Contacts of the helix formed by residues 3104 - 3108 (chain 2) in PDB entry 1BMV
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 ILE3104 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20142 TRP* 3.5 44.6 - - + +
30892 ALA* 4.9 4.9 - - + -
31032 ASP* 1.3 89.4 - - - +
31052 TYR* 1.3 59.2 + - - +
31062 THR 3.3 1.1 - - - -
31072 ILE* 3.7 11.2 - - + +
31082 CYS* 2.4 53.0 + - + +
31122 CYS* 4.6 9.6 - - - -
31142 LEU* 4.0 24.5 - - + -
31512 ILE* 4.0 7.9 - - + -
31532 VAL* 3.9 22.7 - - + -
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Residues in contact with TYR3105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20132 ARG* 4.2 11.4 - - + -
20142 TRP* 3.9 30.1 - - + +
20372 GLY 3.7 2.1 + - - -
20382 GLY* 2.7 17.3 - - - -
20392 ALA* 3.2 28.5 - - + -
20462 LEU* 2.5 40.6 + - + -
20472 MET* 3.4 11.8 - - - -
20482 ASN* 3.6 31.2 - - - +
20512 ASN* 2.7 37.6 + - - +
21872 LEU* 4.9 4.9 - - + -
31032 ASP* 3.1 15.3 + - - +
31042 ILE* 1.3 82.3 - - - +
31062 THR* 1.3 62.6 + - - +
31082 CYS* 3.5 10.2 + - - -
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Residues in contact with THR3106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11751 ASN* 3.8 13.3 + - - -
11771 LEU* 3.5 24.7 - - + +
11781 MET 3.9 12.6 - - - +
20462 LEU* 3.7 12.5 - - + +
20472 MET 3.7 31.2 - - - +
20482 ASN* 4.4 1.8 - - - +
30932 ASN* 4.0 1.0 - - - +
31012 SER* 2.9 39.7 + - - +
31032 ASP* 3.3 13.6 - - - +
31052 TYR* 1.3 80.7 - - - +
31072 ILE* 1.3 57.9 + - - +
31082 CYS 3.7 0.7 + - - -
31092 SER* 4.1 3.8 + - - -
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Residues in contact with ILE3107 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11771 LEU* 4.7 10.5 - - + -
30892 ALA* 5.4 2.9 - - + -
30912 ALA* 2.7 39.9 - - + +
30932 ASN* 3.4 19.0 + - - +
31012 SER 4.2 4.5 - - - +
31022 SER* 3.7 12.6 - - - -
31032 ASP 3.6 28.5 - - - +
31042 ILE* 3.5 11.5 + - + -
31052 TYR 3.3 0.8 - - - -
31062 THR* 1.3 77.7 - - - +
31082 CYS* 1.4 56.8 + - + +
31112 ASP 5.7 0.2 - - - -
31122 CYS* 3.8 1.8 - - + +
31492 ASP* 4.0 8.7 - - + +
31512 ILE* 3.4 43.3 - - + -
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Residues in contact with CYS3108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20122 ASN* 3.4 22.8 - - - +
20132 ARG 4.8 0.4 - - - -
20142 TRP* 4.1 23.6 - - + -
21652 LYS* 3.7 17.2 + - + +
30932 ASN* 5.2 0.2 - - - -
31042 ILE* 2.4 38.1 - - + +
31052 TYR* 3.5 14.6 + - - -
31062 THR 3.7 1.6 - - - -
31072 ILE* 1.4 76.9 - - - +
31092 SER* 1.3 62.8 + - - +
31102 GLN 3.7 2.8 - - - -
31112 ASP 5.1 0.2 - - - -
31122 CYS* 3.7 31.4 + - - +
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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