Contacts of the strand formed by residues 2144 - 2152 (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 LEU2144 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20152 MET* 6.1 0.7 - - + -
20292 LYS 3.7 0.9 - - - +
20312 MET* 2.9 77.9 + - + +
20332 LEU* 4.4 13.2 - - + +
20662 PHE* 4.6 34.3 - - + -
20822 PHE* 4.1 15.7 - - + -
20832 PHE 2.9 23.3 - - - +
20842 ILE* 4.2 7.4 - - + -
21172 PHE* 4.0 21.5 - - + -
21432 TYR* 1.4 69.6 - - - +
21452 TYR* 1.3 65.0 + - - +
21462 ALA 3.8 0.2 + - - -
21642 VAL* 4.7 1.8 - - + -
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Residues in contact with TYR2145 (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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20282 VAL* 4.2 12.6 - - + -
20292 LYS 3.4 4.7 - - - -
20302 ARG* 2.9 61.3 + - + +
20812 SER 3.8 1.0 - - - +
20822 PHE* 3.4 5.6 - - - +
20832 PHE* 2.9 71.2 + + + +
20852 ALA* 3.5 22.7 - - + -
20862 PHE 2.4 37.2 + - - -
20872 GLY* 3.4 6.2 - - - -
20892 LEU* 3.6 12.4 + - + +
20962 PHE* 4.7 9.4 - + - -
21432 TYR* 4.2 11.4 - - + -
21442 LEU* 1.3 75.8 - - - +
21462 ALA* 1.3 59.9 + - - +
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Residues in contact with ALA2146 (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* 3.6 30.5 - - + -
20202 PHE* 4.0 13.9 - - + -
20282 VAL* 3.5 4.9 - - - +
20292 LYS* 2.8 32.6 + - + +
20312 MET* 4.5 2.0 - - + -
20802 VAL* 4.5 0.7 - - + -
20812 SER 3.4 4.7 - - - -
20822 PHE* 3.8 23.1 - - + -
21442 LEU 3.8 0.2 + - - -
21452 TYR* 1.3 74.7 - - - +
21472 MET* 1.3 61.5 - - - +
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Residues in contact with MET2147 (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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20202 PHE* 4.1 4.0 - - - -
20262 ARG* 3.3 34.5 - - + +
20282 VAL* 3.3 24.2 - - + -
20802 VAL* 3.2 8.2 - - - +
20812 SER* 2.6 44.6 + - - +
20832 PHE* 3.2 20.9 - - + -
20962 PHE* 3.0 47.1 - - + -
20972 GLU* 4.1 26.7 - - + +
21462 ALA* 1.3 72.8 - - - +
21482 VAL* 1.3 63.2 + - - +
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Residues in contact with VAL2148 (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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20202 PHE* 3.0 40.6 - - + -
20212 PRO 5.9 1.3 - - - +
20232 GLY 5.3 1.1 - - - +
20252 SER 3.7 25.1 - - - +
20262 ARG* 3.2 29.7 + - - +
20272 SER* 4.2 1.6 - - - -
20782 CYS* 3.2 26.5 - - - -
20792 THR 3.7 2.0 - - - -
21472 MET* 1.3 74.5 - - - +
21492 HIS* 1.3 62.6 + - - +
21502 ASP 3.3 4.9 - - - +
21512 SER* 3.7 28.3 - - - +
21522 SER* 4.3 3.4 - - - +
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Residues in contact with HIS2149 (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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20792 THR* 3.0 35.0 + - + +
20812 SER* 3.9 11.4 - - - -
20972 GLU* 2.5 48.9 + - - +
21032 LEU* 3.4 26.3 - - + +
21472 MET* 3.7 1.0 + - - -
21482 VAL* 1.3 74.0 - - - +
21502 ASP* 1.3 66.1 + - - +
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Residues in contact with ASP2150 (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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20242 THR* 4.6 11.3 - - - -
20252 SER 6.1 0.3 - - - -
20782 CYS* 5.0 0.2 - - - -
20792 THR* 2.4 57.0 + - - +
21482 VAL* 4.0 7.1 - - - +
21492 HIS* 1.3 88.9 - - - +
21512 SER* 1.3 79.7 + - - +
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Residues in contact with SER2151 (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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20232 GLY 3.3 17.7 - - - -
20242 THR* 4.8 5.1 - - - +
20772 LYS 3.5 2.4 - - - +
20782 CYS* 3.4 21.0 - - - -
20792 THR 4.1 0.2 + - - -
21482 VAL* 3.7 12.3 - - - +
21502 ASP* 1.3 101.2 + - - +
21522 SER* 1.3 66.7 - - - +
21532 VAL* 3.7 14.3 - - - +
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Residues in contact with SER2152 (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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20202 PHE* 3.5 15.7 + - - -
20212 PRO 3.3 22.4 - - - -
20222 GLN* 3.4 19.2 - - - +
20232 GLY* 3.2 22.1 + - - +
20762 ILE* 4.5 2.3 - - - +
20772 LYS 3.3 6.4 + - - -
20782 CYS* 4.4 7.2 - - - -
21482 VAL* 4.3 3.6 - - - +
21512 SER* 1.3 74.0 - - - +
21532 VAL* 1.3 64.9 + - - +
21602 PHE* 3.7 16.3 + - - +
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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