Contacts of the helix formed by residues 140 - 157 (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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO 5.4 0.2 + - - -
36A GLY* 4.1 1.9 - - - -
37A ARG* 3.3 27.6 + - - +
133A VAL* 4.4 0.2 - - - -
138A GLY* 3.2 6.3 - - - +
139A LEU* 1.3 94.5 + - - +
141A SER* 1.3 65.4 + - - +
142A SER* 3.2 7.6 - - - +
143A ALA* 4.2 4.4 - - - +
144A SER* 3.1 21.0 + - - -
186A ASP* 3.5 38.1 + - - +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 4.8 1.3 + - - -
131A SER* 5.4 1.1 - - - -
133A VAL* 3.7 25.0 - - - +
134A PRO 4.0 5.7 + - - -
135A LEU* 3.6 36.9 - - - +
136A GLY 3.8 7.1 + - - -
139A LEU 3.5 2.2 - - - +
140A SER* 1.3 73.8 - - - +
142A SER* 1.3 62.0 + - - +
144A SER* 3.2 5.3 + - - -
145A LEU* 2.8 30.8 + - - +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.3 37.9 - - - -
140A SER* 4.6 5.9 - - - -
141A SER* 1.3 81.0 + - - +
143A ALA* 1.3 67.8 + - - +
145A LEU* 3.1 7.6 + - - +
146A GLU* 2.9 33.8 + - - +
174A GLU* 3.4 20.2 + - - -
186A ASP* 5.3 2.4 + - - -
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Residues in contact with ALA 143 (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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140A SER* 3.6 7.9 + - - +
142A SER* 1.3 81.2 + - - +
144A SER* 1.3 58.5 + - - +
146A GLU* 3.5 11.7 - - - +
147A VAL* 2.8 38.0 + - + +
186A ASP* 3.5 45.8 - - + +
187A GLN* 3.9 13.0 - - - +
190A SER* 4.7 2.5 - - - -
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Residues in contact with SER 144 (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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34A ALA* 2.8 23.4 + - - +
35A PRO 3.6 21.6 + - - -
36A GLY* 4.0 2.6 + - - -
61A THR* 2.8 25.7 + - - -
133A VAL* 4.2 3.2 - - - +
140A SER 3.1 15.2 + - - -
141A SER* 3.4 12.3 - - - -
143A ALA* 1.3 76.9 - - - +
145A LEU* 1.3 62.4 + - - +
148A ALA* 3.0 27.4 + - - +
190A SER* 4.2 4.0 - - - -
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Residues in contact with LEU 145 (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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61A THR* 4.2 9.6 + - + +
63A LEU* 5.7 0.9 - - + -
106A TRP* 4.1 20.9 - - + +
109A TYR* 3.7 27.8 - - + -
110A VAL* 4.0 24.0 - - + -
129A VAL* 3.8 34.8 - - + -
141A SER 2.8 16.7 + - - +
142A SER* 3.5 9.2 - - - +
144A SER* 1.3 73.4 - - - +
146A GLU* 1.3 58.9 + - - +
148A ALA* 3.8 1.6 - - + +
149A THR* 2.9 35.2 + - - +
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Residues in contact with GLU 146 (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* 3.4 28.9 - - + +
113A VAL* 3.8 25.7 - - + +
142A SER 2.9 15.5 + - - +
143A ALA* 3.2 7.3 + - - +
145A LEU* 1.3 76.5 - - - +
147A VAL* 1.3 57.7 + - - +
149A THR* 3.2 5.3 + - - -
150A TYR* 2.8 28.2 + - - +
170A CYS* 3.2 29.3 - - + +
173A ALA* 5.3 0.7 - - + -
174A GLU* 2.7 34.4 - - - +
187A GLN* 3.3 21.0 + - - +
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Residues in contact with VAL 147 (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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34A ALA* 4.0 1.6 - - + -
143A ALA 2.8 23.7 + - - +
146A GLU* 1.3 68.6 - - - +
148A ALA* 1.3 64.2 + - - +
150A TYR* 3.3 1.9 + - + +
151A THR* 2.8 30.5 + - - -
170A CYS* 4.0 13.9 - - + -
187A GLN* 4.0 12.8 - - + +
190A SER* 3.8 26.2 - - - +
191A LEU* 3.4 44.6 - - + -
387A ALA* 3.6 21.8 - - + -
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Residues in contact with ALA 148 (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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32A VAL* 3.2 26.4 - - + +
34A ALA* 3.4 15.1 - - + +
61A THR* 4.0 23.8 - - + +
63A LEU* 4.2 9.4 - - + -
144A SER 3.0 20.1 + - - +
145A LEU* 3.8 4.7 - - + +
147A VAL* 1.3 76.8 - - - +
149A THR* 1.3 63.1 + - - +
151A THR* 4.5 0.7 - - - -
152A PHE* 2.9 19.6 + - - +
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Residues in contact with THR 149 (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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63A LEU* 3.9 17.4 - - + +
110A VAL* 3.8 34.4 - - + +
113A VAL* 3.6 24.9 - - + -
