 0.2 - - - +
75A VAL* 2.7 42.3 + - - +
76A PHE* 2.4 25.9 - - - +
78A ARG* 1.3 75.1 - - - +
80A TYR* 1.3 69.3 + - - +
82A TYR* 3.2 19.5 - - - +
83A ARG* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.2 31.5 + - + +
21A LEU* 3.6 29.6 - - + +
22A SER* 3.8 4.7 + - - -
27A ASN* 4.1 12.1 - - - -
28A PHE* 3.8 19.5 - + + -
52A MET* 5.0 10.3 - - + +
56A ASP* 4.7 3.5 + - - -
59A LEU* 3.5 41.4 - - + +
76A PHE* 3.0 22.0 + + + +
77A TRP* 3.8 23.3 - + - +
79A ASN* 1.3 86.5 + - - +
81A PHE* 1.3 73.5 + + - +
83A ARG* 3.3 6.3 + - - +
84A VAL* 3.3 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.4 5.4 - - + -
40A PHE* 3.7 20.2 - + + -
45A MET* 3.1 56.8 - - + -
48A VAL* 4.8 4.3 - - + -
49A ALA* 4.2 22.2 - - + -
52A MET* 4.4 22.9 - - + -
77A TRP* 3.0 31.0 + + + +
78A ARG 3.5 2.8 + - - +
80A TYR* 1.3 81.4 - + - +
82A TYR* 1.3 59.2 + - - +
84A VAL* 2.5 42.4 + - + -
85A SER* 2.8 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 3.4 32.7 - - + +
33A PRO* 4.2 8.7 - - + +
36A VAL* 4.2 22.0 - - + +
38A PHE* 3.4 46.9 - + + -
78A ARG 3.0 15.7 + - - +
79A ASN* 3.2 11.9 - - - +
81A PHE* 1.3 76.7 - - - +
83A ARG* 1.3 99.8 + - - +
85A SER* 3.6 4.3 + - - -
86A LEU* 3.2 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.2 24.5 - - + -
27A ASN* 3.8 14.0 + - + +
30A ARG* 2.9 53.1 + - - +
31A ASP* 3.8 15.2 + - - +
32A PRO* 4.3 0.8 - - - +
33A PRO* 5.9 0.4 - - - +
79A ASN* 3.4 22.6 + - - +
80A TYR* 3.3 8.6 + - - +
81A PHE 3.1 0.6 - - - -
82A TYR* 1.3 104.8 - - + +
84A VAL* 1.3 67.8 + - - +
86A LEU* 3.2 27.6 + - + +
87A ILE* 3.2 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.6 37.7 - - + -
21A LEU* 3.8 10.3 - - + -
52A MET* 5.3 4.7 - - + -
80A TYR* 3.3 22.9 + - + +
81A PHE* 2.5 32.4 + - + +
83A ARG* 1.3 69.4 - - - +
85A SER* 1.3 59.0 + - - +
87A ILE* 2.5 35.2 + - - +
88A LYS* 3.0 35.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.3 18.4 - - - -
81A PHE* 2.8 12.6 + - - -
82A TYR 3.8 8.7 - - - -
84A VAL* 1.3 73.9 - - - +
86A LEU* 1.3 59.2 + - - +
88A LYS* 4.0 12.3 - - - +
89A GLN* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 6.4 1.3 - - + -
82A TYR* 3.2 46.4 - - + +
83A ARG* 3.2 19.5 - - + +
84A VAL 2.8 0.8 + - - -
85A SER* 1.3 79.8 - - - +
87A ILE* 1.3 57.2 + - + +
89A GLN* 3.9 4.5 - - + +
90A SER* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.0 16.0 - - + +
17A GLN* 3.1 60.1 + - + +
18A ILE* 4.1 12.3 - - + +
21A LEU* 4.0 19.5 - - + -
83A ARG* 3.3 19.3 - - + +
84A VAL* 2.5 23.0 + - - +
86A LEU* 1.3 70.2 - - + +
88A LYS* 1.3 66.4 + - - +
90A SER* 3.3 18.3 - - - -
91A ALA 3.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.7 33.5 - - + +
18A ILE* 4.4 4.9 - - + -
84A VAL* 3.0 37.6 + - + +
85A SER* 4.0 7.5 - - - +
87A ILE* 1.3 70.7 - - - +
89A GLN* 1.3 67.6 + - - +
91A ALA* 3.1 21.8 + - - +
92A GLN* 4.1 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 2.8 28.7 + - - +
86A LEU* 3.9 6.3 - - + +
88A LYS* 1.3 72.0 - - - +
90A SER* 1.3 66.2 + - - +
92A GLN* 2.8 31.4 + - - +
93A LEU* 2.9 24.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 3.0 16.4 + - - -
87A ILE* 3.3 13.7 - - - -
89A GLN* 1.3 74.9 - - - +
91A ALA* 1.3 66.6 + - - +
92A GLN 2.7 2.3 + - - -
93A LEU* 2.9 17.6 + - - +
94A THR* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 5.9 5.3 - - + +
10A ASP* 4.3 19.2 - - + +
14A ILE* 3.7 24.7 - - + -
87A ILE 3.6 2.0 + - - -
88A LYS 3.1 15.7 + - - +
90A SER* 1.3 78.7 - - - +
92A GLN* 1.3 59.1 + - + +
94A THR* 3.5 16.2 - - - +
95A SER* 5.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 4.1 0.6 + - - +
89A GLN* 2.8 24.3 + - - +
90A SER 2.7 2.4 + - - -
91A ALA* 1.3 72.6 - - + +
93A LEU* 1.3 55.8 + - - +
94A THR 2.9 2.0 - - - -
95A SER* 2.5 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 2.9 24.1 + - + +
90A SER* 3.7 17.9 - - - +
92A GLN* 1.3 76.5 - - - +
94A THR* 1.3 57.2 + - - +
95A SER* 2.9 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 2.8 33.1 + - - +
91A ALA* 3.5 15.3 - - - +
92A GLN 2.8 3.0 + - - -
93A LEU* 1.3 70.8 - - - +
95A SER* 1.3 66.3 + - - +
96A GLY* 3.1 6.2 + - - -
----------------------------------------------------------
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