Contacts of the strand formed by residues 2023 - 2031 (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 GLY2023 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20212 PRO 3.6 3.2 + - - +
20222 GLN* 1.3 73.5 - - - +
20242 THR* 1.3 64.0 - - - -
20252 SER* 3.5 6.2 + - - +
21482 VAL* 5.3 0.9 - - - +
21512 SER* 3.3 10.5 - - - -
21522 SER* 3.2 33.9 + - - -
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Residues in contact with THR2024 (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* 1.3 73.8 - - - -
20252 SER* 1.3 58.2 - - - +
20262 ARG 4.1 1.4 + - - -
21482 VAL* 6.4 0.2 - - - -
21502 ASP 4.6 11.9 - - - -
21512 SER* 4.8 6.3 - - - -
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Residues in contact with SER2025 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20212 PRO* 5.5 8.8 + - - +
20232 GLY* 3.5 4.7 + - - +
20242 THR* 1.3 76.9 - - - +
20262 ARG* 1.3 56.5 + - - +
20272 SER* 2.5 39.1 + - - -
21482 VAL* 3.7 15.0 - - - +
21502 ASP 6.1 0.4 - - - -
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Residues in contact with ARG2026 (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 4.1 2.8 + - - -
20252 SER* 1.3 70.2 + - - +
20272 SER* 1.3 52.7 + - - +
20282 VAL* 2.5 28.4 + - + +
20912 ASP* 3.4 16.3 + - + +
20922 ASP* 4.7 1.8 - - - -
20932 THR 2.4 44.2 + - - +
20942 ILE* 3.9 18.0 + - - +
20962 PHE* 2.7 25.2 - - - -
20972 GLU* 6.0 2.0 - - - +
21472 MET* 3.3 34.1 - - + +
21482 VAL* 3.2 36.9 + - - +
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Residues in contact with SER2027 (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* 3.6 13.6 - - - -
20212 PRO* 3.4 31.5 - - - +
20252 SER* 2.5 30.9 + - - +
20262 ARG* 1.3 71.5 - - - +
20282 VAL* 1.3 53.6 + - - +
20292 LYS* 2.6 44.4 + - - +
21482 VAL* 4.2 8.3 - - - -
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Residues in contact with VAL2028 (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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20262 ARG* 2.5 19.2 + - + +
20272 SER* 1.3 70.9 - - - +
20292 LYS* 1.3 65.5 + - - +
20302 ARG* 4.2 13.5 + - + +
20912 ASP* 3.8 40.8 - - + +
20962 PHE* 4.6 4.0 - - + -
21452 TYR* 4.2 24.5 - - + -
21462 ALA 3.5 5.2 - - - +
21472 MET* 3.3 35.2 - - + -
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Residues in contact with LYS2029 (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* 3.4 41.1 - - + -
20192 THR* 3.1 32.3 + - - +
20202 PHE* 4.4 5.8 - - + -
20212 PRO* 4.5 2.2 - - - +
20272 SER* 2.6 49.5 + - - +
20282 VAL* 1.3 76.2 + - - +
20302 ARG* 1.3 62.3 + - - +
20312 MET* 4.6 1.8 - - + +
21442 LEU 3.7 3.1 - - - +
21452 TYR* 3.4 2.3 - - - +
21462 ALA* 2.8 40.9 + - + +
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Residues in contact with ARG2030 (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* 4.1 9.9 + - + +
20292 LYS* 1.3 73.2 - - - +
20312 MET* 1.3 61.7 + - - +
20322 PRO* 4.0 5.9 - - - +
20872 GLY* 4.7 4.0 - - - -
20892 LEU 2.6 30.6 + - - -
20902 ALA* 4.1 3.6 + - - +
20912 ASP* 2.1 41.6 + - - +
20962 PHE* 5.3 0.2 - - - -
21362 LEU* 3.6 33.7 - - + +
21432 TYR* 4.3 14.9 - - + -
21442 LEU 4.1 2.7 - - - -
21452 TYR* 2.9 60.1 - - + +
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Residues in contact with MET2031 (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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20152 MET* 3.7 35.4 - - - +
20182 LEU* 3.2 41.5 - - + -
20292 LYS 4.6 0.4 - - - +
20302 ARG* 1.3 77.4 - - - +
20322 PRO* 1.3 72.5 - - + +
20332 LEU 3.4 0.3 + - - -
20662 PHE* 6.3 0.2 - - - -
20822 PHE* 4.4 6.1 - - + -
21432 TYR* 3.1 7.1 - - - -
21442 LEU* 2.9 73.6 + - + +
21462 ALA* 4.5 1.1 - - + -
21642 VAL* 3.4 27.4 - - + -
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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
------------------------------------------------------------
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