Contacts of the helix formed by residues 82 - 93 (chain r) 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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81r HIS* 1.3 80.0 - - - +
83r ASP* 1.3 65.0 + - - -
84r SER* 3.3 5.8 - - - -
85r SER* 3.4 16.5 + - - -
86r ILE* 3.4 15.1 + - - +
122t ARG* 3.4 24.1 - - - -
8v C 3.2 12.6 + - - -
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Residues in contact with ASP 83 (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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71r VAL* 3.9 14.1 - - + +
75r MET* 3.5 28.7 - - + +
81r HIS 3.7 1.6 + - - -
82r GLY* 1.3 70.1 - - - -
84r SER* 1.3 67.3 + - - +
86r ILE* 3.3 3.6 + - - +
87r TYR* 2.9 30.8 + - - +
121r MET* 3.8 20.1 - - + +
83t ASP* 5.6 2.3 - - - +
121t MET* 6.0 7.2 - - + -
122t ARG* 4.6 13.1 - - - +
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Residues in contact with SER 84 (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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82r GLY* 4.7 3.1 - - - -
83r ASP* 1.3 85.8 + - - +
85r SER* 1.3 62.6 + - - +
87r TYR* 4.6 5.2 - - - +
88r GLU* 3.0 45.4 + - - +
121r MET* 5.2 1.6 - - - -
2009v G 5.1 10.2 + - - -
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Residues in contact with SER 85 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45r VAL* 4.3 1.6 - - - +
81r HIS* 5.1 1.1 - - - -
82r GLY* 3.4 13.3 + - - -
83r ASP 3.3 0.6 - - - -
84r SER* 1.3 78.7 + - - +
86r ILE* 1.3 61.1 + - - +
88r GLU* 4.4 5.3 - - - +
89r ALA* 3.4 21.8 + - - +
6v T 4.4 12.9 - - - +
7v A 3.7 51.4 + - - -
8v C 4.1 11.6 + - - -
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Residues in contact with ILE 86 (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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45r VAL* 4.1 8.5 - - + -
49r ILE* 3.5 25.9 - - + +
70r ILE* 6.4 0.4 - - + -
71r VAL* 3.9 26.5 - - + +
74r VAL* 4.1 9.0 - - + -
75r MET* 3.7 38.8 - - + +
79r HIS* 3.6 37.9 - - + +
81r HIS 4.2 1.8 - - - +
82r GLY 3.4 13.9 + - - +
83r ASP 3.3 5.7 + - - +
84r SER 3.2 0.4 - - - -
85r SER* 1.3 74.1 - - - +
87r TYR* 1.3 66.5 + - - +
89r ALA* 3.2 2.3 + - - +
90r MET* 3.1 20.0 + - + +
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Residues in contact with TYR 87 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67r SER* 3.6 11.9 - - - -
71r VAL* 4.0 12.3 - - + +
83r ASP 2.9 20.7 + - - +
84r SER* 4.1 3.6 - - - +
86r ILE* 1.3 71.7 - - - +
88r GLU* 1.3 64.6 + - + +
90r MET* 3.1 22.5 + - + +
91r VAL* 2.8 51.1 + - + +
110r PHE* 4.7 1.3 - + - -
118r ALA* 4.0 7.8 - - + +
119r ALA 2.8 28.8 + - - -
120r ALA* 3.8 1.9 + - - -
121r MET* 3.6 39.5 - - + -
124r THR* 2.7 36.6 + - - +
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Residues in contact with GLU 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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84r SER* 3.0 34.4 + - - +
85r SER* 4.4 4.4 - - - +
87r TYR* 1.3 82.6 - - + +
89r ALA* 1.3 61.4 + - - +
91r VAL* 3.5 10.5 - - + +
92r ARG* 3.1 24.6 + - - +
6v T 4.2 20.6 + - + +
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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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45r VAL* 4.0 28.3 - - + -
46r HIS* 3.9 12.3 - - + +
49r ILE* 4.1 3.8 - - + -
85r SER 3.4 17.7 + - - +
86r ILE 3.2 5.9 + - - +
88r GLU* 1.3 78.9 - - - +
90r MET* 1.3 61.2 + - - +
92r ARG* 3.8 3.7 + - - +
93r MET* 3.4 28.4 + - - +
6v T 4.0 16.6 - - - +
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Residues in contact with MET 90 (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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49r ILE* 3.9 21.9 - - + +
53r LEU* 5.4 2.0 - - - -
67r SER* 3.5 27.6 - - - +
70r ILE* 4.1 27.1 - - - -
71r VAL* 5.2 4.7 - - + -
86r ILE* 3.1 13.7 + - + +
87r TYR* 3.1 28.0 + - + +
89r ALA* 1.3 74.3 - - - +
91r VAL* 1.3 66.6 + - - +
93r MET* 3.2 22.0 + - - +
94r ALA* 3.4 10.9 + - - +
104r VAL* 4.1 15.7 - - + +
110r PHE* 4.3 10.8 - - + -
126r ALA* 3.9 21.8 - - + -
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Residues in contact with VAL 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 TYR* 2.8 43.9 + - + +
88r GLU* 3.5 12.1 - - + +
90r MET* 1.3 74.6 - - - +
92r ARG* 1.3 54.4 + - - +
94r ALA* 2.8 28.1 + - - +
95r GLN* 3.3 33.2 + - - +
110r PHE* 3.7 21.4 - - + +
118r ALA* 3.6 34.5 - - + +
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Residues in contact with ARG 92 (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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46r HIS* 4.5 2.2 + - - -
88r GLU 3.1 13.7 + - - +
89r ALA* 3.9 6.3 - - - +
90r MET 3.3 0.2 - - - -
91r VAL* 1.3 76.9 - - - +
93r MET* 1.3 58.0 + - - +
94r ALA 3.1 4.3 + - - -
95r GLN* 3.1 35.2 + - - +
98r SER* 3.6 22.8 + - - +
99r TYR* 3.1 54.4 + - + -
171r GLY 5.8 1.2 + - - -
172r ALA* 5.6 7.5 - - - +
173r SER* 5.6 2.8 + - - +
266r PHE* 5.8 2.6 - - - -
267r GLN* 5.3 4.4 - - - +
5v G 3.3 42.2 + - - +
6v T 3.5 33.9 + - - -
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Residues in contact with MET 93 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46r HIS* 3.9 25.8 - - + +
49r ILE* 3.6 40.6 - - + -
50r LEU* 4.1 19.5 - - + -
89r ALA 3.4 18.6 + - - +
90r MET* 3.2 14.0 + - - +
92r ARG* 1.3 75.0 - - - +
94r ALA* 1.3 56.7 + - - +
95r GLN 3.5 0.2 - - - -
99r TYR* 3.5 32.8 - - + +
102r PRO* 3.5 8.7 - - - +
103r LEU* 3.0 40.0 + - + -
104r VAL* 3.2 16.2 + - + -
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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