Contacts of the helix formed by residues 75 - 89 (chain s) 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 75 (chain s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100k ASP* 3.1 26.0 + - - -
41s LEU* 5.5 0.4 - - - -
66s TYR* 5.0 1.8 + - - -
73s ARG 3.6 2.5 + - - -
74s ILE* 1.3 79.2 - - - +
76s VAL* 1.3 65.2 + - - +
77s ALA* 3.6 2.8 + - - +
78s ALA* 3.0 22.1 + - - +
79s ALA* 3.0 22.9 + - - +
105s ASP* 3.1 28.5 - - - -
107s ARG* 4.1 4.0 - - - -
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Residues in contact with VAL 76 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41s LEU* 4.5 8.1 - - + -
74s ILE 5.5 0.9 - - - +
75s SER* 1.3 73.8 - - - +
77s ALA* 1.3 58.6 + - - +
79s ALA* 3.2 6.4 + - - +
80s SER* 3.0 30.4 + - - -
101s ILE* 3.8 26.1 - - + +
103s GLY* 3.7 32.3 - - - +
104s TRP 4.0 4.7 - - - +
105s ASP* 3.3 19.3 + - + +
110s GLY* 4.1 15.7 - - - +
112s TYR* 3.6 24.2 - - + -
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Residues in contact with ALA 77 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99k GLU* 4.4 17.5 - - + -
100k ASP* 4.9 0.2 - - - +
75s SER* 4.0 1.3 - - - +
76s VAL* 1.3 78.4 - - - +
78s ALA* 1.3 57.2 + - - +
80s SER* 2.9 19.8 + - - -
81s LYS* 2.9 14.6 + - - +
105s ASP* 4.4 1.6 + - - -
107s ARG* 3.9 22.7 - - - +
112s TYR* 3.6 23.8 - - - +
120s ARG* 3.0 17.9 + - - +
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Residues in contact with ALA 78 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97k THR 4.1 4.6 - - - +
98k VAL* 3.7 36.8 - - + +
99k GLU 4.9 0.4 - - - +
100k ASP* 4.8 0.4 + - - -
66s TYR* 5.9 0.7 - - + -
74s ILE* 3.7 21.1 - - + -
75s SER* 3.0 19.7 + - - +
77s ALA* 1.3 78.7 - - - +
79s ALA* 1.4 55.4 + - - +
81s LYS* 3.7 6.0 - - - +
82s LEU* 2.9 32.1 + - - +
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Residues in contact with ALA 79 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41s LEU* 3.8 28.7 - - + -
59s LEU* 3.6 17.2 - - + +
63s CYS* 4.2 10.1 - - - -
74s ILE* 3.9 8.7 - - + +
75s SER 3.0 16.7 + - - +
76s VAL* 3.2 6.2 + - - +
78s ALA* 1.4 72.1 - - - +
80s SER* 1.3 64.8 + - - +
82s LEU* 3.1 4.7 + - - +
83s LEU* 3.0 20.6 + - - +
101s ILE* 4.3 9.0 - - + -
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Residues in contact with SER 80 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76s VAL 3.0 14.0 + - - -
77s ALA 2.9 19.6 + - - -
79s ALA* 1.3 76.4 - - - +
81s LYS* 1.3 60.2 + - - +
83s LEU* 3.4 3.4 + - - +
84s ALA* 3.0 24.9 + - - +
101s ILE* 4.2 15.3 - - - +
112s TYR* 3.4 33.1 - - - -
114s VAL* 3.8 14.2 - - - +
120s ARG* 3.1 16.4 + - - -
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Residues in contact with LYS 81 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96k LEU* 2.8 35.6 + - - +
97k THR 4.0 11.4 - - - +
98k VAL* 5.1 1.3 - - - +
99k GLU* 4.1 9.3 + - - +
54r VAL* 4.6 7.2 - - - -
58r GLU* 2.2 46.3 + - - +
77s ALA 2.9 19.7 + - - +
78s ALA* 3.7 5.6 - - - +
80s SER* 1.3 76.9 + - - +
82s LEU* 1.3 62.7 + - - +
84s ALA* 3.6 2.7 - - - +
85s ASN* 3.0 49.5 + - - +
120s ARG* 3.3 33.0 - - - +
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Residues in contact with LEU 82 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97k THR* 4.6 15.0 + - + +
98k VAL* 5.9 3.1 - - + -
59s LEU* 4.1 10.1 - - + -
62s GLN* 3.9 38.1 - - + +
66s TYR* 6.0 2.5 - - + -
74s ILE* 3.9 27.4 - - + -
