Contacts of the strand formed by residues 2160 - 2173 (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 PHE2160 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20182 LEU 3.7 1.2 - - - +
20192 THR* 3.4 2.1 - - - -
20202 PHE* 2.8 63.4 + + + +
20702 LYS* 5.3 6.7 - - + -
20722 THR* 3.9 15.9 - - + -
20762 ILE* 3.5 33.5 - - + +
20772 LYS* 4.5 0.2 - - - -
20782 CYS* 3.6 44.6 - - + -
20802 VAL* 3.8 16.8 - - + -
21062 PHE* 4.0 21.1 - + + -
21522 SER* 3.7 13.6 + - - +
21592 ASP* 1.3 71.0 - - - +
21612 VAL* 1.3 59.2 + - - +
21622 ILE* 3.3 29.6 - - + -
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Residues in contact with VAL2161 (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* 4.1 21.8 - - + +
20182 LEU 3.4 10.3 - - - +
20192 THR* 4.6 9.4 - - - +
20702 LYS* 3.8 0.3 - - - -
20712 MET* 2.9 31.3 + - - +
20722 THR* 3.2 18.2 + - - +
21592 ASP* 2.9 26.6 + - + +
21602 PHE* 1.3 75.4 - - - +
21622 ILE* 1.3 68.8 + - - +
21902 ILE* 5.8 1.1 - - + -
21922 GLN* 5.1 9.4 - - + +
31542 THR* 3.5 32.3 - - + +
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Residues in contact with ILE2162 (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* 4.9 0.4 - - - -
20182 LEU* 2.9 36.9 + - + +
20202 PHE* 3.8 22.7 - - + -
20682 VAL* 3.6 28.7 - - + -
20692 SER 2.9 15.0 - - - +
20702 LYS* 4.3 3.4 - - + -
20712 MET* 4.4 2.9 - - - -
20802 VAL* 5.1 2.7 - - + -
20822 PHE* 4.0 11.4 - - + -
21062 PHE* 4.2 12.8 - - + -
21602 PHE* 3.3 36.1 - - + -
21612 VAL* 1.3 80.0 - - - +
21632 GLY* 1.3 57.8 + - - +
21642 VAL* 3.8 15.9 + - + -
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Residues in contact with GLY2163 (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 24.2 - - - -
20162 GLY 3.5 8.1 - - - -
20172 LYS* 4.5 1.6 - - - -
20672 GLU 3.3 4.5 - - - +
20682 VAL* 3.4 1.7 - - - -
20692 SER* 2.9 35.7 + - - -
20712 MET* 3.9 10.6 - - - -
21622 ILE* 1.3 74.9 - - - +
21642 VAL* 1.3 61.0 + - - -
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Residues in contact with VAL2164 (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* 3.7 6.0 - - - -
20152 MET* 2.7 37.6 + - + -
20162 GLY 2.8 15.6 + - - +
20182 LEU* 3.8 11.0 - - + -
20312 MET* 3.4 33.9 - - + -
20662 PHE* 3.8 34.5 - - + -
20672 GLU 3.5 2.5 - - - -
20682 VAL* 4.4 12.8 - - + -
20822 PHE* 4.6 2.5 - - + -
21442 LEU* 4.7 2.2 - - + -
21622 ILE* 3.8 17.0 - - + -
21632 GLY* 1.3 76.3 - - - +
21652 LYS* 1.3 58.6 + - - +
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Residues in contact with LYS2165 (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* 3.6 35.9 + - - -
20132 ARG 3.1 17.9 - - - +
20142 TRP* 4.2 19.5 - - + -
20662 PHE* 4.4 2.9 - - - -
20672 GLU* 2.9 59.5 + - + +
20692 SER* 6.0 1.1 - - - +
21642 VAL* 1.3 75.9 - - - +
21662 LEU* 1.3 63.3 + - - +
21672 THR* 3.2 12.2 + - - +
31082 CYS* 3.7 19.6 + - + -
31122 CYS* 3.5 30.7 + - - +
31132 GLU* 5.9 0.6 + - - -
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Residues in contact with LEU2166 (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 33.0 - - + +
20122 ASN* 2.9 22.6 + - - -
20132 ARG* 2.9 16.7 + - + -
20152 MET* 3.8 19.6 - - + +
20352 ILE* 4.6 5.6 - - + -
20642 LEU* 4.1 11.7 - - + -
20652 VAL 3.6 9.2 - - - +
20662 PHE* 2.4 62.0 - - + -
21652 LYS* 1.3 68.4 - - - +
21672 THR* 1.3 63.0 + - - +
21682 ILE 4.9 3.6 - - - +
21692 ILE* 3.4 29.4 - - + -
