Contacts of the helix formed by residues 1231 - 1235 (chain B) in PDB entry 1VDV
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 ALA1231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B PHE 6.0 1.1 - - - +
144B GLN* 5.7 2.5 - - - +
146B ASN 5.5 1.3 - - - +
147B LEU* 4.5 7.4 - - + -
153B TYR* 3.4 19.0 - - - -
426B ARG* 3.8 28.0 - - - +
428B GLU* 3.8 22.2 - - + +
1229B ILE 3.4 1.6 + - - -
1230B PRO* 1.3 73.0 - - - +
1232B PHE* 1.3 68.9 + - - +
1233B GLY 3.1 1.8 - - - +
1234B SER* 2.9 24.0 + - - +
1235B ILE* 4.0 1.2 + - - +
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Residues in contact with PHE1232 (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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120B ILE* 3.9 21.3 - - + -
140B GLU* 4.9 12.1 - - + +
143B PHE* 3.4 43.2 + + + +
146B ASN* 3.5 17.9 - - + -
153B TYR* 3.2 43.9 - + + -
156B ILE* 3.7 33.2 - - + -
157B LEU* 3.5 42.4 - - + +
1231B ALA* 1.3 77.1 - - - +
1233B GLY* 1.3 60.1 + - - +
1234B SER 3.3 0.7 + - - -
1235B ILE* 3.6 23.4 - - - +
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Residues in contact with GLY1233 (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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140B GLU* 4.1 18.5 + - - +
427B ARG* 3.3 21.4 + - - -
428B GLU* 3.8 24.4 - - - +
551B LYS* 5.6 6.6 - - - +
1231B ALA* 3.1 4.0 - - - +
1232B PHE* 1.3 78.8 - - - +
1234B SER* 1.3 59.8 + - - +
1235B ILE 3.4 5.9 + - - +
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Residues in contact with SER1234 (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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426B ARG* 4.1 5.2 - - - +
427B ARG* 5.1 2.0 - - - +
428B GLU* 4.1 3.6 + - - -
1173B ASN* 2.7 30.9 + - - +
1203B LEU* 3.6 6.4 - - - +
1208B LEU* 3.6 20.5 - - - +
1230B PRO* 3.9 13.9 - - - -
1231B ALA* 2.9 39.0 + - - +
1233B GLY* 1.3 78.0 - - - +
1235B ILE* 1.3 60.0 + - - +
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Residues in contact with ILE1235 (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 GLY 3.2 29.4 - - - +
153B TYR* 3.8 23.1 - - + -
154B ARG* 3.9 23.8 - - + +
157B LEU* 4.5 11.2 - - + -
556B ASN* 5.6 2.5 - - - +
1173B ASN* 3.9 5.7 - - - +
1200B VAL* 4.1 15.5 - - + -
1203B LEU* 4.6 1.8 - - - -
1231B ALA 4.3 0.9 - - - +
1232B PHE 3.6 14.6 - - - +
1233B GLY 4.2 5.2 - - - +
1234B SER* 1.3 82.1 - - - +
1236B PRO* 1.3 83.8 - - + +
1237B THR* 3.2 6.0 + - - -
1239B PHE* 4.6 5.2 - - + -
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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