Contacts of the strand formed by residues 1028 - 1034 (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 CYS1028 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10161 THR* 3.9 12.3 - - + -
10171 PRO* 5.0 2.0 - - + -
10201 PHE* 4.4 7.6 - - + -
10271 PHE* 1.3 75.6 - - - +
10291 GLN* 1.3 62.3 + - - +
10421 ASP* 3.2 10.5 - - - +
10441 THR* 4.6 1.8 - - - +
10471 TRP* 3.3 31.0 - - + -
11501 LEU* 3.6 4.7 - - - +
11511 VAL* 2.8 58.7 + - - -
11541 PRO* 3.8 18.1 - - + +
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Residues in contact with GLN1029 (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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10271 PHE* 4.1 16.5 - - + -
10281 CYS* 1.3 75.6 - - - +
10301 PHE* 1.3 65.6 + - - +
10411 VAL 4.1 0.7 - - - -
10421 ASP* 2.5 43.4 + - - +
10471 TRP* 3.6 4.1 - - - -
10941 PHE* 6.0 0.5 - - - -
11491 PHE 3.5 11.9 - - - +
11501 LEU* 3.0 33.7 - - + +
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Residues in contact with PHE1030 (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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10141 VAL* 3.1 46.7 - - + -
10291 GLN* 1.3 75.9 - - - +
10311 SER* 1.4 67.5 - - - +
10321 VAL* 4.3 7.2 - - + -
10391 ILE* 4.4 1.8 - - + -
10401 SER 3.7 11.7 - - - +
10411 VAL* 4.6 2.9 - - + -
10471 TRP* 3.7 24.0 - + + -
11481 SER* 3.3 2.1 - - - -
11491 PHE* 2.4 94.2 + + + +
11511 VAL* 4.4 5.4 - - + -
11601 PHE* 3.3 38.6 - + + -
11621 VAL* 5.8 2.0 - - + -
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Residues in contact with SER1031 (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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10301 PHE* 1.4 77.9 - - - +
10321 VAL* 1.3 63.5 + - - +
10331 ASP 4.3 0.2 - - - -
10381 GLY 4.5 0.7 - - - -
10391 ILE* 3.4 9.4 - - - +
10401 SER* 3.1 43.5 + - - +
10991 ASN* 3.8 20.2 + - - -
11461 HIS* 4.5 5.7 - - - -
11471 LEU 3.5 4.9 + - - -
11481 SER* 2.7 29.6 + - - -
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Residues in contact with VAL1032 (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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10111 MET* 4.0 17.9 - - + -
10121 ALA* 4.3 17.3 - - + -
10301 PHE* 4.3 14.8 - - + -
10311 SER* 1.3 78.0 - - - +
10331 ASP* 1.3 60.0 + - - +
10341 LEU* 3.0 32.0 + - + +
10381 GLY 3.6 4.5 - - - +
10391 ILE* 3.9 19.5 - - + -
11461 HIS* 3.5 3.7 - - - -
11471 LEU* 2.7 44.9 + - + +
11491 PHE* 4.8 2.0 - - + -
11621 VAL* 4.4 13.7 - - + -
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Residues in contact with ASP1033 (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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10111 MET* 3.4 3.3 - - - +
10321 VAL* 1.3 69.2 - - - +
10341 LEU* 1.3 56.1 + - - +
10351 LEU 3.1 4.5 + - - -
10361 GLY* 2.4 33.1 + - - -
10371 GLY* 2.5 37.8 + - - -
10381 GLY* 2.9 23.5 + - - +
11351 TRP* 2.5 32.2 + - - -
11441 SER* 3.3 10.0 + - - -
11451 TRP 3.7 5.0 - - - +
11461 HIS* 3.8 28.1 + - + +
30972 ARG* 5.7 0.2 - - - -
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Residues in contact with LEU1034 (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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10111 MET* 3.2 21.1 - - + +
10321 VAL* 3.0 38.1 + - + +
10331 ASP* 1.3 73.9 + - - +
10351 LEU* 1.3 61.1 + - - +
10361 GLY 3.8 0.2 + - - -
10371 GLY 4.6 0.7 + - - -
10601 LEU* 3.8 20.1 - - - +
10701 LEU* 5.6 0.6 - - + +
10721 VAL* 3.5 29.4 - - + -
10951 LEU* 4.9 7.6 - - + -
11231 ILE* 3.8 27.1 - - + -
11451 TRP* 3.3 13.8 + - + +
11471 LEU* 3.8 23.3 - - + +
11621 VAL* 4.9 3.6 - - + -
11641 LEU* 4.0 16.6 - - + +
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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