Contacts of the helix formed by residues 106 - 117 (chain B) in PDB entry 6GR2
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 TRP 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LEU* 4.0 34.8 - - + -
77B THR* 3.7 26.5 - - + -
82B ALA* 4.2 11.4 - - + -
83B ASP* 3.0 34.7 + - + +
85B PRO 3.0 21.5 + - - -
86B GLN* 3.6 26.9 - - - +
87B ARG 4.5 0.4 - - - -
88B LEU* 4.6 7.2 - - + -
104B PRO* 3.4 17.6 - - + +
105B ARG* 1.3 77.8 - - - +
107B ALA* 1.3 75.7 + - + +
108B ASN 3.2 0.9 + - - -
109B TYR* 3.4 28.5 + - + +
110B VAL* 4.1 11.3 - - + +
129B VAL* 5.1 7.4 - - + -
135B LEU* 6.4 0.7 - - + -
145B LEU* 4.1 13.4 - - + +
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Residues in contact with ALA 107 (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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75B LEU* 4.9 3.8 - - + -
88B LEU* 3.5 31.2 - - + -
104B PRO* 3.4 16.0 + - + +
105B ARG 3.2 1.2 + - - -
106B TRP* 1.3 98.7 - - + +
108B ASN* 1.3 59.5 + - - +
109B TYR 3.2 0.4 - - - -
110B VAL* 3.4 6.6 + - + +
111B LYS* 2.8 38.0 + - + +
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Residues in contact with ASN 108 (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 PRO* 3.4 6.7 - - - +
102B GLY 3.0 44.5 + - - +
104B PRO 3.9 1.7 - - - +
105B ARG* 3.0 26.1 + - - +
107B ALA* 1.3 77.5 - - - +
109B TYR* 1.3 57.1 + - + +
111B LYS* 3.6 10.6 + - - +
112B GLY 2.7 29.3 + - - -
177B PHE* 3.4 40.5 + - + +
178B ALA* 4.7 3.6 - - - +
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Residues in contact with TYR 109 (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 ARG* 4.1 13.0 - - + -
106B TRP* 3.4 22.2 - - - +
107B ALA 3.2 0.8 - - - -
108B ASN* 1.3 78.5 - - + +
110B VAL* 1.3 60.4 + - - +
112B GLY* 4.0 1.3 - - - -
113B VAL* 3.1 31.2 + - - +
142B SER* 3.7 25.0 - - - -
145B LEU* 4.1 19.7 - - + -
146B GLU* 3.2 38.3 - - + +
149B THR* 5.4 0.4 - - - -
173B ALA* 4.5 4.4 - - - +
174B GLU* 4.4 8.6 + - + -
177B PHE* 5.4 1.1 - - - -
178B ALA* 3.5 32.0 + - + +
180B MET* 5.5 2.6 - - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.4 34.3 - - + -
90B PHE* 4.7 1.3 - - + -
106B TRP* 4.1 14.6 - - + +
107B ALA* 3.7 20.4 - - - +
109B TYR* 1.3 71.5 - - - +
111B LYS* 1.3 67.3 + - - +
113B VAL* 3.3 1.6 + - - +
114B ILE* 3.0 45.2 + - + +
125B PHE* 5.3 2.0 - - + -
129B VAL* 5.9 2.9 - - + -
145B LEU* 4.6 11.9 - - + -
149B THR* 3.7 30.0 - - + +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.8 29.6 - - - +
90B PHE* 3.5 38.3 - - + +
99B LEU* 3.4 22.4 - - + +
100B GLU 3.9 22.8 + - - +
102B GLY* 4.6 8.3 - - - +
103B THR 4.4 13.1 + - - -
107B ALA* 2.8 27.9 + - - +
108B ASN* 3.6 12.6 + - - +
110B VAL* 1.3 78.8 - - - +
112B GLY* 1.3 56.5 + - - +
114B ILE* 3.2 3.1 + - - -
115B GLN* 2.9 25.6 + - - +
177B PHE* 4.2 10.5 - - + -
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Residues in contact with GLY 112 (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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108B ASN 2.7 17.1 + - - -
109B TYR 4.0 1.6 - - - -
111B LYS* 1.3 74.6 - - - +
113B VAL* 1.3 61.4 + - - +
115B GLN* 3.2 1.2 + - - +
116B TYR* 3.0 29.5 + - - -
173B ALA* 3.6 10.8 - - - -
177B PHE* 3.3 33.6 - - - -
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Residues in contact with VAL 113 (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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109B TYR 3.1 19.7 + - - +
110B VAL 3.8 3.8 - - - +
112B GLY* 1.3 74.4 - - - +
114B ILE* 1.3 57.6 + - - +
116B TYR 3.4 0.5 + - - -
117B TYR* 2.8 28.9 + - - +
146B GLU* 3.8 29.2 - - + +
149B THR* 3.9 20.0 - - + -
150B TYR* 3.9 35.7 - - + +
153B LEU* 4.2 4.9 - - + -
169B VAL* 4.4 6.8 - - + +
170B CYS* 4.6 5.4 - - - -
173B ALA* 3.6 15.0 - - + +
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Residues in contact with ILE 114 (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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73B VAL* 4.3 5.8 - - + -
90B PHE* 4.2 19.7 - - + -
92B LEU* 4.5 6.3 - - + -
93B PRO* 3.9 29.0 - - + +
99B LEU* 4.0 2.7 - - + -
110B VAL* 3.0 34.1 + - + +
111B LYS* 3.5 6.1 - - - +
113B VAL* 1.3 76.3 - - - +
115B GLN* 1.3 63.8 + - - +
117B TYR* 3.2 15.6 + - - +
122B LEU* 4.0 19.5 - - + +
125B PHE* 3.9 24.5 - - + -
149B THR* 4.8 2.0 - - + -
153B LEU* 4.1 19.5 - - + -
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Residues in contact with GLN 115 (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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93B PRO* 3.4 17.5 - - - +
98B SER* 3.3 26.4 + - - -
99B LEU* 2.7 36.8 + - + +
111B LYS 2.9 16.3 + - - +
112B GLY 3.2 5.1 + - - +
114B ILE* 1.3 77.8 - - - +
116B TYR* 1.3 71.5 + - + +
117B TYR 3.8 2.3 + - - +
177B PHE* 3.7 25.1 - - + -
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Residues in contact with TYR 116 (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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112B GLY 3.0 23.3 + - - +
113B VAL 3.6 1.1 - - - -
115B GLN* 1.3 84.7 - - + +
117B TYR* 1.3 67.0 + - - +
118B PRO* 3.3 7.6 - - - +
169B VAL* 3.7 27.8 - - + +
172B GLN* 4.0 24.4 + - + -
173B ALA* 4.0 14.4 - - - -
176B SER* 3.1 30.4 + - - -
177B PHE* 3.6 29.5 - + - -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL 2.8 14.7 + - - +
114B ILE* 3.2 12.7 + - - +
115B GLN 4.7 2.3 - - - +
116B TYR* 1.3 77.5 - - - +
118B PRO* 1.3 69.3 - - + +
119B ALA* 3.4 50.2 + - + +
122B LEU* 4.2 24.5 - - + -
150B TYR* 3.6 39.0 - + - -
153B LEU* 3.7 32.8 - - + -
154B GLN* 3.3 18.5 - - - +
157B CYS* 2.6 25.5 + - + -
159B ASP* 3.6 9.7 + - + +
169B VAL* 4.6 1.6 - - - -
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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