Contacts of the strand formed by residues 644 - 652 (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 THR 644 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ASN* 4.6 6.1 + - - +
607A VAL* 5.5 0.5 - - - +
642A GLY 3.9 1.9 + - - -
643A THR* 1.3 78.5 - - - +
645A ILE* 1.3 59.6 + - - +
646A GLN* 4.3 2.2 + - + +
666A THR* 3.4 23.8 - - - +
667A TYR 3.5 6.1 - - - +
668A THR* 2.8 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 3.6 37.0 - - + -
606A ASN* 3.6 5.8 - - - +
607A VAL* 4.1 30.1 - - + -
610A LEU* 4.1 11.9 - - + -
639A VAL* 4.9 2.9 - - + -
640A PRO* 5.1 3.4 - - + -
643A THR* 4.0 14.4 - - + +
644A THR* 1.3 77.2 - - - +
646A GLN* 1.3 64.9 + - - +
647A PHE* 4.0 13.0 - - + -
666A THR* 3.1 19.2 + - - -
667A TYR* 2.8 37.8 + - + +
669A VAL* 4.3 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLY* 3.2 2.6 - - - -
606A ASN* 2.9 54.0 + - - +
610A LEU* 4.5 0.2 - - - +
613A TRP* 3.8 6.1 - - + -
644A THR* 5.6 1.8 - - + +
645A ILE* 1.3 78.6 - - - +
647A PHE* 1.3 61.9 + - - +
664A ASN* 2.8 39.5 + - + +
665A HIS 3.2 8.7 - - - +
666A THR* 4.5 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 3.9 17.7 - + - -
603A LEU* 3.7 22.7 - - + -
604A THR 3.2 15.5 - - - +
605A GLY* 4.2 2.2 - - - -
610A LEU* 4.2 6.3 - - + -
613A TRP* 3.9 7.1 - - - -
645A ILE* 4.0 16.2 - - + -
646A GLN* 1.3 77.5 - - - +
648A LYS* 1.3 64.7 + - - +
649A PHE* 3.8 24.2 - + - -
664A ASN* 3.8 0.5 - - - +
665A HIS* 2.9 69.8 + + + +
666A THR 4.0 1.1 - - - -
667A TYR* 3.8 24.0 - - + -
677A VAL* 4.1 23.1 - - + -
679A VAL* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU* 3.9 4.4 - - - +
604A THR* 3.0 33.1 + - - +
613A TRP* 3.9 5.9 - - + -
647A PHE* 1.3 79.7 - - - +
649A PHE* 1.3 69.4 + - - +
659A TRP* 4.1 25.6 - - + -
660A GLU* 2.8 43.7 + - + +
661A GLY* 3.3 11.2 + - - -
662A GLY 2.8 28.3 + - - -
663A SER 3.9 8.3 - - - -
664A ASN* 3.5 25.3 + - - +
665A HIS* 4.4 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 4.3 13.0 - - + -
589A VAL 4.5 4.7 - - - -
590A VAL* 3.7 26.2 - - + -
601A VAL* 4.0 5.8 - - + -
602A TYR 3.3 15.7 - - - +
603A LEU* 3.7 24.5 - - + -
622A MET* 3.6 35.0 - - + -
647A PHE* 3.8 19.3 - + - -
648A LYS* 1.3 74.4 - - - +
650A ILE* 1.3 65.4 + - - +
660A GLU* 2.8 45.3 + - - +
665A HIS* 4.5 0.7 - + - -
679A VAL* 3.5 26.5 - - + -
681A TRP* 3.5 23.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A VAL* 3.2 6.4 - - - +
602A TYR* 2.9 50.7 + - + +
604A THR* 4.1 13.0 - - + -
615A THR* 3.9 24.0 - - + -
618A ALA* 3.8 24.7 - - + -
649A PHE* 1.3 79.8 - - - +
651A LYS* 1.3 63.7 + - - +
652A LYS* 4.3 11.2 - - + -
657A ILE* 4.0 11.9 - - + -
658A THR 3.2 7.6 - - - +
659A TRP* 3.7 40.6 - - + +
681A TRP* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ASN 5.3 0.2 + - - -
593A ALA* 4.2 4.3 - - - +
594A SER* 2.7 43.7 + - - +
595A THR* 4.1 11.7 - - + -
599A GLU* 3.7 25.6 - - + +
600A ASN 3.3 4.5 - - - +
601A VAL* 4.2 4.5 - - + -
650A ILE* 1.3 78.3 - - - +
652A LYS* 1.3 62.1 + - - +
656A THR 3.9 0.9 - - - +
657A ILE* 3.4 3.2 - - - +
658A THR* 2.7 46.6 + - + +
681A TRP* 3.5 50.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A GLY 4.3 0.3 - - - +
599A GLU* 3.6 0.8 - - - +
600A ASN* 3.0 30.4 + - - +
602A TYR* 3.5 54.6 + - + +
615A THR 2.8 29.6 + - - +
616A SER* 4.1 12.5 + - - +
618A ALA* 4.5 2.2 + - - +
650A ILE* 4.3 9.6 - - + -
651A LYS* 1.3 77.0 - - - +
653A ASN* 1.3 66.6 + - - +
656A THR 3.8 5.6 - - - +
657A ILE* 3.8 29.6 - - + +
----------------------------------------------------------
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