Contacts of the strand formed by residues 2011 - 2020 (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 LEU2011 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20092 PHE* 3.8 19.2 + - + -
20102 VAL* 1.3 74.8 - - - +
20122 ASN* 1.3 73.4 + - - +
20132 ARG* 3.3 35.0 - - + -
20352 ILE* 4.6 5.6 - - + -
20482 ASN* 4.3 0.7 - - - +
20502 PRO* 2.8 57.5 - - - +
20512 ASN* 4.3 9.4 - - - +
20542 LEU* 3.9 17.0 - - + -
21662 LEU* 3.3 30.3 - - + +
21672 THR 3.1 7.1 + - - +
21692 ILE* 4.2 10.1 - - + -
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Residues in contact with ASN2012 (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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20102 VAL* 2.8 36.5 - - - +
20112 LEU* 1.3 81.6 - - - +
20132 ARG* 1.3 59.6 + - - +
20142 TRP 4.3 0.2 + - - -
20482 ASN* 3.5 12.8 - - - +
21652 LYS* 3.6 25.3 + - - +
21662 LEU 2.9 16.3 + - - -
21672 THR* 3.2 15.6 + - - +
31082 CYS* 3.4 23.3 - - - +
31092 SER* 3.1 22.5 + - - +
31102 GLN 4.5 4.0 + - - -
31802 ARG* 5.3 1.2 - - - +
1M G 5.2 6.7 + - - +
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Residues in contact with ARG2013 (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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20112 LEU* 3.3 28.5 - - + -
20122 ASN* 1.3 76.9 - - - +
20142 TRP* 1.3 68.0 + - - +
20152 MET* 2.9 20.7 + - - -
20322 PRO 5.8 0.2 + - - -
20342 SER 4.6 1.6 + - - -
20352 ILE* 3.5 51.5 + - - +
20382 GLY* 3.2 28.1 + - - +
20482 ASN* 4.6 3.1 - - - +
20512 ASN* 3.1 23.4 + - + +
21652 LYS* 3.1 8.3 - - - +
21662 LEU* 2.9 30.2 + - + +
21872 LEU* 3.3 30.9 - - - +
31052 TYR* 4.2 12.9 - - + -
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Residues in contact with TRP2014 (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* 1.3 82.2 + - - +
20152 MET* 1.3 58.5 + - - +
20162 GLY* 3.7 27.4 - - - -
20172 LYS* 3.8 11.7 - - + +
20692 SER* 5.5 3.4 - - - -
20712 MET* 3.7 31.9 - - + -
21632 GLY* 3.8 22.9 - - - -
21642 VAL 4.0 7.2 - - - -
21652 LYS* 4.2 25.1 - - + -
21872 LEU* 3.3 27.0 - - + +
21882 GLY 4.9 4.0 + - - -
31032 ASP* 5.1 2.2 - - - -
31042 ILE* 3.5 40.1 - - + +
31052 TYR* 3.9 29.3 - - + +
31082 CYS* 4.1 11.3 - - - -
31142 LEU* 4.2 13.9 - - + -
31532 VAL* 4.3 8.0 - - + +
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Residues in contact with MET2015 (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* 2.9 22.9 + - - +
20142 TRP* 1.3 73.9 - - - +
20162 GLY* 1.3 57.2 + - - +
20312 MET* 3.7 29.7 - - - +
20322 PRO 3.8 14.6 - - - +
20332 LEU* 3.6 30.3 - - + -
20352 ILE* 3.1 34.8 - - + -
20662 PHE* 3.8 22.2 - - + -
21442 LEU* 6.1 0.4 - - - -
21642 VAL* 2.7 29.4 + - + +
21662 LEU* 3.8 14.6 - - + +
21872 LEU* 4.1 12.5 - - - +
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Residues in contact with GLY2016 (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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20142 TRP* 3.3 18.9 + - - -
20152 MET* 1.3 81.5 - - - +
20172 LYS* 1.3 62.1 - - - -
20182 LEU* 3.5 12.4 - - - +
21632 GLY* 3.5 2.1 - - - -
21642 VAL 2.8 32.3 + - - +
21872 LEU* 4.5 8.5 - - - -
21882 GLY* 4.8 6.5 - - - -
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Residues in contact with LYS2017 (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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20142 TRP* 3.8 13.8 - - + +
20162 GLY* 1.3 71.2 - - - -
20182 LEU* 1.3 63.2 + - - +
20192 THR* 3.6 11.7 + - + +
20712 MET* 5.0 7.4 - - + -
21612 VAL* 4.1 15.0 - - + +
21622 ILE 4.1 2.7 - - - -
21632 GLY* 4.5 2.5 - - - -
21882 GLY* 3.7 28.4 + - - +
21892 THR* 3.5 20.9 - - - +
21902 ILE* 2.8 30.0 + - + +
21912 PRO 2.5 32.1 + - - -
31532 VAL* 3.2 18.1 + - + -
31542 THR* 2.8 24.5 + - - -
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Residues in contact with LEU2018 (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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20162 GLY* 3.5 24.9 - - - +
20172 LYS* 1.3 72.0 - - - +
20192 THR* 1.3 60.4 + - - +
20202 PHE* 3.8 15.2 - - + -
20292 LYS* 3.4 33.9 - - + -
20312 MET* 3.2 44.9 - - + -
21462 ALA* 3.6 15.5 - - + -
21602 PHE 3.7 1.0 - - - +
21612 VAL* 3.4 4.3 - - - +
21622 ILE* 2.9 44.4 + - + +
21642 VAL* 3.8 7.9 - - + -
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Residues in contact with THR2019 (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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20172 LYS* 3.8 11.4 - - + +
20182 LEU* 1.3 74.4 - - - +
20202 PHE* 1.3 61.3 + - - +
20212 PRO* 3.6 4.4 - - - +
20292 LYS* 3.1 31.5 + - - +
21592 ASP* 2.8 26.9 + - - +
21602 PHE 3.4 5.8 - - - -
21612 VAL* 4.5 13.2 - - - +
21882 GLY* 6.4 0.4 - - - -
21892 THR 5.2 2.0 - - - +
21902 ILE* 4.0 34.7 - - + +
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Residues in contact with PHE2020 (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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20182 LEU* 3.8 18.2 - - + -
20192 THR* 1.3 75.8 + - - +
20212 PRO* 1.4 71.5 - - - +
20272 SER* 3.6 20.4 - - - -
20292 LYS* 4.4 3.8 - - + -
20782 CYS* 5.0 2.9 - - - -
20802 VAL* 3.8 17.3 - - + -
21462 ALA* 4.0 25.1 - - + -
21472 MET 4.1 13.0 - - - -
21482 VAL* 3.0 35.7 - - + -
21522 SER* 3.5 3.3 + - - +
21592 ASP* 4.2 1.6 - - - -
21602 PHE* 2.8 61.8 + + + +
21622 ILE* 3.8 24.5 - - + -
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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