Contacts of the helix formed by residues 75 - 90 (chain p) 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 ARG 75 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107h TYR* 3.6 53.9 + - + +
145h GLU* 4.2 21.0 + - - +
41p ILE* 3.6 8.6 - - - +
73p LEU 4.5 5.6 - - - +
74p PRO* 1.3 78.6 - - - +
76p VAL* 1.3 65.6 + - - +
77p VAL* 3.9 15.0 - - + +
78p THR* 3.3 27.6 + - - +
79p ALA* 3.6 4.5 + - - +
104p ASP* 3.1 18.6 - - + +
105p VAL* 4.1 32.1 - - + +
106p THR* 4.2 23.3 - - - +
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Residues in contact with VAL 76 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41p ILE* 3.9 13.5 - - + -
75p ARG* 1.3 71.1 - - - +
77p VAL* 1.3 64.9 + - - +
78p THR 3.1 0.2 - - - -
79p ALA* 3.1 3.6 + - - +
80p ASN* 2.9 20.8 + - - +
100p LEU* 4.1 14.8 - - + +
101p GLY 4.8 0.4 - - - -
102p GLY* 3.7 35.2 - - - +
103p VAL 4.1 0.2 - - - +
104p ASP* 2.8 31.3 + - - +
109p HIS* 3.9 21.1 - - + +
111p TYR* 3.6 26.0 - - + -
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Residues in contact with VAL 77 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105h TYR 3.7 9.0 - - - +
106h GLY* 4.0 24.7 - - - +
107h TYR* 4.8 2.0 - - + -
75p ARG* 3.9 26.0 - - + +
76p VAL* 1.3 73.8 - - - +
78p THR* 1.3 58.7 + - - +
80p ASN* 3.5 10.2 - - + +
81p ARG* 2.8 37.7 + - + +
104p ASP* 4.3 2.8 + - - +
109p HIS* 6.3 0.2 - - - -
111p TYR* 3.5 24.6 + - + +
121p LYS* 5.4 2.9 - - - +
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Residues in contact with THR 78 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105h TYR* 2.9 33.8 + - + -
107h TYR* 3.2 20.6 - - - -
63p LEU* 3.5 25.8 - - + -
66p HIS* 4.6 7.6 + - + -
75p ARG* 3.3 18.4 + - - +
76p VAL 3.1 0.8 - - - -
77p VAL* 1.3 79.2 - - - +
79p ALA* 1.3 63.3 + - - +
81p ARG* 3.2 1.6 + - - +
82p MET* 3.0 41.3 + - + +
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Residues in contact with ALA 79 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37p ILE* 4.7 1.8 - - + -
41p ILE* 4.5 7.2 - - + -
59p ILE* 4.3 12.1 - - + +
63p LEU* 3.9 25.0 - - + +
75p ARG 3.6 4.9 + - - +
76p VAL 3.1 8.8 + - - +
78p THR* 1.3 78.4 - - - +
80p ASN* 1.3 59.1 + - - +
82p MET* 3.4 2.3 + - - +
83p LEU* 2.9 37.3 + - + +
100p LEU* 3.9 22.2 - - + -
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Residues in contact with ASN 80 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76p VAL 2.9 13.2 + - - +
77p VAL* 3.5 15.0 + - - +
79p ALA* 1.3 77.6 - - - +
81p ARG* 1.3 60.4 + - - +
83p LEU* 3.8 3.7 - - - +
84p LYS* 2.9 41.5 + - - +
100p LEU* 3.6 9.9 - - + +
111p TYR* 3.3 41.9 - - + +
113p ILE* 3.6 5.7 - - - +
119p THR* 3.4 35.7 + - - +
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Residues in contact with ARG 81 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102h LYS* 3.0 35.4 + - - +
103h TYR* 3.4 20.9 + - - +
104h LYS 3.5 18.4 - - - +
105h TYR 4.6 1.1 - - - -
106h GLY* 3.2 21.6 + - - -
57o ASP* 3.7 34.4 + - - -
77p VAL* 2.8 28.0 + - + +
78p THR 3.8 1.6 - - - +
80p ASN* 1.3 70.6 - - - +
82p MET* 1.3 68.3 + - - +
84p LYS* 3.6 14.5 - - + +
85p GLN* 3.0 41.2 + - - +
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Residues in contact with MET 82 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104h LYS 4.4 9.0 - - - +
105h TYR* 3.3 35.2 - - + -
59p ILE* 3.5 21.7 - - + +
62p ASN* 4.0 37.0 - - + +
63p LEU* 4.1 23.6 - - + -
66p HIS* 4.8 3.8 - - + -
78p THR* 3.0 26.9 + - + +
79p ALA 3.8 2.7 - - - +
81p ARG* 1.3 76.4 - - - +
83p LEU* 1.3 62.4 + - - +
85p GLN* 4.1 3.2 - - - +
86p MET* 3.0 25.6 + - - +
