Contacts of the strand formed by residues 557 - 565 (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 HIS 557 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ASN 4.8 3.2 + - - -
535B SER* 5.3 2.9 - - - -
552B CYS* 4.3 13.2 - - + +
554B GLN* 2.9 57.3 + - + +
555B GLN 3.3 7.0 + - - -
556B GLY* 1.3 84.3 + - - +
558B VAL* 1.3 63.6 + - - +
586B ASN* 2.9 23.6 + - - -
600B CYS* 4.7 8.1 - - + -
601B CYS* 3.2 11.4 - - - +
602B HIS* 3.3 43.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B CYS* 4.1 3.6 - - - -
556B GLY 4.7 6.3 - - - +
557B HIS* 1.3 77.6 - - - +
559B LEU* 1.3 60.3 + - - +
560B THR* 3.7 12.4 + - + +
586B ASN* 3.9 5.6 - - - +
600B CYS* 3.5 2.4 - - - -
601B CYS* 2.9 40.4 + - + +
603B ALA* 5.2 6.3 - - + +
606B LEU* 4.5 27.4 - - + +
607B GLU* 5.6 0.2 - - - -
608B CYS* 3.9 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B CYS* 3.8 9.7 - - - -
558B VAL* 1.3 72.7 - - - +
560B THR* 1.3 60.1 + - - +
561B GLY 3.4 20.9 - - - +
562B CYS* 3.9 5.2 - - - -
586B ASN* 3.4 36.3 + - - +
587B GLN 3.8 16.6 - - - +
588B CYS* 3.6 17.9 - - - -
598B ALA* 3.4 23.3 - - + -
599B SER 3.3 17.7 - - - +
608B CYS* 4.4 9.7 - - - +
610B VAL* 5.9 5.6 - - + -
677B ILE* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 2.7 45.1 + - + +
558B VAL* 4.0 22.7 - - + +
559B LEU* 1.3 78.5 - - - +
561B GLY* 1.3 58.1 + - - +
599B SER* 3.1 18.8 + - - -
601B CYS* 4.1 16.7 - - + -
606B LEU* 5.2 3.8 - - + -
633B THR* 2.7 40.5 + - - +
634B GLY* 3.5 2.8 - - - -
677B ILE* 3.6 7.7 - - - +
679B CYS* 4.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU 3.3 10.3 + - - -
485B SER* 3.8 11.9 - - - -
500B MET* 4.2 2.6 - - - +
559B LEU* 3.4 8.9 - - - +
560B THR* 1.3 84.9 + - - +
562B CYS* 1.3 65.2 + - - -
597B HIS 3.9 0.2 - - - +
598B ALA* 3.5 0.5 - - - -
599B SER* 2.9 28.1 + - - -
634B GLY* 4.6 1.3 - - - -
677B ILE* 3.6 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B SER* 5.0 1.4 - - - -
486B CYS 3.8 8.7 + - - +
498B GLU* 4.6 0.3 - - - +
559B LEU* 3.9 11.4 - - - -
561B GLY* 1.3 76.4 - - - -
563B SER* 1.3 67.3 + - - +
587B GLN 4.4 1.1 - - - -
588B CYS* 2.0 52.3 - - + -
589B VAL 5.1 1.6 - - - +
596B ILE* 5.0 2.9 - - + -
597B HIS 3.4 4.3 - - - -
634B GLY* 5.7 0.6 - - - -
635B CYS 5.1 1.9 - - - +
636B SER* 4.4 28.1 + - - +
677B ILE* 4.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B CYS* 2.7 34.2 + - - +
498B GLU* 3.3 24.5 - - - -
499B ARG* 4.6 2.7 - - - -
500B MET* 3.5 16.4 - - - +
562B CYS* 1.3 73.0 + - - +
564B SER* 1.3 62.1 + - - +
596B ILE* 3.2 10.9 - - - +
597B HIS* 2.9 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B GLY* 3.2 6.8 - - - -
498B GLU* 2.7 41.8 + - - +
563B SER* 1.3 77.7 - - - +
565B HIS* 1.3 54.1 + - - +
566B TRP* 4.0 12.2 - - - -
590B GLY* 4.9 6.2 - - - -
591B HIS 5.1 0.9 + - - -
594B ALA* 3.3 17.5 - - - +
595B SER 3.0 18.9 + - - -
596B ILE* 4.3 9.1 - - - +
597B HIS* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ARG* 3.1 17.5 - - - +
497B GLY 4.1 0.7 - - - -
498B GLU 3.6 15.9 - - - +
499B ARG* 3.7 32.0 + - + +
512B HIS* 4.2 19.1 - + + -
564B SER* 1.3 77.0 + - - +
566B TRP* 1.3 69.9 + - - +
567B GLU* 4.0 20.4 + - - -
595B SER* 3.0 48.0 + - - -
597B HIS* 2.8 34.3 + + - -
----------------------------------------------------------
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