Contacts of the helix formed by residues 76 - 91 (chain r) in PDB entry 5GJQ
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 SER 76 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103j GLU* 3.4 14.6 + - - -
141j LYS* 3.9 19.7 - - - +
42r ILE* 4.2 0.7 - - - -
74r GLU 3.9 0.6 + - - -
75r LEU* 1.3 76.5 - - - +
77r PRO* 1.3 77.6 - - - +
78r THR* 3.8 9.5 + - - -
79r ALA* 3.1 26.6 + - - +
80r ALA* 2.9 21.3 + - - +
108r ASP* 4.1 15.7 - - - -
111r GLU* 5.8 3.8 - - - -
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Residues in contact with PRO 77 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42r ILE* 3.8 20.9 - - + -
75r LEU 4.1 3.6 - - - +
76r SER* 1.3 89.5 - - - +
78r THR* 1.3 55.5 + - - +
80r ALA* 3.6 2.1 - - + +
81r ALA* 2.9 28.1 + - - +
104r LEU* 3.6 13.7 - - + +
106r GLY* 3.7 36.6 - - - +
107r TYR 3.8 14.4 - - - +
108r ASP* 3.9 19.3 - - + +
112r GLY 5.4 0.7 - - - +
114r ALA* 5.2 10.3 - - + -
116r TYR* 4.1 4.1 - - + -
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Residues in contact with THR 78 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101j TYR 5.3 2.2 - - - +
102j GLN 5.3 5.8 - - - +
103j GLU* 5.6 4.0 - - + +
76r SER* 3.0 9.4 - - - -
77r PRO* 1.3 77.7 - - - +
79r ALA* 1.3 67.7 + - - +
81r ALA* 3.2 2.1 + - - +
82r ASN* 3.0 42.5 + - - +
111r GLU* 5.7 5.5 - - - +
114r ALA* 5.0 5.2 - - - +
116r TYR* 2.9 30.7 + - + +
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Residues in contact with ALA 79 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101j TYR* 3.5 36.9 - - + +
103j GLU* 4.1 13.0 + - - +
75r LEU* 3.9 21.1 - - + -
76r SER* 3.1 20.3 + - - +
78r THR* 1.3 80.5 - - - +
80r ALA* 1.3 62.8 + - - +
82r ASN* 3.5 1.7 + - - +
83r PHE* 3.1 22.3 + - - +
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Residues in contact with ALA 80 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38r MET* 4.2 19.1 - - + -
42r ILE* 4.0 18.8 - - + -
64r VAL* 5.1 2.9 - - + -
75r LEU* 4.5 15.2 - - + +
76r SER 2.9 16.5 + - - +
77r PRO* 3.6 5.6 - - + +
79r ALA* 1.3 75.3 - - - +
81r ALA* 1.3 63.1 + - - +
83r PHE* 2.9 14.7 + - - +
84r THR* 2.9 22.8 + - - +
104r LEU* 4.2 2.9 - - + -
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Residues in contact with ALA 81 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77r PRO 2.9 19.3 + - - +
78r THR* 3.4 5.6 - - - +
80r ALA* 1.3 76.6 - - - +
82r ASN* 1.3 62.9 + - - +
84r THR* 3.4 3.7 + - - -
85r ARG* 3.0 25.3 + - - +
104r LEU* 3.5 18.7 - - + +
116r TYR* 3.7 31.2 - - + -
118r MET* 4.2 1.6 - - - +
124r LEU* 4.0 15.6 - - + +
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Residues in contact with ASN 82 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99j LEU 5.6 0.2 - - - +
100j GLN 3.6 9.4 - - - +
101j TYR 4.0 15.5 - - - +
102j GLN* 3.3 30.6 - - + +
65q GLN* 3.4 14.8 + - - +
78r THR* 3.0 41.3 + - - +
79r ALA 4.1 0.7 - - - +
81r ALA* 1.3 77.7 - - - +
83r PHE* 1.3 58.1 - - - +
85r ARG* 3.7 5.9 + - - +
86r ARG* 2.9 29.3 + - - +
116r TYR* 5.6 1.0 - - - -
124r LEU* 3.7 22.3 - - - +
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Residues in contact with PHE 83 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100j GLN* 3.0 48.8 + - + -
101j TYR* 3.4 31.4 - + + -
59r TYR* 5.5 0.7 - + - -
60r ILE* 4.1 20.0 - - + -
63r ASN* 3.5 40.2 - - + -
64r VAL* 5.5 5.4 - - + -
75r LEU* 6.0 1.6 - - + -
79r ALA 3.1 14.1 + - - +
80r ALA* 2.9 13.5 + - - +
82r ASN* 1.3 74.4 - - - +
84r THR* 1.3 67.1 + - - +
86r ARG* 3.2 3.2 + - - +
87r ASN* 3.1 46.9 + - - -
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Residues in contact with THR 84 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38r MET* 4.7 1.3 - - + -
