Contacts of the helix formed by residues 138 - 143 (chain A) in PDB entry 2VM6
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 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE 3.4 0.2 + - - -
135A ARG 4.0 4.5 + - - -
136A GLN 3.7 2.4 + - - -
137A ASN* 1.3 74.8 - - - +
139A GLY* 1.3 67.0 + - - +
141A GLU 4.4 0.2 + - - -
142A ASN* 3.3 19.3 + - - +
143A GLY* 3.0 16.2 + - - -
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Residues in contact with GLY 139 (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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86A TRP* 3.2 9.6 - - - -
134A ILE* 2.9 27.0 + - - -
135A ARG* 4.7 3.6 + - - +
137A ASN 3.5 0.8 + - - -
138A GLY* 1.3 78.2 - - - +
140A TRP* 1.3 58.5 + - - -
141A GLU 3.3 0.9 - - - -
143A GLY* 2.8 23.4 + - - -
144A PHE 3.1 8.0 + - - -
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Residues in contact with TRP 140 (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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8A TYR* 3.5 37.7 - + + +
9A ILE* 3.9 16.8 - - + +
12A LEU* 3.7 26.7 - - + -
33A THR* 3.9 4.7 - - + -
37A LEU* 4.4 7.0 - - + -
86A TRP* 3.8 11.0 - + - -
89A ILE* 3.6 24.5 - - + -
93A PHE* 3.7 18.8 - + - -
126A ILE* 4.4 9.4 - - + -
134A ILE* 3.9 38.3 - - + +
139A GLY* 1.3 72.7 - - - -
141A GLU* 1.3 58.6 + - + +
144A PHE* 3.3 39.0 + + + +
145A VAL* 2.9 35.8 + - - +
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Residues in contact with GLU 141 (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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8A TYR* 2.6 34.8 + - + +
31A SER* 5.6 0.5 + - - -
32A LYS* 5.8 2.1 - - - +
33A THR* 2.9 21.9 + - - -
138A GLY 4.4 0.4 + - - +
139A GLY* 3.3 0.6 - - - -
140A TRP* 1.3 79.2 - - + +
142A ASN* 1.3 62.5 + - - +
145A VAL* 3.6 19.0 - - - +
146A LYS* 4.2 10.0 + - - +
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Residues in contact with ASN 142 (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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138A GLY* 3.3 19.1 + - - +
141A GLU* 1.3 80.7 - - - +
143A GLY* 1.3 63.1 + - - +
146A LYS* 3.3 43.7 - - - +
165B ARG 5.2 1.9 - - - +
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Residues in contact with GLY 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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86A TRP* 3.6 8.4 + - - -
137A ASN 3.5 21.1 - - - -
138A GLY* 3.0 5.3 + - - -
139A GLY 2.8 18.9 + - - -
142A ASN* 1.3 74.9 - - - +
144A PHE* 1.3 64.7 + - - +
146A LYS* 4.4 0.2 - - - +
147A LYS* 3.4 22.3 + - - +
165B ARG 5.0 2.6 - - - +
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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