Contacts of the helix formed by residues 147 - 156 (chain B) in PDB entry 2GM4
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 ASP 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B LYS 3.4 5.2 + - - +
146B ILE* 1.3 71.2 - - - +
148B ARG* 1.3 60.3 + - - +
149B ASP* 4.1 13.3 + - - +
150B ALA* 3.0 39.2 + - + +
151B VAL* 3.4 7.4 + - - +
168B MET* 5.1 2.6 - - - +
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Residues in contact with ARG 148 (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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144B ARG* 3.1 50.5 - - + +
146B ILE* 2.7 22.1 + - + +
147B ASP* 1.3 67.0 + - - +
149B ASP* 1.3 56.1 + - - +
150B ALA 2.7 15.7 + - - -
151B VAL* 2.8 10.5 + - - +
152B LEU* 2.7 32.9 + - + +
177B LYS* 5.0 9.5 - - - +
178B VAL* 4.0 33.4 - - + +
181B GLU* 3.7 25.6 + - - +
25K A 3.8 6.1 + - - +
26K T 2.5 40.2 + - - -
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Residues in contact with ASP 149 (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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147B ASP* 3.4 9.5 + - - +
148B ARG* 1.3 78.2 - - - +
150B ALA* 1.3 56.1 + - - +
152B LEU* 4.4 14.9 - - - +
153B ASN* 3.2 34.7 + - - +
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Residues in contact with ALA 150 (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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147B ASP* 3.0 32.5 + - + +
148B ARG 2.7 1.8 + - - -
149B ASP* 1.3 78.1 - - - +
151B VAL* 1.3 63.3 + - - +
152B LEU 3.3 0.2 - - - -
153B ASN* 3.1 7.9 + - - +
154B MET* 3.0 28.7 + - + +
168B MET* 4.8 10.3 - - + -
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Residues in contact with VAL 151 (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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146B ILE* 4.5 8.1 - - + -
147B ASP 3.4 6.7 + - - +
148B ARG* 2.8 15.2 + - - +
150B ALA* 1.3 72.1 - - - +
152B LEU* 1.3 56.6 + - - +
154B MET* 2.8 23.4 + - - +
155B TRP* 3.1 11.1 + - - +
164B ILE* 4.5 5.1 - - + +
168B MET* 3.5 33.7 - - + -
170B ILE* 4.4 15.0 - - + -
175B VAL* 3.9 30.7 - - + +
178B VAL* 4.2 22.2 - - + -
179B ILE* 5.1 4.5 - - + -
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Residues in contact with LEU 152 (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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148B ARG* 2.7 21.8 + - + +
149B ASP* 4.4 17.3 - - - +
151B VAL* 1.3 76.4 - - - +
153B ASN* 1.3 59.9 + - - +
155B TRP* 3.5 6.3 + - + +
156B GLN* 3.1 57.4 + - + +
178B VAL* 5.3 10.0 - - + +
179B ILE* 5.4 20.0 - - + +
182B SER* 3.3 29.6 - - - +
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Residues in contact with ASN 153 (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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149B ASP* 3.2 22.3 + - - +
150B ALA* 3.1 10.4 + - - +
152B LEU* 1.3 78.5 - - - +
154B MET* 1.3 59.5 + - + +
155B TRP 3.5 0.4 - - - -
156B GLN* 3.6 27.6 + - - +
157B GLN* 3.5 27.7 + - - -
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Residues in contact with MET 154 (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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150B ALA* 3.0 12.0 + - + +
151B VAL* 2.8 12.3 + - - +
153B ASN* 1.3 81.5 - - + +
155B TRP* 1.3 57.9 + - - +
157B GLN* 3.7 8.4 - - - +
159B LEU* 3.1 47.8 + - + +
163B HIS* 5.9 0.9 - - + -
164B ILE* 4.0 23.4 - - + +
167B THR* 4.5 24.9 - - + -
168B MET* 3.6 27.1 - - + -
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Residues in contact with TRP 155 (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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151B VAL 3.1 8.9 + - - +
152B LEU* 3.5 7.2 + - + +
153B ASN 3.5 0.2 - - - -
154B MET* 1.3 75.2 - - - +
156B GLN* 1.3 56.1 + - - +
157B GLN 2.6 5.3 + - - -
158B GLY* 2.3 42.3 + - - +
159B LEU 4.5 13.8 + - - +
161B ALA* 5.2 12.6 - - + +
164B ILE* 4.5 4.7 - - + +
176B TYR* 6.4 0.6 - - - -
179B ILE* 3.4 44.1 - - + +
6J G 4.8 15.7 + - - -
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Residues in contact with GLN 156 (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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152B LEU* 3.1 41.1 + - + +
153B ASN* 3.6 26.2 + - - +
155B TRP* 1.3 81.8 - - - +
157B GLN* 1.3 59.0 + - - +
158B GLY 3.5 0.3 + - - -
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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