Contacts of the helix formed by residues 57 - 75 (chain A) in PDB entry 4H7Y
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 ASN 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.5 15.5 - - - +
14A GLU* 3.0 26.8 + - - +
54A TYR* 2.9 32.8 + - + +
55A GLY 3.5 0.4 - - - -
56A GLN* 1.3 77.3 - - - +
58A GLU* 1.3 63.9 + - - +
59A SER* 3.0 13.9 + - - -
60A PHE* 3.0 23.8 + - + +
61A ALA* 3.1 21.0 + - - +
90A CYS* 4.8 0.2 - - - -
93A PHE* 4.0 1.4 - - - -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN 3.6 4.2 + - - -
57A ASN* 1.3 73.7 + - - +
59A SER* 1.3 57.2 + - - +
61A ALA* 3.2 3.3 + - - +
62A ARG* 3.0 55.8 + - - +
93A PHE* 3.7 31.8 - - + -
95A PHE* 4.3 13.6 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.8 26.2 - - - -
14A GLU* 3.6 20.5 + - - +
17A LEU* 3.9 17.8 - - - +
57A ASN* 3.0 9.2 + - - -
58A GLU* 1.3 75.7 - - - +
60A PHE* 1.3 61.7 + - - +
62A ARG* 3.1 18.1 + - - +
63A ILE* 2.9 32.8 + - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.6 9.1 - - + +
46A ILE* 5.4 6.1 - - + -
49A LEU* 3.6 44.0 - - + -
51A PRO* 3.7 36.8 - - + -
54A TYR* 3.5 35.2 - + + -
57A ASN* 3.0 17.4 + - - +
59A SER* 1.3 76.9 - - - +
61A ALA* 1.3 63.0 + - - +
63A ILE* 3.3 6.2 + - + +
64A GLN* 3.1 58.2 + - + +
89A ASN* 4.2 3.1 - - + -
90A CYS* 3.5 23.6 - - - -
81D ASP* 4.2 0.7 - - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASN 3.1 8.5 + - - +
58A GLU 3.4 8.7 - - - +
60A PHE* 1.3 79.1 - - - +
62A ARG* 1.3 57.0 + - - +
64A GLN* 3.3 3.8 + - - +
65A VAL* 3.0 32.6 + - - +
86A ALA* 6.2 0.2 - - - -
90A CYS* 3.7 21.9 - - + -
93A PHE* 3.7 27.1 - - + -
95A PHE* 3.6 17.5 - - + -
96A VAL* 4.0 3.3 - - + +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.6 31.4 - - + +
21A LEU* 5.5 4.8 - - - +
58A GLU* 3.0 46.5 + - - +
59A SER* 3.1 23.1 + - - +
61A ALA* 1.3 74.1 - - - +
63A ILE* 1.3 60.2 + - - +
65A VAL* 4.0 0.8 - - - +
66A ARG* 2.9 40.5 + - + +
95A PHE* 3.7 23.1 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.5 27.8 - - + +
16A TRP* 3.8 12.8 - - + -
17A LEU* 3.9 17.9 - - + +
20A LEU* 4.3 5.8 - - + -
42A TYR* 3.6 24.1 - - + -
45A ALA* 4.3 10.1 - - + -
46A ILE* 4.0 24.0 - - + +
49A LEU* 3.7 26.2 - - + -
59A SER 2.9 16.3 + - - +
60A PHE* 3.6 10.1 - - + +
61A ALA 3.3 0.2 - - - -
62A ARG* 1.3 77.5 - - - +
64A GLN* 1.3 57.7 + - + +
66A ARG 3.5 0.2 + - - -
67A PHE* 3.0 24.6 + - - +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.8 17.3 - - + +
60A PHE* 3.1 42.7 + - + +
61A ALA* 3.9 3.8 - - - +
62A ARG 3.3 0.2 - - - -
63A ILE* 1.3 77.6 - - - +
65A VAL* 1.3 58.5 + - - +
67A PHE* 3.3 9.1 + - - +
68A ALA* 3.0 26.7 + - - +
82A TYR 4.7 1.6 - - - +
85A MET* 3.7 21.5 - - + +
86A ALA* 3.6 31.7 - - + +
89A ASN* 2.9 24.3 + - - +
90A CYS* 5.0 1.5 - - - -
81D ASP* 3.2 23.2 + - - -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 19.5 + - - +
62A ARG 4.0 2.7 - - - +
64A GLN* 1.3 72.7 - - - +
66A ARG* 1.3 64.0 + - + +
68A ALA* 3.2 7.1 + - - +
69A GLU* 2.8 42.3 + - - +
83A PHE* 6.1 1.1 - - + -
86A ALA* 4.1 11.4 - - + -
95A PHE* 3.8 17.7 - - + -
96A VAL* 3.7 33.9 - - + +
99A SER* 3.4 26.9 - - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.2 4.5 - - + -
21A LEU* 4.9 4.3 - - + -
24A GLU* 4.7 2.2 + - - -
42A TYR* 3.4 32.1 - - + +
62A ARG* 2.9 27.5 + - + +
65A VAL* 1.3 78.4 - - + +
