Contacts of the strand formed by residues 1090 - 1096 (chain 1) 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 LEU1090 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10891 SER* 1.3 81.3 + - - +
10911 VAL* 1.3 80.8 + - - +
10921 GLN* 3.7 35.7 - - + +
11101 THR* 4.1 12.8 - - + -
11111 LYS 3.5 9.4 - - - +
11121 SER* 4.1 14.8 - - - +
11501 LEU* 4.6 2.9 - - + +
11511 VAL* 4.0 0.5 - - - +
11521 ASP* 3.2 45.9 + - + +
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Residues in contact with VAL1091 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10901 LEU* 1.3 81.5 - - - +
10921 GLN* 1.3 59.2 + - - +
10931 VAL* 3.6 6.9 + - + +
11111 LYS 3.2 24.6 + - - +
11171 TRP* 2.7 52.3 - - + +
11491 PHE* 4.1 18.6 - - + -
11501 LEU 2.9 20.6 - - - +
11511 VAL* 4.4 5.2 - - + -
11571 SER* 5.0 4.3 - - - +
11601 PHE* 3.8 23.3 - - + -
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Residues in contact with GLN1092 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10901 LEU* 3.7 12.0 - - + +
10911 VAL* 1.3 71.4 - - - +
10931 VAL* 1.3 62.2 + - - +
10941 PHE* 3.7 26.3 - - + -
11081 ARG* 5.8 1.4 - - - +
11091 TRP 3.7 3.1 - - - +
11101 THR* 3.8 29.6 + - + +
11491 PHE* 3.6 2.3 - - - -
11501 LEU* 2.7 60.5 + - + +
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Residues in contact with VAL1093 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10911 VAL* 3.6 11.9 + - + +
10921 GLN* 1.3 74.2 - - - +
10941 PHE* 1.3 68.6 - - - +
11081 ARG* 3.5 3.8 - - - +
11091 TRP* 2.6 61.7 + - + +
11111 LYS* 5.7 2.2 - - + +
11171 TRP* 4.1 13.9 - - + -
11191 LEU* 4.6 11.9 - - + -
11471 LEU* 3.3 29.8 - - + -
11481 SER 3.4 8.5 - - - +
11491 PHE* 3.5 33.2 - - + -
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Residues in contact with PHE1094 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10291 GLN* 6.0 0.2 - - - -
10921 GLN* 3.7 46.0 - - + -
10931 VAL* 1.3 74.3 - - - +
10951 LEU* 1.3 60.4 + - - +
10961 THR* 4.2 2.9 - - - +
11051 ASP* 3.3 26.7 - - - +
11071 CYS 3.7 5.4 - - - -
11081 ARG* 3.1 45.8 - - + -
11091 TRP* 4.7 1.6 - - - -
11471 LEU* 3.1 14.0 - - - +
11481 SER* 3.1 49.8 + - - +
11491 PHE* 4.9 1.6 - - - -
11501 LEU* 4.4 14.4 - - + -
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Residues in contact with LEU1095 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10341 LEU* 4.9 6.5 - - + -
10941 PHE* 1.3 74.1 - - - +
10961 THR* 1.3 59.3 + - - +
11051 ASP* 4.7 0.2 + - - -
11061 ALA* 2.8 56.7 + - + +
11071 CYS* 3.1 22.9 + - + +
11091 TRP* 4.1 9.9 - - + -
11211 PHE* 3.5 35.2 - - + -
11221 PRO 5.6 2.7 - - - +
11231 ILE* 4.4 13.5 - - + -
11451 TRP* 4.2 24.2 - - + -
11461 HIS 3.1 14.4 - - - +
11471 LEU* 4.4 4.5 - - + -
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Residues in contact with THR1096 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10941 PHE* 4.2 3.3 - - - +
10951 LEU* 1.3 72.9 + - - +
10971 ASN* 1.3 69.0 + - - +
10981 SER 3.1 26.0 - - - +
11001 SER 4.9 2.7 - - - +
11031 HIS* 4.1 12.3 - - + +
11041 PHE 3.9 19.7 - - - +
11051 ASP* 2.5 27.9 + - - +
11061 ALA* 4.9 0.7 - - - +
11451 TRP* 3.4 8.6 - - - -
11461 HIS* 2.5 47.2 + - - +
11481 SER* 5.2 5.1 + - - -
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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