Contacts of the strand formed by residues 557 - 562 (chain B) in PDB entry 2V4M
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 SER 557 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LYS* 5.1 4.0 + - - +
557A SER* 3.6 10.6 + - - -
584A HIS* 2.9 32.8 + - - +
555B GLN* 3.6 5.3 + - - +
556B LYS* 1.3 81.4 + - - +
558B VAL* 1.3 63.4 + - - +
583B MET* 4.5 2.4 - - - +
584B HIS* 3.2 7.2 - - - +
605B MET* 3.9 22.5 - - - +
606B PRO* 3.0 27.0 - - - +
----------------------------------------------------------
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 LEU* 5.1 8.3 - - + -
557B SER* 1.3 76.0 - - - +
559B LEU* 1.3 67.0 + - - +
560B ILE* 3.7 3.8 + - + +
577B ILE* 4.2 6.7 - - + -
583B MET* 3.8 27.1 - - + -
584B HIS 3.0 5.4 + - - -
585B SER* 3.3 24.1 - - - -
586B GLU 3.2 20.4 + - - -
605B MET* 4.7 0.4 - - - -
606B PRO* 3.5 21.3 - - + +
608B ILE* 3.7 34.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
584A HIS* 3.8 29.2 - - + +
558B VAL* 1.3 73.2 - - - +
560B ILE* 1.3 61.5 + - - +
561B MET* 4.0 27.4 - - + -
586B GLU* 3.6 6.7 - - + +
588B ILE* 4.2 22.2 - - + -
597B PRO 5.0 1.8 - - - +
600B LEU* 3.9 29.8 - - + -
601B VAL* 4.7 5.6 - - + -
605B MET* 3.7 30.7 - - + -
606B PRO 3.1 9.2 + - - +
607B VAL* 3.4 9.1 - - + +
608B ILE 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B VAL* 4.2 9.9 - - + +
559B LEU* 1.3 74.6 - - - +
561B MET* 1.3 56.4 + - - +
570B CYS* 3.4 32.1 - - + +
573B GLY 3.7 7.6 - - - -
574B ALA* 3.5 31.9 - - + +
577B ILE* 4.0 12.8 - - + -
585B SER* 4.8 2.5 - - - -
586B GLU 3.0 10.5 + - - +
587B GLY* 3.3 2.9 - - - -
588B ILE 2.7 30.5 + - - -
608B ILE* 3.2 29.6 - - + +
610B ILE* 4.5 4.9 - - + -
671B LEU* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LEU* 4.0 19.5 - - + +
560B ILE* 1.3 75.9 - - - +
562B GLY* 1.3 58.0 + - - +
570B CYS* 4.3 2.5 - - - -
588B ILE* 3.3 17.5 - - + +
590B ALA* 4.8 7.4 - - + -
593B LEU* 3.7 42.0 - - + -
601B VAL* 4.0 15.7 - - + -
607B VAL* 3.6 36.6 - - + -
608B ILE 2.8 9.7 + - - +
609B MET* 3.4 30.7 - - + +
610B ILE* 2.9 27.7 + - - +
627B VAL* 3.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B MET* 1.3 74.3 - - - +
563B ARG* 1.3 59.8 + - - -
566B HIS 3.9 20.0 - - - -
567B TYR* 4.2 3.5 - - - -
570B CYS* 4.1 6.1 - - - +
588B ILE 3.2 7.1 + - - -
589B LEU* 3.3 15.1 - - - +
590B ALA* 3.1 23.8 + - - +
610B ILE* 4.5 11.0 - - - -
620B CYS* 6.0 0.2 - - - -
----------------------------------------------------------
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