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Residues in contact with THR2167 (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* 4.0 0.9 - - - -
20112 LEU* 3.1 23.1 + - - -
20122 ASN* 3.2 22.4 + - - +
20652 VAL* 3.0 31.5 + - + -
20672 GLU* 3.8 26.3 + - + +
21142 VAL* 6.5 0.4 - - + -
21652 LYS* 3.2 12.7 + - - -
21662 LEU* 1.3 74.0 - - - +
21682 ILE* 1.3 71.4 + - + +
1M G 3.4 22.1 - - - -
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Residues in contact with ILE2168 (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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20082 PRO* 3.8 19.1 - - + -
20092 PHE 3.3 15.7 - - - +
20102 VAL* 4.1 6.7 - - + -
20632 ASP 3.4 2.4 - - - +
20642 LEU* 4.1 0.2 - - - -
20652 VAL* 3.1 37.6 + - + +
21662 LEU* 3.7 2.2 - - - -
21672 THR* 1.3 96.1 - - + +
21692 ILE* 1.3 63.2 + - - +
21702 GLU* 3.8 19.7 + - + +
1M G 3.2 55.0 - - + +
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Residues in contact with ILE2169 (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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20072 ASN* 4.5 0.2 - - - +
20082 PRO 3.8 0.5 - - - -
20092 PHE* 3.1 50.3 + - + +
20112 LEU* 4.2 7.2 - - + -
20352 ILE* 4.3 2.2 - - + -
20542 LEU* 4.1 17.9 - - + -
20602 PHE* 3.6 31.4 - - + -
20612 VAL 4.3 9.4 - - - +
20622 GLY* 4.5 1.6 - - - -
20632 ASP 3.2 3.8 - - - +
20642 LEU* 3.0 27.6 - - + -
21662 LEU* 3.4 26.9 - - + -
21682 ILE* 1.3 74.1 - - - +
21702 GLU* 1.3 59.8 + - - +
21712 ASN 4.2 0.5 + - - -
21722 MET* 4.5 11.8 - - + +
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Residues in contact with GLU2170 (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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20072 ASN* 3.6 5.6 - - - +
20082 PRO* 3.7 26.3 - - + +
20632 ASP* 2.5 55.1 + - - +
20652 VAL* 4.3 4.3 - - + +
21162 LYS* 3.1 35.9 + - - +
21682 ILE* 3.8 17.5 - - + +
21692 ILE* 1.3 71.8 - - - +
21712 ASN* 1.3 67.5 + - + +
21722 MET 3.3 0.7 - - - -
1M G 5.0 8.5 + - - -
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Residues in contact with ASN2171 (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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20072 ASN* 2.9 32.5 + - - +
20622 GLY* 3.6 4.3 - - - -
20632 ASP* 3.4 12.2 - - - +
21192 GLN* 3.4 26.8 + - - +
21692 ILE 4.2 0.2 + - - -
21702 GLU* 1.3 82.2 - - - +
21722 MET* 1.3 65.9 - - - +
21732 CYS* 5.1 1.2 - - - +
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Residues in contact with MET2172 (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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20052 PRO* 4.6 9.9 - - + -
20062 GLN 5.1 8.3 - - - +
20072 ASN* 4.6 1.8 + - - -
20092 PHE* 4.0 21.5 - - + -
20542 LEU* 3.3 18.8 - - + -
20572 TRP* 2.4 51.4 - - + -
20602 PHE* 4.2 13.0 - - + -
20612 VAL 3.3 18.4 - - - +
20622 GLY* 4.0 2.0 - - - -
21692 ILE* 4.5 17.3 - - + +
21702 GLU 3.3 0.4 - - - -
21712 ASN* 1.3 80.7 - - - +
21732 CYS* 1.3 70.3 + - - +
21742 ALA* 4.9 2.5 - - + +
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Residues in contact with CYS2173 (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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20602 PHE* 3.4 4.7 - - - +
20612 VAL* 3.0 46.0 + - + +
21192 GLN* 5.8 2.9 - - - +
21712 ASN 5.1 1.3 - - - +
21722 MET* 1.3 78.6 - - - +
21742 ALA* 1.3 61.6 + - - +
21752 TYR* 3.4 41.7 + - - -
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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