Contacts of the helix formed by residues 2049 - 2057 (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 MET2049 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10621 VAL* 3.0 10.4 - - + +
10631 ALA* 4.8 4.7 - - + +
11721 ILE* 3.2 35.0 - - + -
11731 ALA* 3.5 11.9 - - - -
11741 GLY 3.4 30.7 - - - +
11751 ASN* 2.9 16.9 + - + +
20482 ASN* 1.3 68.3 - - - +
20502 PRO* 1.3 60.0 - - + +
20512 ASN 2.5 13.7 + - - -
20522 ALA* 2.6 23.4 + - - -
20532 VAL* 2.6 27.4 + - + +
31822 TYR* 2.7 51.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2050 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20092 PHE* 3.7 12.7 - - + -
20102 VAL 3.9 8.3 - - - +
20112 LEU* 2.8 61.1 - - - +
20482 ASN* 2.5 21.3 - - - +
20492 MET* 1.3 94.8 - - + +
20512 ASN* 1.3 52.0 + - - -
20532 VAL* 3.8 8.3 - - + -
20542 LEU* 3.8 3.6 - - - +
31092 SER* 3.1 31.4 - - - +
31822 TYR* 4.3 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2051 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20112 LEU* 4.4 4.0 - - + +
20132 ARG* 3.1 26.2 + - + +
20352 ILE* 2.3 27.9 + - - +
20362 GLY* 4.0 2.4 - - - -
20372 GLY 4.7 0.2 - - - -
20382 GLY* 3.3 8.9 - - - -
20472 MET* 3.4 4.7 - - + -
20482 ASN* 2.6 20.8 + - - +
20492 MET 2.5 4.2 + - - -
20502 PRO* 1.3 73.1 - - - +
20522 ALA* 1.3 65.5 + - - +
20532 VAL 3.2 1.3 - - - -
20542 LEU* 3.7 12.7 - - - +
20552 SER* 3.0 29.1 + - - -
31052 TYR* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2052 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10551 PRO 4.1 6.8 - - - +
10581 ASN 4.8 0.4 - - - +
10591 LEU* 3.6 38.1 - - + +
10621 VAL* 4.9 1.3 - - + -
20472 MET* 2.8 26.8 - - + +
20482 ASN 3.2 2.1 + - - +
20492 MET* 2.6 26.9 + - - +
20512 ASN* 1.3 75.9 - - - +
20532 VAL* 1.3 61.1 + - - +
20552 SER* 3.4 13.9 - - - -
20562 MET* 3.4 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2053 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10591 LEU* 4.0 13.2 - - + -
11721 ILE* 4.7 2.5 - - + -
20012 CYS 5.4 0.7 - - - +
20022 VAL* 4.0 22.0 - - + +
20092 PHE* 3.7 17.5 - - + -
20492 MET* 2.6 43.7 - - + +
20502 PRO* 3.8 8.5 - - + -
20522 ALA* 1.3 70.9 - - - +
20542 LEU* 1.3 60.9 + - - +
20552 SER 3.0 1.8 - - - -
20562 MET* 2.5 38.0 + - - +
20572 TRP* 3.6 26.6 + - + -
31822 TYR* 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2054 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20092 PHE* 3.6 16.4 - - + -
20112 LEU* 3.9 7.2 - - + -
20352 ILE* 3.5 48.0 - - + +
20362 GLY* 5.0 0.7 - - - +
20502 PRO 3.8 9.6 + - - +
20512 ASN* 3.2 13.1 + - - +
20532 VAL* 1.3 79.9 - - - +
20552 SER* 1.3 57.5 + - - +
20572 TRP* 3.0 48.2 + - + +
20602 PHE* 4.2 11.2 - - + -
21282 THR* 4.0 10.0 + - - +
21692 ILE* 4.1 8.5 - - + -
21722 MET* 3.3 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2055 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10551 PRO* 3.3 18.2 - - - +
20362 GLY* 2.7 35.3 - - - -
20372 GLY* 3.0 8.9 + - - -
20472 MET* 4.5 4.7 - - - -
20512 ASN 3.0 12.6 + - - -
20522 ALA 3.4 8.1 - - - -
20542 LEU* 1.3 73.2 - - - +
20562 MET* 1.3 64.6 + - - +
20572 TRP 3.1 2.9 - - - -
21282 THR* 3.9 12.1 - - - -
21292 GLN* 5.1 5.4 - - - -
21782 ASN* 3.2 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2056 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10091 ASN* 4.5 10.1 - - - +
10551 PRO* 4.1 5.8 - - - -
10561 ILE* 3.4 54.7 - - + -
10591 LEU* 4.1 8.7 - - + -
11661 ILE* 3.8 36.1 - - + -
20022 VAL* 3.6 25.4 - - + -
20032 LEU* 5.5 3.4 - - + -
20522 ALA 3.4 10.5 + - - +
20532 VAL* 2.5 25.7 + - - +
20552 SER* 1.3 73.6 - - - +
20572 TRP* 1.3 60.4 + - + +
21772 LEU* 3.5 14.0 - - - +
21782 ASN* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2057 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10021 ILE* 3.3 29.2 - - + +
20022 VAL* 2.7 25.6 + - - -
20032 LEU* 4.6 2.2 - - + -
20052 PRO* 3.4 22.4 - - + -
20092 PHE* 3.9 19.3 - + - -
20532 VAL* 3.7 23.7 + - + -
20542 LEU* 3.0 29.5 + - + +
20552 SER 3.3 5.0 - - - +
20562 MET* 1.3 84.2 - - + +
20582 ARG* 1.3 64.9 + - - +
20592 TYR 4.5 3.6 - - - +
20602 PHE* 4.8 5.6 - - + -
21282 THR* 3.6 6.7 - - - +
21722 MET* 2.4 48.7 - - + -
21742 ALA* 4.1 18.2 - - + -
21762 GLY 4.1 9.0 - - - +
21782 ASN* 2.8 22.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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