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Residues in contact with LEU 83 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37p ILE* 6.0 1.3 - - + -
43p CYS* 5.1 1.8 - - - -
55p THR* 3.4 25.5 - - + +
56p THR* 5.1 3.1 - - - +
59p ILE* 3.4 33.2 - - + -
79p ALA 2.9 27.1 + - - +
80p ASN 3.8 2.9 - - - +
82p MET* 1.3 75.4 - - - +
84p LYS* 1.3 60.0 + - - +
86p MET* 3.4 3.3 + - - +
87p LEU* 2.8 35.9 + - + +
98p LEU* 3.6 18.4 - - + -
100p LEU* 4.0 18.4 - - + -
113p ILE* 3.4 33.7 - - + -
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Residues in contact with LYS 84 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53o GLN* 2.8 33.9 + - - +
57o ASP* 4.6 11.4 + - - +
80p ASN* 2.9 29.6 + - - +
81p ARG* 3.6 20.8 - - - +
83p LEU* 1.3 78.6 - - - +
85p GLN* 1.3 67.6 + - + +
87p LEU* 4.4 1.8 - - - -
88p PHE* 3.0 28.9 + - - +
113p ILE* 5.1 0.9 - - - -
117p GLY* 3.2 35.2 - - - +
119p THR* 3.0 29.7 + - + -
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Residues in contact with GLN 85 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103h TYR* 3.3 56.6 + - - +
104h LYS* 4.7 8.7 - - - +
57o ASP* 5.4 2.7 + - - +
81p ARG* 3.0 28.8 + - - +
82p MET* 4.1 3.4 - - - +
84p LYS* 1.3 81.7 - - + +
86p MET* 1.3 66.6 + - - +
88p PHE* 3.8 6.2 - - - +
89p ARG* 3.0 24.1 + - - +
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Residues in contact with MET 86 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54p MET 5.9 0.7 - - - +
55p THR* 4.0 33.0 - - + +
58p LEU* 3.8 31.2 - - + -
59p ILE* 5.3 1.8 - - + -
82p MET 3.0 18.2 + - - +
83p LEU* 3.7 4.0 - - - +
85p GLN* 1.3 78.7 - - - +
87p LEU* 1.3 66.1 + - - +
89p ARG* 3.2 13.0 + - - +
90p TYR* 3.4 33.0 + - + +
94p ILE* 3.9 29.4 - - + -
96q TYR* 5.6 4.9 - - + +
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Residues in contact with LEU 87 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55p THR* 4.8 5.2 - - + +
83p LEU* 2.8 24.1 + - + +
84p LYS 3.9 3.8 - - - +
86p MET* 1.3 83.6 - - - +
88p PHE* 1.3 61.5 + - - +
90p TYR* 3.2 12.8 + - - +
91p GLN 3.3 8.8 + - - -
92p GLY 3.9 1.0 + - - -
94p ILE* 3.8 42.7 - - + +
96p ALA* 4.2 19.7 - - + +
98p LEU* 5.0 5.4 - - + -
113p ILE* 3.8 28.7 - - + -
114p TYR 3.9 10.5 - - - +
115p PRO 3.7 18.2 - - - +
116p HIS 4.1 2.2 - - - +
117p GLY* 4.0 6.3 - - - -
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Residues in contact with PHE 88 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50o ALA* 4.0 15.0 - - + -
51o ASP* 3.7 22.0 - - - -
54o ALA* 3.4 31.2 - - + -
94o LEU* 4.4 15.5 - - + -
84p LYS 3.0 19.2 + - - +
85p GLN* 3.8 7.2 - - - +
86p MET 3.4 0.2 - - - -
87p LEU* 1.3 72.6 - - - +
89p ARG* 1.3 70.7 + - + +
91p GLN* 3.1 29.6 + - - +
116p HIS 3.6 19.2 + - - +
117p GLY* 4.9 1.3 - - - +
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Residues in contact with ARG 89 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85p GLN 3.0 13.4 + - - +
86p MET* 3.4 13.1 - - - +
87p LEU 3.2 0.4 - - - -
88p PHE* 1.3 84.5 - - + +
90p TYR* 1.3 100.4 + - + +
91p GLN* 3.7 6.8 + - - +
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Residues in contact with TYR 90 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86p MET* 3.4 34.9 + - + +
87p LEU 3.2 6.7 + - - +
88p PHE 3.1 0.8 - - - -
89p ARG* 1.3 113.4 + - + +
91p GLN* 1.3 71.1 + - - +
92p GLY 3.2 2.2 - - - -
93p TYR* 2.9 23.2 + - + +
94p ILE* 3.6 31.4 - - + -
100q PHE* 4.0 35.4 - + - -
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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
------------------------------------------------------------
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