67A PHE* 1.3 57.3 + - - +
69A GLU* 2.4 36.9 + - - +
70A LEU* 2.9 52.7 + - - +
29B PRO* 3.6 38.6 + - - +
30B LEU 2.9 32.3 + - - -
31B SER* 4.0 3.4 - - - -
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.7 33.4 - - + -
42A TYR* 3.6 26.0 - - + -
43A SER* 4.1 13.0 - - - -
46A ILE* 3.8 20.0 - - + -
63A ILE 3.0 14.2 + - - +
64A GLN 3.5 7.2 - - - +
65A VAL 3.2 0.2 - - - -
66A ARG* 1.3 78.3 - - - +
68A ALA* 1.3 58.1 + - - +
70A LEU* 3.4 4.3 + - - +
71A LYS* 2.9 46.8 + - + +
82A TYR* 3.6 28.7 - + + -
85A MET* 4.5 3.8 - - + -
85D MET* 3.6 29.2 - - + -
88D ALA* 4.0 15.3 - - + -
89D ASN* 5.6 0.7 - - - -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN 3.0 14.8 + - - +
65A VAL* 3.6 7.0 - - - +
67A PHE* 1.3 75.8 - - - +
69A GLU* 1.3 58.3 + - - +
71A LYS* 3.2 3.4 + - - +
72A ALA* 2.9 24.1 + - - +
79A ALA* 4.3 0.3 - - - +
82A TYR* 3.8 30.1 - - + +
83A PHE* 3.5 43.6 - - + -
86A ALA* 5.5 0.7 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 2.8 31.1 + - - +
66A ARG* 2.4 42.5 + - - +
68A ALA* 1.3 73.2 - - - +
70A LEU* 1.3 61.7 + - - +
72A ALA* 3.2 13.5 + - - +
73A ILE* 3.4 18.3 + - - +
83A PHE* 4.0 10.1 - - + -
99A SER* 2.7 33.9 + - - +
102A GLN* 6.1 0.3 - - - +
30B LEU 4.9 0.9 - - - +
31B SER* 4.2 14.4 - - - -
32B ASP 4.9 2.7 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 5.0 1.3 - - - +
35A LEU* 3.6 24.8 - - + +
38A LEU* 4.0 18.6 - - + -
39A ILE* 3.7 23.9 - - + +
42A TYR* 3.7 36.3 - - + -
66A ARG* 2.9 37.6 + - - +
67A PHE* 3.8 4.5 - - - +
69A GLU* 1.3 75.0 - - - +
71A LYS* 1.3 59.6 + - - +
73A ILE* 3.1 11.7 + - + +
74A GLN* 2.9 27.5 + - - +
30B LEU* 3.9 18.6 - - + +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 3.8 21.2 - - + +
67A PHE* 2.9 33.3 + - + +
68A ALA 3.2 4.2 + - - +
70A LEU* 1.3 75.3 - - - +
72A ALA* 1.3 57.6 + - - +
74A GLN* 2.7 30.3 + - - +
75A GLU* 2.6 50.6 + - - +
78A ASP* 6.3 0.7 - - - -
79A ALA* 3.7 5.6 - - + -
82A TYR* 3.8 45.3 - - + -
88D ALA* 3.8 26.3 + - - +
89D ASN* 5.8 0.6 + - - -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 2.9 13.2 + - - +
69A GLU* 3.4 12.6 - - - +
70A LEU 3.1 0.4 - - - -
71A LYS* 1.3 76.9 - - - +
73A ILE* 1.3 59.9 + - + +
76A PRO* 3.2 26.7 - - - +
79A ALA* 3.6 9.6 - - - +
83A PHE* 4.1 7.0 - - + -
103A PHE* 3.9 26.5 - - + -
32B ASP* 4.9 13.9 - - + +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.8 8.5 - - + -
69A GLU 3.7 11.0 - - - +
70A LEU* 3.1 14.5 + - + +
72A ALA* 1.3 80.7 - - - +
74A GLN* 1.3 65.7 + - - +
75A GLU 3.4 0.3 + - - -
76A PRO* 3.7 8.1 - - - +
30B LEU* 3.9 26.2 - - + +
31B SER* 3.5 29.2 - - - +
32B ASP* 3.7 23.6 - - + +
35B LEU* 3.8 12.6 - - + -
73B ILE* 3.6 40.7 - - + +
74B GLN* 4.5 8.1 - - + +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 5.9 1.3 - - - +
35A LEU* 4.8 7.4 - - + -
36A ASN* 2.9 35.0 + - - +
39A ILE* 3.5 33.9 - - + +
70A LEU 2.9 6.8 + - - +
71A LYS* 2.7 38.0 + - - +
73A ILE* 1.3 79.7 - - - +
75A GLU* 1.3 83.4 + - + +
76A PRO* 4.0 1.7 - - - +
73B ILE 5.2 4.2 - - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 2.6 30.2 + - + +
74A GLN* 1.3 108.5 + - - +
76A PRO* 1.3 68.7 - - - +
77A ASP 3.2 2.7 - - - -
78A ASP* 2.9 34.0 + - + +
79A ALA* 3.2 8.7 + - - +
91D LYS* 3.4 30.4 + - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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