44r LEU* 5.2 2.7 - - + -
56r PHE* 3.5 10.9 - - - -
60r ILE* 3.7 42.4 - - + -
80r ALA 2.9 20.9 - - - +
81r ALA 3.4 2.1 + - - -
83r PHE* 1.3 76.3 - - + +
85r ARG* 1.3 60.8 + - - +
87r ASN* 3.4 0.9 + - - -
88r LEU* 2.9 30.8 + - - +
102r LEU* 4.1 7.2 - - + +
104r LEU* 3.9 15.6 - - + +
118r MET* 3.1 22.0 - - - +
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Residues in contact with ARG 85 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58q THR* 3.1 16.2 + - - +
61q GLN* 4.0 11.9 + - - +
62q THR* 2.7 33.1 + - - +
65q GLN* 2.4 42.4 + - - +
81r ALA 3.0 15.7 + - - +
82r ASN* 3.7 8.2 + - - +
84r THR* 1.3 83.1 + - - +
86r ARG* 1.3 68.8 + - - +
88r LEU* 3.7 1.4 - - - +
89r ALA* 2.9 42.9 + - - +
118r MET* 3.6 24.9 - - + -
122r ALA* 2.9 27.0 + - - +
124r LEU* 3.8 25.4 - - + -
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Residues in contact with ARG 86 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99j LEU* 3.7 39.6 + - - +
100j GLN* 4.2 31.9 - - + +
62q THR* 3.9 16.6 + - - +
65q GLN* 2.1 40.2 + - - +
66q ARG* 3.9 15.9 - - - +
82r ASN 2.9 18.2 + - - +
83r PHE* 3.2 8.0 + - - +
85r ARG* 1.3 87.0 - - - +
87r ASN* 1.3 61.2 - - - +
89r ALA* 3.7 3.2 - - - +
90r ASP* 3.0 65.6 + - - +
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Residues in contact with ASN 87 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100j GLN* 4.0 11.2 + - - +
56r PHE* 4.5 6.1 - - + -
59r TYR* 3.8 29.7 + - + -
60r ILE* 3.9 10.3 - - + +
83r PHE* 3.1 58.0 + - - +
84r THR 4.0 2.9 - - - +
86r ARG* 1.3 82.6 - - - +
88r LEU* 1.3 64.4 - - - +
89r ALA 3.4 0.3 + - - -
90r ASP* 3.5 5.4 + - - +
91r CYS* 3.4 27.8 + - - -
98r TYR* 5.4 0.6 - - - -
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Residues in contact with LEU 88 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56r PHE* 3.8 14.2 - - + -
84r THR 2.9 19.1 + - - +
85r ARG* 3.7 4.9 - - - +
87r ASN* 1.3 78.7 - - - +
89r ALA* 1.3 59.3 + - - +
91r CYS* 3.6 4.1 + - - +
92r LEU* 3.4 18.9 + - - +
98r TYR* 3.5 37.4 + - + +
100r VAL* 3.6 24.9 - - + +
102r LEU* 4.1 5.6 - - + -
118r MET* 3.4 25.6 - - + -
119r ASP 3.7 15.9 - - - +
120r TYR 4.3 6.2 - - - +
122r ALA* 3.7 12.4 - - + +
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Residues in contact with ALA 89 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58q THR* 4.7 5.3 - - + +
62q THR* 4.3 7.6 - - + +
85r ARG* 2.9 40.2 + - - +
86r ARG* 3.2 7.6 + - - +
88r LEU* 1.3 76.9 - - - +
90r ASP* 1.3 68.9 + - - +
92r LEU* 3.3 20.2 + - - +
93r ARG* 4.6 6.9 + - - -
121r LEU 4.9 0.4 - - - -
122r ALA* 3.7 15.3 - - + -
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Residues in contact with ASP 90 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62q THR* 5.5 0.9 - - - +
66q ARG* 3.9 12.9 + - - -
86r ARG* 3.0 57.8 + - - +
87r ASN* 3.5 7.2 + - - +
88r LEU 3.4 0.2 - - - -
89r ALA* 1.3 79.3 - - - +
91r CYS* 1.3 64.6 + - - +
92r LEU 3.6 0.3 + - - -
93r ARG* 4.4 5.7 + - - +
94r SER* 4.4 7.8 + - - -
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Residues in contact with CYS 91 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87r ASN* 3.4 17.5 + - - +
88r LEU 4.1 2.7 - - - +
89r ALA 3.2 0.6 - - - -
90r ASP* 1.3 80.3 - - - +
92r LEU* 1.3 64.1 + - - +
93r ARG 3.3 0.9 - - - -
94r SER* 2.6 26.0 + - - +
96r THR* 3.6 20.6 - - - +
97r PRO* 3.2 13.2 - - + +
98r TYR* 4.0 26.2 - - + -
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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
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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