Contacts of the strand formed by residues 583 - 591 (chain A) in PDB entry 3BMW
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 GLN 583 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 4.4 3.3 + - - -
241A LYS* 4.1 5.4 - - + +
242A ASN* 3.4 16.5 - - - +
245A ASP* 2.8 38.7 + - + +
579A LEU* 3.7 16.8 - - + +
581A GLY 2.9 22.8 + - - -
582A ASN* 1.3 77.0 - - - +
584A ILE* 1.3 69.2 + - - +
609A GLU* 2.9 31.0 + - - +
638A SER* 2.7 47.2 + - - +
639A VAL 3.4 3.5 + - - -
640A PRO* 4.0 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 5.1 3.4 - - - +
242A ASN* 3.6 8.5 - - - -
583A GLN* 1.3 82.9 - - - +
585A CYS* 1.3 72.4 + - - +
586A VAL* 4.1 6.3 - - + -
637A VAL 3.4 1.4 - - - +
638A SER* 3.4 1.7 - - - -
639A VAL* 2.8 30.5 + - - +
641A ALA* 3.6 16.6 - - + -
669A VAL* 3.7 20.9 - - + -
670A PRO* 3.4 17.5 - - + +
671A SER 3.9 3.8 - - - +
672A SER* 3.3 43.3 - - - +
673A SER 3.2 21.8 - - - +
674A THR* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLN* 3.2 35.1 + - - +
213A LYS* 5.4 0.2 - - - +
238A GLY 4.0 3.1 - - - -
239A TRP* 3.6 37.7 - - + -
242A ASN* 3.6 28.3 + - + +
584A ILE* 1.3 73.8 - - - +
586A VAL* 1.3 60.9 + - - +
636A ASP* 3.9 14.4 - - - -
637A VAL 3.6 6.1 - - - -
674A THR* 3.4 12.5 - - + +
675A GLY 3.3 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLN* 4.1 0.7 - - - -
584A ILE* 3.6 13.7 + - + -
585A CYS* 1.3 76.1 - - - +
587A ARG* 1.3 72.4 + - - +
588A PHE* 3.6 23.4 + - + -
636A ASP* 4.4 1.3 - - - -
637A VAL 2.8 36.2 + - - +
639A VAL* 3.5 27.8 - - + -
667A TYR* 3.9 26.9 - - + -
669A VAL* 4.1 9.0 - - + -
670A PRO* 4.1 4.9 - - + -
675A GLY 3.2 12.8 - - - +
677A VAL* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A HIS* 5.1 2.4 + - - -
192A TYR* 3.6 19.2 - - - -
202A ASN* 4.8 5.5 + - - +
204A GLN* 3.6 36.6 - - - +
586A VAL* 1.3 71.6 - - - +
588A PHE* 1.3 62.3 + - - +
589A VAL* 3.8 13.7 - - + -
627A VAL* 3.7 23.6 - - - +
628A TYR* 4.2 21.6 + - - -
634A TYR* 4.4 9.8 - - + -
635A TYR 3.5 4.9 - - - +
636A ASP* 2.7 38.9 + - - +
675A GLY 2.9 9.5 + - - -
676A THR* 3.4 21.6 + - + +
677A VAL 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A VAL* 3.6 31.2 - - + -
587A ARG* 1.3 72.3 - - - +
589A VAL* 1.3 60.2 + - - +
603A LEU* 3.6 27.8 - - + -
610A LEU* 4.5 2.5 - - + -
622A MET* 3.8 6.0 - - + +
634A TYR* 3.1 6.9 - - - +
635A TYR 2.9 31.3 + - - +
637A VAL* 3.7 28.7 - - + -
639A VAL* 4.3 11.7 - - + -
645A ILE* 3.6 32.3 - - + -
647A PHE* 3.9 26.7 - + + -
649A PHE* 4.3 11.2 - + + -
667A TYR* 5.2 0.2 - + - -
677A VAL* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ARG* 3.8 14.4 - - + -
588A PHE* 1.3 79.1 - - - +
590A VAL* 1.3 63.7 + - - +
591A ASN* 4.3 1.6 - - - +
628A TYR* 3.7 38.1 - - + +
632A THR* 3.5 27.8 - - + -
633A TRP 3.4 5.6 - - - +
634A TYR* 4.2 1.8 - - + -
649A PHE* 4.5 3.3 - - - -
676A THR* 4.2 2.5 - - + -
677A VAL 2.9 8.8 + - - +
678A ILE* 3.4 34.3 - - + -
679A VAL* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL* 1.3 74.5 - - - +
591A ASN* 1.3 67.0 + - - +
593A ALA* 4.4 5.6 - - + -
601A VAL* 4.0 11.2 - - + -
622A MET* 4.3 0.4 - - + -
631A PRO 3.8 1.4 - - - +
632A THR* 3.3 3.1 - - - -
633A TRP* 2.9 53.4 + - + +
649A PHE* 3.7 47.6 - - + -
679A VAL* 3.3 6.1 - - + +
681A TRP* 3.7 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL* 4.3 2.1 - - - +
590A VAL* 1.3 71.8 - - - +
592A ASN* 1.3 76.3 + - - +
593A ALA 3.3 3.1 - - - -
628A TYR* 5.6 0.9 - - - -
632A THR* 2.8 36.8 + - - +
678A ILE* 3.6 26.1 - - - +
679A VAL 2.9 8.1 + - - -
680A ASN* 3.2 25.5 + - - +
681A TRP* 2.9 28.2 + - - +
----------------------------------------------------------
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