Contacts of the helix formed by residues 57 - 76 (chain A) in PDB entry 3ZYQ
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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18A GLN* 4.0 21.8 + - - +
55A ASP* 3.2 10.7 - - + +
56A LYS* 1.3 76.4 - - - +
58A PRO* 1.3 64.9 - - - +
59A HIS* 2.9 39.2 + - - +
60A VAL* 3.3 24.1 + - + +
61A ALA 3.0 21.7 + - - -
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP 5.2 0.2 - - - +
56A LYS 3.4 9.6 - - - +
57A ASN* 1.3 84.2 - - - +
59A HIS* 1.3 60.7 + - + +
61A ALA* 3.7 3.4 - - + -
62A LEU* 2.9 31.0 + - - +
99A GLN* 4.8 4.7 - - - +
101A GLU* 3.6 38.5 - - + +
104A VAL* 3.4 13.7 - - + +
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 2.8 20.1 + - - -
18A GLN* 3.5 23.4 + - + -
20A LEU 3.1 19.1 - - - -
57A ASN* 2.9 12.1 + - - +
58A PRO* 1.3 77.3 - - + +
60A VAL* 1.3 69.3 + - - +
62A LEU* 3.4 5.1 + - - +
63A TYR* 2.5 67.1 + + - +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.5 35.6 - - - +
18A GLN* 4.6 10.1 - - + +
52A LYS* 4.0 17.7 - - + +
55A ASP* 3.8 26.5 - - + +
57A ASN* 3.3 29.7 + - + +
59A HIS* 1.3 86.2 - - + +
61A ALA* 1.3 56.5 + - - +
63A TYR* 3.8 2.0 - - - +
64A ALA* 2.9 28.1 + - - +
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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
----------------------------------------------------------
52A LYS 3.7 11.0 + - - -
53A VAL* 3.3 22.4 - - - +
55A ASP 3.9 9.6 - - - +
57A ASN 3.0 15.5 + - - +
58A PRO* 3.9 6.5 - - + +
59A HIS 3.2 0.2 - - - -
60A VAL* 1.3 76.7 - - - +
62A LEU* 1.3 58.0 + - - +
64A ALA* 3.3 2.6 + - - +
65A LEU* 2.9 34.5 + - + +
99A GLN* 5.1 3.8 - - - +
104A VAL* 4.1 18.2 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 2.9 18.8 + - - +
59A HIS* 3.9 4.7 - - - +
61A ALA* 1.3 77.6 - - - +
63A TYR* 1.3 67.2 + - + +
65A LEU* 3.1 7.3 + - - +
66A GLU* 3.1 35.0 + - - +
101A GLU* 5.5 0.2 - - - +
103A ASN* 3.7 41.3 - - + +
104A VAL* 4.0 9.3 - - + +
107A LYS* 3.8 26.0 - - + -
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Residues in contact with TYR 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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15A ALA 3.6 18.5 - - - +
16A THR* 4.0 8.3 - - - -
17A SER 3.9 5.8 - - - -
20A LEU* 3.3 27.5 + - + -
21A LEU 3.4 4.0 + - - -
22A GLU* 3.1 26.2 + - - -
23A THR* 3.8 19.7 - - + -
28A ILE* 5.3 0.7 - - - +
59A HIS* 2.5 60.1 + + - +
60A VAL 3.9 3.4 - - - +
62A LEU* 1.3 80.0 - - + +
64A ALA* 1.3 62.2 + - - +
66A GLU* 3.2 29.9 + - - +
67A VAL* 3.1 23.6 + - - +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.9 0.2 - - - -
16A THR* 3.8 10.6 - - + +
49A ILE* 3.5 10.4 - - + +
52A LYS* 3.4 17.5 - - + -
53A VAL* 3.4 33.7 - - + +
60A VAL 2.9 17.7 + - - +
61A ALA 3.6 3.1 - - - +
62A LEU 3.2 0.2 - - - -
63A TYR* 1.3 76.7 - - - +
65A LEU* 1.3 58.2 + - - +
67A VAL* 3.1 7.9 + - - +
68A MET 2.9 23.4 + - - -
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Residues in contact with LEU 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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53A VAL* 3.8 28.5 - - + -
61A ALA 2.9 19.3 + - - +
62A LEU* 3.1 9.4 + - - +
64A ALA* 1.3 76.5 - - - +
66A GLU* 1.3 58.1 + - - +
68A MET* 3.3 15.6 + - - +
69A GLU* 2.9 27.0 + - - +
92A LEU* 4.7 5.8 - - + -
104A VAL* 4.0 24.9 - - + +
107A LYS* 3.8 23.1 - - + -
108A ILE* 4.0 28.5 - - + -
111A LEU* 3.8 23.0 - - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 2.6 34.6 + - + +
25A TRP* 5.7 4.4 - - + -
28A ILE* 4.4 9.5 - - + +
62A LEU* 3.1 27.0 + - + +
63A TYR* 3.4 30.9 - - - +
65A LEU* 1.3 74.5 - - - +
67A VAL* 1.3 64.5 + - - +
69A GLU* 3.3 11.6 + - - +
70A SER* 3.1 26.3 + - - -
107A LYS* 4.0 21.4 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.2 8.5 - - + -
15A ALA* 4.1 19.1 - - + +
16A THR* 4.3 6.7 - - + -
28A ILE* 4.0 27.4 - - + -
31A ILE* 4.4 14.1 - - + -
49A ILE* 3.8 30.1 - - + -
63A TYR 3.1 15.3 + - - +
