Contacts of the strand formed by residues 653 - 658 (chain B) in PDB entry 2PMW
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 653 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B THR* 3.9 18.2 - - + +
624B VAL 3.6 14.6 - - - +
625B ALA* 3.5 16.4 - - + +
632B LEU* 3.4 7.8 - - - +
649B ALA* 3.4 0.3 - - - -
650B VAL* 2.8 43.4 + - - +
651B ASP* 3.5 0.4 - - - +
652B ASN* 1.3 78.8 + - - +
654B CYS* 1.3 71.2 + - - +
655B VAL* 3.8 6.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B VAL 4.0 0.3 - - - +
623B THR* 3.1 7.8 - - - -
624B VAL* 2.7 44.2 + - + +
632B LEU* 3.6 4.2 - - + +
635B CYS* 2.0 56.1 - - + -
636B SER 3.5 12.6 - - - -
653B THR* 1.3 71.8 - - - +
655B VAL* 1.3 59.6 + - - +
656B VAL* 4.4 7.4 - - - -
674B ALA* 4.3 1.6 - - - +
675B VAL 3.6 13.2 - - - -
676B ALA* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B GLN* 4.0 27.8 - - - +
622B VAL 3.8 2.2 - - - -
623B THR* 4.0 13.7 - - + -
647B ALA* 3.1 5.7 - - - +
648B TYR* 3.0 64.2 + - + +
650B VAL* 3.5 29.2 - - + -
653B THR* 4.3 8.7 - - + +
654B CYS* 1.3 77.2 - - - +
656B VAL* 1.3 69.6 + - - +
657B ARG* 4.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B GLN* 3.3 5.7 - - - +
622B VAL* 2.8 38.2 + - + +
636B SER 3.9 14.1 - - - +
637B ALA* 3.6 23.3 - - + -
644B VAL* 4.3 9.6 - - + -
646B GLY 3.6 9.2 - - - +
647B ALA* 3.9 10.8 - - + -
654B CYS* 4.4 2.5 - - - -
655B VAL* 1.3 77.7 - - - +
657B ARG* 1.3 65.1 + - - +
658B SER* 4.0 0.5 + - - -
672B VAL* 3.9 22.6 - - + +
674B ALA* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU 5.7 3.0 + - - -
435B VAL* 4.1 14.8 - - - +
489B PHE* 4.0 24.4 - - + -
620B GLU* 4.1 7.9 - - - -
621B GLN* 4.2 20.9 + - + -
644B VAL* 3.3 6.1 - - - +
645B LEU* 2.5 68.5 + - + +
646B GLY 2.9 15.6 + - - +
648B TYR* 3.4 33.2 + - + +
655B VAL* 4.4 3.4 - - + -
656B VAL* 1.3 77.2 - - - +
658B SER* 1.3 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B PRO* 3.2 39.9 + - - +
620B GLU* 3.2 27.8 + - - +
621B GLN* 4.3 1.2 + - - -
622B VAL* 5.2 0.2 - - - +
643B HIS 3.8 8.3 - - - -
644B VAL* 4.2 3.8 - - - +
645B LEU* 4.2 9.0 - - - +
656B VAL 4.0 1.0 + - - -
657B ARG* 1.3 74.9 + - - +
659B ARG* 1.3 66.3 + - - +
672B VAL* 4.2 17.2 - - - +
----------------------------------------------------------
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