Contacts of the helix formed by residues 75 - 90 (chain b) 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 b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B TYR* 2.8 58.7 + - + -
145B GLU* 3.4 32.3 - - - +
41b ILE* 3.6 9.7 - - - +
63b LEU* 4.9 0.3 - - - +
73b LEU 4.5 5.6 - - - +
74b PRO* 1.3 78.9 - - - +
76b VAL* 1.3 64.1 + - - +
77b VAL* 3.3 21.8 - - + -
78b THR* 3.2 27.4 + - - +
79b ALA 3.6 2.3 + - - -
104b ASP* 3.2 20.4 - - - +
105b VAL* 4.2 23.2 - - + +
106b THR* 4.1 24.1 - - - +
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Residues in contact with VAL 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41b ILE* 3.8 15.5 - - + -
75b ARG* 1.3 70.6 - - - +
77b VAL* 1.3 67.9 + - - +
79b ALA* 3.1 4.2 + - - +
80b ASN* 3.0 19.4 + - - +
100b LEU* 4.1 13.0 - - + -
101b GLY 4.3 4.3 - - - -
102b GLY* 3.8 36.3 - - - +
104b ASP* 2.8 26.8 + - - +
109b HIS* 3.9 20.9 - - + +
111b TYR* 3.6 24.7 - - + -
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Residues in contact with VAL 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR 4.1 4.3 - - - +
106B GLY* 4.8 16.2 - - - +
107B TYR* 5.7 3.8 - - + -
75b ARG* 3.6 26.2 - - + +
76b VAL* 1.3 75.1 - - - +
78b THR* 1.3 60.4 + - - +
80b ASN* 3.3 9.2 + - + +
81b ARG* 2.8 32.7 + - + +
104b ASP* 4.3 3.1 + - - +
111b TYR* 3.2 26.6 + - + +
121b LYS* 5.5 2.7 - - - +
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Residues in contact with THR 78 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 5.6 3.1 - - - -
104B LYS 5.1 0.2 - - - +
105B TYR* 3.1 55.3 + - + +
107B TYR* 5.7 2.4 - - - +
63b LEU* 3.8 14.1 - - + -
66b HIS* 4.8 7.1 - - + -
75b ARG* 3.2 24.7 + - - +
76b VAL 3.1 1.4 - - - -
77b VAL* 1.3 77.4 - - - +
79b ALA* 1.3 63.1 + - - +
81b ARG* 3.1 2.4 + - - +
82b MET* 2.9 37.3 + - + +
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Residues in contact with ALA 79 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37b ILE* 4.7 0.2 - - + -
41b ILE* 4.5 9.2 - - + -
59b ILE* 4.3 12.5 - - + +
63b LEU* 3.9 24.8 - - + +
75b ARG 3.6 2.0 + - - -
76b VAL 3.1 10.2 + - - +
78b THR* 1.3 80.2 - - - +
80b ASN* 1.3 62.1 + - - +
82b MET* 3.8 4.0 - - - +
83b LEU* 3.0 31.9 + - - +
100b LEU* 3.7 22.7 - - + -
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Residues in contact with ASN 80 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76b VAL 3.0 12.6 + - - +
77b VAL* 3.4 14.5 + - - +
79b ALA* 1.3 74.6 - - - +
81b ARG* 1.3 62.0 + - - +
83b LEU* 3.9 0.9 - - - +
84b LYS* 3.0 42.6 + - - +
100b LEU* 3.5 10.4 - - + +
111b TYR* 3.2 43.2 - - + +
113b ILE* 3.5 7.7 - - - +
119b THR* 3.4 34.2 + - - +
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Residues in contact with ARG 81 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS 3.3 16.6 + - - -
103B TYR* 2.9 28.0 + - - +
104B LYS 3.7 13.9 - - - +
105B TYR 4.2 12.1 - - - -
106B GLY* 4.2 7.7 - - - +
57a ASP* 2.8 51.2 + - - +
60a THR* 6.1 1.4 - - - +
77b VAL* 2.8 22.3 + - + +
78b THR 3.1 3.8 + - - +
80b ASN* 1.3 74.1 - - - +
82b MET* 1.3 65.7 + - - +
84b LYS* 3.6 12.1 - - + +
85b GLN* 3.0 51.9 + - - +
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Residues in contact with MET 82 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS 4.4 5.6 + - - +
105B TYR* 2.9 43.3 - - + +
59b ILE* 3.4 24.2 - - + +
62b ASN* 4.0 37.2 - - + +
63b LEU* 4.1 24.5 - - + -
66b HIS* 4.8 0.4 - - + -
78b THR* 2.9 29.0 + - + +
79b ALA* 3.8 4.5 - - - +
81b ARG* 1.3 72.8 - - - +
83b LEU* 1.3 64.2 + - - +
85b GLN* 4.0 4.0 - - - +
86b MET* 3.1 26.9 + - - +