78s ALA* 2.9 12.0 + - + +
79s ALA 3.1 9.4 + - - +
81s LYS* 1.3 78.2 - - - +
83s LEU* 1.3 58.4 + - - +
85s ASN* 3.3 5.9 + - + +
86s MET* 2.9 43.8 + - + +
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Residues in contact with LEU 83 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55s TRP* 3.9 31.6 - - + +
56s GLU* 4.1 8.5 - - + -
59s LEU* 4.2 8.7 - - + +
79s ALA 3.0 9.3 + - - +
80s SER* 3.7 8.1 - - - +
82s LEU* 1.3 79.8 - - - +
84s ALA* 1.3 63.7 + - - +
86s MET* 3.2 14.3 + - + +
87s VAL* 3.0 24.3 + - + +
97s MET* 3.6 34.3 - - + -
99s THR* 3.6 17.7 - - + -
101s ILE* 4.0 19.7 - - + -
114s VAL* 3.9 7.9 - - + -
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Residues in contact with ALA 84 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55r GLN* 4.3 3.5 + - - +
80s SER 3.0 18.0 + - - +
81s LYS* 3.6 6.5 - - + +
83s LEU* 1.3 75.7 - - - +
85s ASN* 1.3 63.9 + - - +
87s VAL* 3.9 6.0 - - - +
88s TYR* 3.0 30.3 + - - +
114s VAL* 4.1 12.7 - - + +
115s ASP 5.4 0.9 - - - -
118s GLY* 5.4 10.5 - - - +
119s ASN 4.9 2.2 - - - +
120s ARG* 4.1 24.9 - - + -
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Residues in contact with ASN 85 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96k LEU* 4.7 5.7 + - - +
97k THR* 4.7 13.3 - - - +
55r GLN* 2.8 26.8 + - - +
58r GLU* 4.7 1.9 + - - +
81s LYS* 3.0 52.3 + - - +
82s LEU* 3.8 5.3 - - + +
84s ALA* 1.3 77.5 - - - +
86s MET* 1.3 66.1 + - - +
88s TYR* 3.6 7.8 + - - +
89s GLN* 3.8 18.7 + - - +
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Residues in contact with MET 86 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55s TRP* 3.9 36.6 - - + +
58s LEU* 4.1 28.5 - - + +
59s LEU* 4.0 18.2 - - + +
62s GLN* 4.8 11.4 - - + +
82s LEU* 2.9 27.6 + - + +
83s LEU* 3.5 28.5 - - + +
85s ASN* 1.3 75.2 - - - +
87s VAL* 1.3 63.3 + - - +
89s GLN* 3.6 12.0 + - - +
90s TYR* 3.9 15.8 - - - -
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Residues in contact with VAL 87 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55s TRP* 4.0 21.3 - - + -
83s LEU* 3.0 19.0 + - + +
84s ALA* 3.9 5.8 - - - +
86s MET* 1.3 73.7 - - - +
88s TYR* 1.3 67.6 + - - +
89s GLN 3.1 3.6 + - - -
90s TYR* 3.1 18.8 + - - +
91s LYS* 4.0 3.8 + - - -
95s LEU* 4.1 15.6 - - + +
97s MET* 3.6 31.0 - - + -
114s VAL* 5.9 0.4 - - + -
115s ASP 3.7 22.9 - - - +
116s SER* 3.8 22.5 - - - +
118s GLY* 5.4 2.7 - - - +
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Residues in contact with TYR 88 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51r GLY 4.0 7.0 - - - -
52r ASP* 2.5 35.4 + - - -
55r GLN* 3.1 49.8 - - + +
96r THR* 5.9 6.4 - - + -
97r PRO 4.6 3.6 + - - -
98r TYR* 3.3 27.8 - + - -
84s ALA 3.0 17.4 + - - +
85s ASN 3.9 4.5 - - - +
86s MET 3.3 0.4 - - - -
87s VAL* 1.3 80.3 - - - +
89s GLN* 1.3 62.6 + - + +
90s TYR 3.1 0.2 - - - -
91s LYS* 3.2 44.6 + - + +
116s SER 5.7 0.4 - - - -
117s GLU 4.2 8.5 - - - -
118s GLY* 4.7 7.4 - - - -
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Residues in contact with GLN 89 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85s ASN 3.8 15.2 + - - +
86s MET* 3.6 8.9 + - - +
87s VAL 3.1 1.6 - - - -
88s TYR* 1.3 84.5 - - + +
90s TYR* 1.3 67.0 + - + +
91s LYS 3.4 1.6 - - - -
93s MET* 4.8 4.5 - - - +
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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