64A ALA* 3.1 11.2 + - - +
66A GLU* 1.3 74.5 - - - +
68A MET* 1.3 58.5 + - - +
70A SER* 3.1 4.0 + - - -
71A VAL* 2.9 35.7 + - + +
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 4.3 12.8 - - + -
49A ILE* 4.0 16.8 - - + +
50A LYS* 3.6 38.6 - - + -
53A VAL* 4.6 7.2 - - + -
64A ALA 2.9 13.6 + - - +
65A LEU* 3.4 26.9 - - + +
67A VAL* 1.3 77.6 - - - +
69A GLU* 1.3 63.4 + - - +
71A VAL* 3.4 9.2 - - + +
72A VAL* 3.0 35.2 + - + +
83A VAL* 4.6 6.3 - - + -
88A THR* 5.3 3.6 - - + -
92A LEU* 5.2 10.8 - - + -
111A LEU* 5.0 0.7 - - + -
115A TRP* 3.9 29.8 - - + -
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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
----------------------------------------------------------
25A TRP* 6.1 4.4 - - - -
65A LEU 2.9 13.1 + - - +
66A GLU* 3.4 13.2 - - - +
68A MET* 1.3 78.2 - - - +
70A SER* 1.3 60.2 + - - +
72A VAL* 3.6 2.3 + - - +
73A LYS* 3.0 40.6 + - + +
107A LYS* 2.7 32.6 + - - -
110A TYR* 3.1 29.7 + - + -
111A LEU* 3.6 22.8 - - + +
115A TRP* 4.7 5.6 + - - +
152A PHE* 5.9 0.2 - - - -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 3.4 22.0 - - - -
28A ILE* 3.3 34.1 - - - +
29A LEU* 5.6 0.7 - - - -
32A CYS* 3.8 6.1 - - - -
66A GLU 3.1 11.7 + - - -
67A VAL 3.1 3.8 + - - -
69A GLU* 1.3 77.7 - - - +
71A VAL* 1.3 60.8 - - - +
73A LYS* 3.6 6.2 - - - +
74A ASN* 2.9 42.1 + - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 5.4 0.4 - - + +
31A ILE* 3.9 28.5 - - + -
32A CYS* 3.9 11.7 - - - -
35A ILE* 3.9 13.9 - - + -
46A VAL* 4.8 7.0 - - + -
49A ILE* 4.0 17.3 - - + -
67A VAL* 2.9 20.4 + - + +
68A MET* 3.4 18.6 - - + +
70A SER* 1.3 75.5 - - - +
72A VAL* 1.3 60.8 + - + +
75A CYS* 3.0 45.1 + - - +
79A VAL* 3.7 17.9 - - + +
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Residues in contact with VAL 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 MET* 3.0 18.6 + - + +
69A GLU 4.0 3.1 - - - +
71A VAL* 1.3 79.9 - - + +
73A LYS* 1.3 61.9 + - - +
74A ASN 3.4 0.2 + - - -
75A CYS 4.0 1.7 + - - -
79A VAL* 3.8 20.4 - - + -
80A HIS* 2.8 35.9 + - + -
83A VAL* 3.9 20.6 - - + -
115A TRP* 3.6 39.7 - - + +
119A PHE* 4.3 7.0 - - + -
152A PHE* 3.7 20.7 - - + -
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Residues in contact with LYS 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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69A GLU* 3.0 31.0 + - + +
70A SER* 3.3 7.8 + - - +
72A VAL* 1.3 79.6 - - - +
74A ASN* 1.3 72.2 + - - +
76A GLY 5.3 0.6 + - - -
80A HIS* 5.2 0.3 + - - -
110A TYR* 5.9 0.9 - - - -
148A SER* 3.2 21.2 + - - -
149A ASP* 4.1 15.7 + - - +
151A MET* 3.0 29.5 + - - +
152A PHE* 3.5 19.7 - - + +
153A ALA 3.0 28.8 + - - +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.9 16.7 - - - +
32A CYS* 3.7 25.5 - - + -
36A ARG* 3.2 22.2 - - - +
70A SER* 2.9 24.4 + - - +
73A LYS* 1.3 97.6 + - - +
75A CYS* 1.3 57.7 + - - +
76A GLY 3.7 2.0 + - - -
153A ALA* 4.1 24.6 - - - +
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Residues in contact with CYS 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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32A CYS* 3.5 41.1 - - - -
35A ILE* 4.0 15.2 - - + +
36A ARG* 3.9 12.5 - - + +
71A VAL* 3.0 31.9 + - - +
73A LYS 3.8 0.4 - - - -
74A ASN* 1.3 80.8 - - - +
76A GLY* 1.3 64.2 + - - +
78A THR* 3.5 16.1 - - - +
79A VAL* 3.6 16.6 - - + -
155A GLU* 5.0 3.1 - - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL 4.4 0.6 + - - -
73A LYS 5.3 0.2 + - - -
74A ASN 3.7 2.2 - - - -
75A CYS* 1.3 76.7 - - - +
77A GLN* 1.3 65.9 - - - -
78A THR 3.2 2.7 - - - -
79A VAL* 3.0 13.7 + - - -
80A HIS* 3.0 34.4 + - - -
153A ALA 5.4 4.1 + - - -
155A GLU* 3.4 24.0 - - - +
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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
------------------------------------------------------------
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