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Residues in contact with LEU 83 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37b ILE* 6.0 0.7 - - + -
43b CYS* 5.0 1.1 - - - -
55b THR* 3.5 19.1 - - + +
56b THR* 5.1 2.2 - - - +
59b ILE* 3.4 33.2 - - + -
79b ALA 3.0 28.1 + - - +
80b ASN 3.9 2.5 - - - +
82b MET* 1.3 76.2 - - - +
84b LYS* 1.3 59.7 - - - +
86b MET* 3.9 4.5 - - - +
87b LEU* 2.9 36.8 + - + +
98b LEU* 3.4 27.1 - - + -
100b LEU* 4.0 18.2 - - + -
113b ILE* 3.5 33.4 - - + -
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Residues in contact with LYS 84 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53a GLN* 3.5 24.3 + - - +
54a ALA* 5.9 0.9 - - - +
57a ASP* 4.4 12.0 + - - +
80b ASN* 3.0 29.1 + - - +
81b ARG* 3.6 24.1 - - - +
83b LEU* 1.3 80.8 - - - +
85b GLN* 1.3 66.5 - - + +
87b LEU* 4.5 0.4 - - - -
88b PHE* 2.9 29.1 + - - +
113b ILE* 4.8 2.7 - - - -
117b GLY* 3.4 34.4 - - - +
119b THR* 2.9 34.2 + - + -
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Residues in contact with GLN 85 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.0 52.9 + - - +
104B LYS* 3.8 14.9 - - - +
57a ASP* 5.4 4.6 + - - +
81b ARG* 3.0 35.6 + - - +
82b MET* 4.0 3.9 - - - +
84b LYS* 1.3 83.7 - - + +
86b MET* 1.3 66.6 + - - +
88b PHE* 3.4 6.1 + - - +
89b ARG* 3.1 22.3 + - - +
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Residues in contact with MET 86 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54b MET 5.3 0.7 - - - +
55b THR* 3.9 42.6 - - + +
58b LEU* 3.8 31.9 - - + -
59b ILE* 4.7 4.7 - - - -
82b MET 3.1 13.7 + - - +
83b LEU* 4.4 7.4 - - - +
85b GLN* 1.3 79.4 - - - +
87b LEU* 1.3 65.7 + - + +
89b ARG* 3.1 17.1 + - - +
90b TYR* 3.2 34.7 - - + -
94b ILE* 4.6 14.8 - - + -
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Residues in contact with LEU 87 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55b THR* 4.6 11.9 - - + +
83b LEU* 2.9 25.9 + - + +
86b MET* 1.3 78.7 - - - +
88b PHE* 1.3 65.8 - - - +
90b TYR* 3.2 13.6 + - - +
91b GLN 3.5 7.3 + - - -
92b GLY 3.9 6.9 + - - -
94b ILE* 3.8 44.6 - - + +
96b ALA* 4.1 26.0 - - + +
98b LEU* 5.2 1.8 - - + -
113b ILE* 3.9 25.4 - - + -
114b TYR 4.1 4.9 - - - +
115b PRO 3.8 12.3 - - - +
116b HIS 4.0 2.2 - - - +
117b GLY* 4.0 9.6 - - - -
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Residues in contact with PHE 88 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50a ALA* 3.8 25.4 - - + +
51a ASP* 3.3 33.0 - - - -
54a ALA* 4.2 21.5 - - + -
55a VAL* 6.1 1.3 - - + -
93a ASP* 6.5 0.2 - - + -
94a LEU* 4.2 16.4 - - + -
84b LYS 2.9 19.1 + - - +
85b GLN* 3.9 5.2 - - - +
87b LEU* 1.3 77.9 - - - +
89b ARG* 1.3 69.8 + - + +
90b TYR 3.1 0.7 + - - -
91b GLN* 3.1 32.9 + - - +
116b HIS 3.5 11.1 + - - +
117b GLY* 4.8 1.8 - - - +
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Residues in contact with ARG 89 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85b GLN 3.1 13.2 + - - +
86b MET* 3.1 14.1 + - - +
88b PHE* 1.3 86.5 - - + +
90b TYR* 1.3 96.9 + - + +
91b GLN* 3.4 7.8 + - - +
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Residues in contact with TYR 90 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86b MET* 3.2 33.2 - - + +
87b LEU* 3.2 7.9 + - - +
88b PHE 3.1 0.8 - - - -
89b ARG* 1.3 113.3 + - + +
91b GLN* 1.3 71.8 + - - +
92b GLY 3.2 2.2 - - - -
93b TYR* 3.0 22.3 + - + +
94b ILE* 3.5 40.4 - - + -
100c PHE* 4.6 22.2 - + - -
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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
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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