Contacts of the helix formed by residues 106 - 117 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.0 40.6 - - + -
76A LEU 5.4 0.2 - - - -
77A THR* 3.8 24.7 - - + +
82A ALA* 4.2 10.8 - - + -
83A ASP* 2.7 54.6 + - + +
85A PRO 3.0 12.3 + - - -
86A GLN* 3.4 31.6 - - - +
87A ARG 4.2 0.7 - - - -
88A LEU* 4.5 9.6 - - + -
104A PRO* 3.0 17.2 - - + +
105A ARG* 1.3 79.3 - - - +
107A ALA* 1.3 66.1 + - + +
108A ASN 3.2 0.7 + - - -
109A TYR* 3.3 28.9 + - + +
110A VAL* 4.2 9.1 + - + +
129A VAL* 5.6 5.4 - - + -
135A LEU* 6.2 2.0 - - + -
145A LEU* 4.1 13.4 - - + +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.8 0.9 - - + -
88A LEU* 3.2 35.2 - - + -
104A PRO* 3.1 18.5 + - + +
106A TRP* 1.3 93.2 - - + +
108A ASN* 1.3 64.3 + - - +
110A VAL* 3.3 10.0 - - + +
111A LYS* 3.0 36.4 + - + +
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Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PRO* 3.3 7.8 - - - +
102A GLY 3.0 45.0 + - - +
104A PRO 4.1 0.7 - - - +
105A ARG* 2.9 30.3 + - - +
107A ALA* 1.3 79.0 - - - +
109A TYR* 1.3 59.4 + - + +
111A LYS* 3.8 8.7 - - - +
112A GLY* 2.9 24.8 + - - -
177A PHE* 3.3 38.9 + - + +
178A ALA* 4.7 4.1 - - - +
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.9 14.1 - - + -
106A TRP* 3.5 17.3 - - - +
107A ALA 3.2 1.0 - - - -
108A ASN* 1.3 79.9 - - + +
110A VAL* 1.3 61.1 + - - +
112A GLY* 4.1 0.7 - - - -
113A VAL* 3.3 27.9 + - - +
142A SER* 3.3 32.7 - - - -
145A LEU* 3.7 27.1 - - + -
146A GLU* 3.4 30.4 - - + +
149A THR* 5.5 0.2 - - - -
173A ALA* 4.5 4.8 - - - +
174A GLU* 4.4 7.6 + - - -
177A PHE* 5.5 0.4 - - - -
178A ALA* 3.8 29.5 + - + +
180A MET* 5.5 2.4 - - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.1 39.7 - - + -
90A PHE* 4.5 3.6 - - + -
106A TRP* 4.6 10.1 - - + +
107A ALA 3.3 11.4 + - - +
109A TYR* 1.3 72.9 - - - +
111A LYS* 1.3 74.4 + - + +
113A VAL* 3.3 2.4 + - - +
114A ILE* 3.0 32.3 + - + +
125A PHE* 6.3 0.9 - - + -
129A VAL* 5.5 4.9 - - + -
145A LEU* 4.0 24.7 - - + -
149A THR* 3.8 29.7 - - + +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.7 19.4 - - - +
90A PHE* 3.7 47.9 - - + +
99A LEU* 3.9 23.4 - - + +
100A GLU 4.1 21.5 + - - +
102A GLY* 4.6 9.3 - - - +
103A THR 4.5 9.5 + - - +
107A ALA* 3.0 25.7 + - - +
108A ASN* 3.8 9.2 + - - +
110A VAL* 1.3 83.1 - - - +
112A GLY* 1.3 57.7 + - - +
114A ILE* 3.2 6.3 + - - +
115A GLN* 2.9 28.8 + - - +
177A PHE* 4.1 11.7 - - + -
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASN 2.9 13.9 + - - -
109A TYR 3.6 0.4 + - - -
111A LYS* 1.3 76.8 - - - +
113A VAL* 1.3 60.2 + - - +
115A GLN* 3.2 1.6 + - - +
116A TYR* 3.1 29.8 + - - -
173A ALA* 3.4 15.7 - - - -
177A PHE* 3.3 30.4 - - - -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR 3.3 15.8 + - - +
110A VAL 3.3 7.4 + - - +
112A GLY* 1.3 74.4 - - - +
114A ILE* 1.3 62.8 + - - +
116A TYR* 3.4 1.4 + - - +
117A TYR* 3.0 22.7 + - - +
146A GLU* 3.8 31.4 - - + +
149A THR* 3.6 22.9 - - + -
150A TYR* 3.9 33.9 - - + +
153A LEU* 4.1 4.9 - - + -
169A VAL* 4.5 5.4 - - + +
170A CYS* 4.5 5.8 - - - -
173A ALA* 3.5 12.8 - - + +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.2 11.9 - - + -
90A PHE* 4.3 19.1 - - + -
92A LEU* 4.9 4.5 - - + -
93A PRO* 3.8 30.8 - - + +
99A LEU* 4.2 4.3 - - + -
110A VAL* 3.0 26.5 + - + +
111A LYS* 3.4 7.2 - - - +
113A VAL* 1.3 75.3 - - - +
115A GLN* 1.3 62.1 + - - +
116A TYR 3.2 0.5 + - - -
117A TYR* 3.3 15.1 + - - +
122A LEU* 4.3 17.3 - - + +
125A PHE* 3.8 31.2 - - + -
149A THR* 4.9 2.9 - - + -
153A LEU* 4.1 20.0 - - + -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 3.4 20.8 - - - +
98A SER* 3.3 27.1 + - - -
99A LEU* 3.1 29.0 + - + +
111A LYS 2.9 15.4 + - - +
112A GLY 3.2 5.4 + - - +
114A ILE* 1.3 79.5 - - - +
116A TYR* 1.3 72.9 + - + +
117A TYR 3.7 2.8 + - - +
177A PHE* 3.9 23.3 - - + -
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLY 3.1 22.0 + - - +
113A VAL 3.7 1.1 - - - -
115A GLN* 1.3 84.5 - - + +
117A TYR* 1.3 66.4 + - - +
118A PRO* 3.3 7.4 - - - +
169A VAL* 3.7 30.6 - - + +
172A GLN* 3.9 34.1 + - + -
173A ALA* 4.0 14.6 - - + -
176A SER* 3.0 26.8 + - - -
177A PHE* 3.9 25.7 - + - -
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL 3.0 14.3 + - - +
114A ILE 3.3 11.9 + - - +
115A GLN 4.5 3.1 - - - +
116A TYR* 1.3 77.0 - - - +
118A PRO* 1.3 69.5 - - + +
119A ALA* 3.3 39.7 + - + +
122A LEU* 4.2 15.3 - - + -
150A TYR* 3.6 38.1 - + - -
153A LEU* 3.6 38.1 - - + -
154A GLN* 3.0 22.5 - - - +
157A CYS* 2.6 34.0 + - + -
159A ASP* 3.5 11.8 + - + -
169A VAL* 4.6 2.0 - - - -
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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