Contacts of the strand formed by residues 2077 - 2085 (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 LYS2077 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20702 LYS* 6.0 0.9 - - - +
20742 PRO 2.5 28.9 + - - +
20752 TYR* 4.2 9.3 - - - +
20762 ILE* 1.3 76.6 - - - +
20782 CYS* 1.3 61.8 + - - +
21062 PHE 4.6 15.7 - - - +
21082 GLU* 3.1 30.8 + - - +
21512 SER 3.5 1.5 - - - +
21522 SER* 3.3 6.1 + - - -
21532 VAL* 2.9 45.2 + - + +
21602 PHE* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2078 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20202 PHE* 5.0 1.3 - - - -
20772 LYS* 1.3 77.0 - - - +
20792 THR* 1.3 72.8 + - - +
20802 VAL* 3.9 11.9 + - - -
21042 VAL 4.1 3.8 - - - +
21052 GLN* 4.5 8.8 - - - +
21062 PHE* 4.8 3.3 + - - +
21482 VAL* 3.2 42.4 - - - -
21502 ASP* 5.0 0.2 - - - -
21512 SER 3.4 11.0 - - - +
21522 SER* 4.4 6.3 - - - -
21602 PHE* 3.6 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2079 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20782 CYS* 1.3 78.3 - - - +
20802 VAL* 1.3 60.3 + - - +
21032 LEU* 5.1 8.3 - - + -
21042 VAL 3.3 12.6 - - - +
21052 GLN* 3.5 29.2 + - + +
21482 VAL* 3.7 3.8 - - - -
21492 HIS* 3.0 46.0 + - + -
21502 ASP* 2.4 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2080 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20202 PHE* 3.8 30.1 - - + -
20782 CYS* 3.9 8.6 + - - +
20792 THR* 1.3 73.9 - - - +
20812 SER* 1.3 63.2 + - - +
20822 PHE* 2.8 41.7 - - + -
21032 LEU* 3.6 2.0 - - - -
21042 VAL* 2.8 43.4 + - + +
21062 PHE* 6.3 2.2 - - + -
21462 ALA* 4.5 0.2 - - + -
21472 MET 3.2 10.5 - - - +
21492 HIS* 4.8 0.9 - - - -
21602 PHE* 3.8 28.9 - - + -
21622 ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2081 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20792 THR 4.0 0.6 + - - -
20802 VAL* 1.3 71.0 - - - +
20822 PHE* 1.3 62.0 + - - +
20832 PHE* 4.3 3.9 - - - -
20972 GLU* 3.3 30.8 + - - +
21012 HIS* 4.2 13.7 - - - +
21022 LYS 3.9 3.8 + - - -
21032 LEU* 4.0 11.0 - - - +
21452 TYR 3.8 1.2 - - - +
21462 ALA* 3.4 2.9 - - - -
21472 MET* 2.6 53.3 + - - +
21492 HIS* 3.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2082 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20312 MET* 4.4 13.7 - - + -
20682 VAL* 3.5 37.0 - - + -
20802 VAL* 2.8 28.9 - - + -
20812 SER* 1.3 73.2 - - - +
20832 PHE* 1.3 61.5 + - - +
21012 HIS* 3.2 4.0 - - - +
21022 LYS* 2.8 44.5 + - + +
21042 VAL* 3.1 32.8 - - + -
21152 LEU* 3.9 9.4 - - + -
21172 PHE* 3.9 17.9 - + + -
21442 LEU* 4.1 20.4 - - + -
21452 TYR 3.4 5.2 - - - -
21462 ALA* 3.8 19.3 - - + -
21622 ILE* 4.0 8.5 - - + -
21642 VAL* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2083 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20812 SER* 4.3 12.6 - - - -
20822 PHE* 1.3 77.9 - - - +
20842 ILE* 1.3 74.4 + - - +
20852 ALA* 4.1 8.3 - - + -
20962 PHE* 3.6 36.3 - + + -
20972 GLU* 5.7 0.7 - - + -
20992 PHE* 4.5 11.2 - + + -
21002 PRO 3.2 22.7 - - - +
21012 HIS* 4.0 8.5 - - + -
21172 PHE* 4.2 5.6 - - - -
21442 LEU* 2.9 25.2 - - - +
21452 TYR* 2.9 57.5 + + + -
21472 MET* 3.2 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2084 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20332 LEU* 4.5 6.3 - - + -
20662 PHE* 5.7 2.7 - - + -
20832 PHE* 1.3 85.8 - - - +
20852 ALA* 1.3 66.6 + - - +
20862 PHE* 6.5 0.4 - - + -
20992 PHE* 4.3 16.5 - - - -
21002 PRO* 4.3 4.1 + - - +
21172 PHE* 3.4 26.2 - - + -
21212 GLU* 3.4 39.5 - - + +
21222 PHE* 3.9 37.0 - - + -
21422 PRO* 4.5 7.0 - - + -
21432 TYR 3.6 12.8 - - - +
21442 LEU* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2085 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20832 PHE* 4.1 4.7 - - + -
20842 ILE* 1.3 77.6 - - - +
20862 PHE* 1.3 71.3 + - + +
20892 LEU* 4.1 8.3 - - + -
20992 PHE* 3.9 25.1 - - + -
21422 PRO* 3.6 6.4 - - - +
21432 TYR 2.7 36.9 + - - -
21452 TYR* 3.5 25.1 - - + -
----------------------------------------------------------
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