114A ILE* 4.9 2.7 - - + -
125A PHE* 5.8 4.0 - - + -
145A LEU* 2.9 22.0 + - - +
146A GLU* 3.3 10.5 - - - -
148A ALA* 1.3 75.7 - - - +
150A TYR* 1.3 63.2 + - - +
152A PHE* 2.9 4.7 + - + +
153A LEU* 2.9 35.2 + - + +
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Residues in contact with TYR 150 (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* 3.9 9.2 - - + +
117A TYR* 3.6 24.2 - + - -
118A PRO* 3.5 18.7 - - + +
146A GLU 2.8 18.9 + - - +
147A VAL* 3.3 6.7 + - + +
149A THR* 1.3 71.5 - - - +
151A THR* 1.3 64.5 + - - +
153A LEU* 3.2 6.5 + - - +
154A GLN* 3.0 36.0 + - - -
159A ASP* 2.6 32.0 + - - -
165A ALA* 5.1 1.4 - - - +
166A ARG* 3.2 30.8 + - + +
169A VAL* 3.6 37.3 - - + +
170A CYS* 3.8 19.1 - - - -
191A LEU* 5.5 2.9 - - + -
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Residues in contact with THR 151 (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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32A VAL* 3.2 27.6 - - + -
33A SER 5.2 0.7 - - - -
147A VAL* 2.8 19.5 + - - +
148A ALA* 3.8 2.4 - - - -
150A TYR* 1.3 75.6 - - - +
152A PHE* 1.3 62.8 + - - +
154A GLN* 3.3 22.6 + - - +
155A GLN* 3.0 27.5 + - - +
191A LEU* 5.1 3.1 - - - +
387A ALA* 3.7 18.1 - - + +
388A LYS* 4.4 11.4 - - - +
389A VAL* 4.0 18.2 - - + -
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Residues in contact with PHE 152 (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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30A LEU* 3.6 34.3 - - + -
32A VAL* 3.9 10.0 - - + +
63A LEU* 3.6 30.3 - - + -
64A VAL 4.5 0.4 - - - -
65A GLY* 3.6 35.0 - - - -
66A SER 4.0 2.9 - - - -
125A PHE* 3.1 43.7 - + + -
127A ALA* 4.0 6.3 - - + -
148A ALA 2.9 14.0 + - - +
149A THR* 3.2 8.7 - - + +
151A THR* 1.3 76.4 - - - +
153A LEU* 1.3 62.1 + - + +
155A GLN* 2.8 32.4 + - + +
156A LEU* 3.3 17.1 + - + +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.1 13.9 - - + -
114A ILE* 4.1 19.5 - - + -
117A TYR* 3.4 46.8 - - + -
122A LEU* 4.2 13.0 - - + +
125A PHE* 4.0 25.8 - - + -
149A THR* 2.9 22.3 + - + +
150A TYR 3.7 1.6 - - - +
152A PHE* 1.3 77.2 - - + +
154A GLN* 1.3 52.7 + - - +
156A LEU* 3.1 27.0 + - + +
157A CYS* 2.7 37.2 + - - +
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Residues in contact with GLN 154 (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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117A TYR* 3.0 18.6 + - - +
150A TYR* 3.0 40.6 + - + +
151A THR* 3.3 28.8 + - - +
152A PHE 3.1 0.2 - - - -
153A LEU* 1.3 76.5 - - - +
155A GLN* 1.3 68.3 + - - +
157A CYS 3.7 0.9 - - - -
158A PRO* 3.0 33.7 - - + +
159A ASP* 3.4 9.2 + - - +
166A ARG* 3.1 41.4 + - - +
191A LEU* 5.3 1.7 - - - +
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Residues in contact with GLN 155 (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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30A LEU* 3.8 37.8 - - + +
31A ALA 5.2 1.1 - - - +
32A VAL* 4.6 4.7 - - + -
151A THR* 3.0 24.4 + - - +
152A PHE* 2.8 18.6 + - + +
154A GLN* 1.3 86.8 - - - +
156A LEU* 1.3 61.4 + - - +
158A PRO* 4.7 3.1 - - - +
389A VAL* 3.3 46.9 - - + +
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Residues in contact with LEU 156 (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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30A LEU* 3.8 22.2 - - + -
67A PRO* 4.1 31.6 - - + -
121A PRO 4.9 0.7 - - - +
122A LEU* 4.3 4.7 - - + -
123A PRO* 3.9 32.8 - - + +
125A PHE* 3.7 36.8 - - + -
152A PHE* 3.9 16.4 - - + +
153A LEU* 3.1 23.5 + - + +
155A GLN* 1.3 77.3 - - - +
157A CYS* 1.3 61.0 + - - +
158A PRO* 4.3 1.7 - - - +
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Residues in contact with CYS 157 (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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117A TYR* 2.6 31.9 + - + -
119A ALA* 3.5 23.6 - - - -
120A ALA 3.6 28.3 - - - -
121A PRO* 3.8 12.8 - - - +
122A LEU* 3.9 21.1 - - + -
153A LEU 2.7 8.1 + - - -
154A GLN 3.4 2.2 - - - -
155A GLN 3.3 0.2 - - - -
156A LEU* 1.3 76.6 - - - +
158A PRO* 1.3 69.8 - - - +
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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