Contacts of the helix formed by residues 82 - 93 (chain J) in PDB entry 6QX2
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 GLY 82 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81J HIS* 1.3 79.3 - - - +
83J ASP* 1.3 68.3 + - - -
84J SER* 3.3 6.7 - - - -
85J SER* 3.4 17.0 + - - -
86J ILE* 3.4 14.6 + - - +
122L ARG* 3.0 24.5 - - - +
8N C 3.3 9.9 + - - -
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Residues in contact with ASP 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL* 3.9 13.3 - - + +
75J MET* 3.5 29.2 - - + +
81J HIS 3.7 1.6 + - - -
82J GLY* 1.3 71.4 - - - -
84J SER* 1.3 67.3 + - - +
86J ILE* 3.3 2.6 + - - +
87J TYR* 2.8 32.7 + - - +
121J MET* 3.8 22.7 - - + +
83L ASP* 5.8 0.2 - - - +
121L MET* 6.1 5.2 - - + -
122L ARG* 4.6 14.5 - - - +
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Residues in contact with SER 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J GLY* 4.6 3.6 - - - -
83J ASP* 1.3 86.4 + - - +
85J SER* 1.3 62.5 + - - -
87J TYR* 4.6 4.5 - - - +
88J GLU* 3.0 46.0 + - - +
2009N G 5.8 1.7 + - - -
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Residues in contact with SER 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J VAL* 4.3 1.6 - - - +
81J HIS* 5.1 0.7 - - - -
82J GLY* 3.4 12.7 + - - -
83J ASP 3.3 0.8 - - - -
84J SER* 1.3 79.4 + - - +
86J ILE* 1.3 60.9 + - - +
88J GLU* 4.5 3.9 - - - +
89J ALA* 3.4 21.8 + - - +
6N T 4.2 13.5 - - - +
7N A 3.3 59.6 + - - -
8N C 4.2 6.1 + - - -
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Residues in contact with ILE 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J VAL* 4.0 7.4 - - + -
49J ILE* 3.5 23.7 - - + +
70J ILE* 6.4 0.4 - - + -
71J VAL* 3.9 27.1 - - + +
74J VAL* 4.1 8.5 - - + -
75J MET* 3.7 35.0 - - + +
79J HIS* 3.6 39.7 - - + +
81J HIS 4.2 2.2 - - - +
82J GLY 3.4 15.0 + - - +
83J ASP 3.3 5.3 + - - +
84J SER 3.2 0.4 - - - -
85J SER* 1.3 73.9 - - - +
87J TYR* 1.3 66.0 + - - +
89J ALA* 3.2 5.5 + - - +
90J MET* 3.1 19.1 + - + +
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Residues in contact with TYR 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67J SER* 3.6 12.6 - - - -
71J VAL* 4.1 16.4 - - + +
83J ASP 2.8 21.9 + - - +
84J SER* 4.2 4.3 - - - +
86J ILE* 1.3 72.9 - - - +
88J GLU* 1.3 65.0 + - + +
90J MET* 3.1 22.8 + - + +
91J VAL* 2.8 52.4 + - + +
110J PHE* 4.7 0.9 - - - -
118J ALA* 4.0 4.8 - - + +
119J ALA 2.8 29.4 + - - -
120J ALA* 3.8 2.5 + - - -
121J MET* 3.7 30.7 - - + -
124J THR* 2.7 35.5 + - - +
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Residues in contact with GLU 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J SER* 3.0 34.9 + - - +
85J SER* 4.5 3.6 - - - +
87J TYR* 1.3 82.4 - - + +
89J ALA* 1.3 60.7 + - - +
91J VAL* 3.4 10.8 + - + +
92J ARG* 3.1 25.3 + - - +
6N T 4.3 20.3 + - + +
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Residues in contact with ALA 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J VAL* 4.0 25.8 - - + -
46J HIS* 3.9 11.5 - - - +
49J ILE* 4.0 7.2 - - + -
85J SER 3.4 18.3 + - - +
86J ILE 3.2 6.1 + - - +
88J GLU* 1.3 79.3 - - - +
90J MET* 1.3 60.9 + - - +
92J ARG* 3.8 3.6 + - - +
93J MET* 3.4 29.7 + - - +
6N T 4.0 17.7 + - - +
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Residues in contact with MET 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J ILE* 3.9 22.8 - - + +
53J LEU* 5.4 2.0 - - + -
67J SER* 3.5 28.3 - - - +
70J ILE* 4.1 27.4 - - - -
71J VAL* 5.1 5.4 - - + -
86J ILE* 3.1 13.7 + - + +
87J TYR* 3.4 27.4 - - + +
89J ALA* 1.3 75.1 - - - +
91J VAL* 1.3 65.1 + - - +
93J MET* 3.2 23.0 + - - +
94J ALA* 3.4 11.1 + - - +
104J VAL* 4.1 14.2 - - + +
110J PHE* 4.2 11.7 - - + -
126J ALA* 3.9 21.5 - - + -
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Residues in contact with VAL 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J TYR* 2.8 52.0 + - + +
88J GLU* 3.4 13.2 + - + +
90J MET* 1.3 75.9 - - - +
92J ARG* 1.3 55.1 + - - +
94J ALA* 2.8 28.1 + - - +
95J GLN* 3.3 33.4 + - - +
110J PHE* 3.8 20.1 - - + +
118J ALA* 3.6 28.0 - - + +
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Residues in contact with ARG 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LYS* 6.1 0.4 - - - +
46J HIS* 4.7 2.2 + - - -
88J GLU 3.1 13.1 + - - +
89J ALA* 3.9 6.5 - - - +
90J MET 3.3 0.2 - - - -
91J VAL* 1.3 78.5 - - - +
93J MET* 1.3 57.3 - - - +
94J ALA 3.0 5.2 + - - -
95J GLN* 3.1 34.0 + - - +
98J SER* 3.6 23.5 + - - +
99J TYR* 3.1 53.3 + - + -
171J GLY 5.7 1.8 + - - -
172J ALA* 5.5 5.1 - - - +
173J SER* 5.5 7.0 + - - +
266J PHE* 5.7 3.2 - - - -
267J GLN* 5.3 4.4 - - - +
5N G 3.4 40.6 + - - +
6N T 3.8 32.8 + - - -
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Residues in contact with MET 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J HIS* 3.9 25.4 - - + +
49J ILE* 3.6 41.1 - - + -
50J LEU* 4.1 18.8 - - + -
89J ALA 3.4 18.4 + - - +
90J MET* 3.2 14.0 + - - +
92J ARG* 1.3 75.5 - - - +
94J ALA* 1.3 55.6 + - - +
95J GLN 3.5 0.4 - - - -
99J TYR* 3.5 32.1 - - + +
102J PRO* 3.4 8.1 - - - +
103J LEU* 3.0 41.6 + - + -
104J VAL* 3.2 16.6 + - + -
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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