Contacts of the helix formed by residues 1436 - 1440 (chain A) in PDB entry 4V1M
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 ILE1436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1063A MET* 3.3 22.7 - - + -
1422A ARG 5.5 1.3 - - - +
1424A VAL* 3.7 34.5 - - + +
1434A ALA* 2.6 22.8 + - + +
1435A PRO* 1.3 85.5 - - + +
1437A GLY* 1.3 72.1 + - - +
1438A THR 2.8 1.7 + - - -
1439A GLY 2.7 15.8 + - - -
1138B MET 5.0 0.2 - - - +
1139B ILE* 3.8 41.3 - - + +
1142B GLY* 3.9 15.7 - - - -
1143B ALA 5.0 0.2 - - - -
1144B ALA* 3.4 14.9 - - + +
1147B LEU* 6.0 2.9 - - + -
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Residues in contact with GLY1437 (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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849A MET* 4.4 0.2 - - - -
1061A GLY* 3.2 34.9 + - - -
1063A MET* 4.2 0.8 - - - +
1436A ILE* 1.3 67.1 - - - +
1438A THR* 1.3 53.1 + - - -
1439A GLY 2.8 1.0 + - - -
1440A ALA* 2.7 35.5 + - - +
1441A PHE* 3.8 4.9 - - - -
1142B GLY* 4.0 4.5 - - - -
88F TYR* 3.7 25.7 - - - +
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Residues in contact with THR1438 (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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500A GLU* 3.2 32.5 + - - +
504A LEU* 4.1 10.9 - - - +
1433A MET* 4.5 0.9 - - - -
1436A ILE 2.8 2.8 + - - -
1437A GLY* 1.3 68.2 - - - -
1439A GLY* 1.3 47.5 + - - -
1440A ALA 3.6 0.4 - - - -
1441A PHE* 3.3 15.0 - - - -
1142B GLY 3.1 17.1 + - - -
1144B ALA* 3.4 20.4 - - + -
1145B SER* 3.4 13.0 - - - +
88F TYR* 3.6 24.2 + - - +
91F ALA* 4.5 1.0 - - - +
92F ARG* 2.8 40.0 + - - +
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Residues in contact with GLY1439 (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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1433A MET* 3.9 18.2 - - - +
1434A ALA 3.6 11.1 - - - +
1435A PRO* 3.2 22.3 - - - +
1436A ILE 2.7 14.1 + - - -
1437A GLY 2.8 0.4 + - - -
1438A THR* 1.3 74.1 - - - +
1440A ALA* 1.4 55.2 + - - -
1441A PHE 3.3 10.0 + - - +
1144B ALA* 3.6 0.6 - - - +
92F ARG* 4.0 3.8 - - - -
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Residues in contact with ALA1440 (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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849A MET* 3.7 31.5 - - + +
852A TYR* 3.8 17.5 - - + +
1060A PRO 5.3 0.2 - - - +
1061A GLY* 4.2 7.0 - - - -
1435A PRO* 4.1 11.0 - - - +
1436A ILE 3.7 0.4 + - - -
1437A GLY 2.7 28.1 + - - +
1439A GLY* 1.4 70.1 - - - +
1441A PHE* 1.3 61.7 + - + +
137F TYR* 4.3 15.0 + - - +
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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