Contacts of the strand formed by residues 651 - 657 (chain A) in PDB entry 2YT4
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 651 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PHE* 3.3 24.9 - - - -
642A GLU 2.9 26.0 - - - -
649A GLN* 3.2 7.9 + - - -
650A LYS* 1.3 72.2 - - - +
652A GLU* 1.3 59.7 + - - +
665A TRP* 3.5 2.9 - - - -
666A CYS* 2.9 37.1 + - - -
667A LYS 5.0 4.0 + - - -
668A ASN* 5.1 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PHE* 4.4 1.0 - - - -
642A GLU* 3.3 51.4 + - + +
651A SER* 1.3 75.9 - - - +
653A TYR* 1.3 65.4 + - - +
654A VAL* 5.1 0.4 - - - -
663A ARG* 3.5 31.3 + - - +
664A GLY 3.0 13.2 - - - +
665A TRP* 3.3 43.3 - - + +
666A CYS* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ILE* 6.3 1.1 - - + -
640A LYS 3.4 12.1 - - - +
641A PHE* 5.1 6.7 - - + -
642A GLU* 5.5 0.4 - - - -
652A GLU* 1.3 75.2 - - - +
654A VAL* 1.3 78.9 + - - +
655A MET 4.5 0.4 - - - -
662A VAL* 3.9 8.3 - - + -
663A ARG* 3.2 24.5 - - - +
664A GLY* 2.9 37.4 + - - -
665A TRP 3.4 13.8 + - - -
666A CYS* 4.0 22.7 - - - -
672A GLY* 4.1 23.8 - - - +
675A LEU* 4.1 10.9 - - + +
676A ALA* 3.6 26.4 + - + -
679A LYS* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ILE* 3.2 2.7 - - - -
640A LYS* 2.8 50.1 + - + +
642A GLU* 5.1 5.4 - - - +
652A GLU* 4.7 4.0 - - - +
653A TYR* 1.3 86.6 - - - +
655A MET* 1.3 63.9 - - - +
656A ALA* 4.0 3.9 + - + +
661A THR* 3.9 19.1 - - - +
662A VAL 3.0 9.2 - - - +
663A ARG* 3.4 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A TYR* 4.3 8.5 - - + -
624A LEU* 3.4 33.2 - - + -
637A THR* 4.0 11.4 - - + -
638A SER 3.4 4.5 - - - +
639A ILE* 3.2 30.1 - - + +
653A TYR* 4.5 0.4 - - - -
654A VAL* 1.3 74.0 - - - +
656A ALA* 1.3 65.6 + - - +
660A HIS 3.7 1.2 - - - +
661A THR* 3.2 1.3 - - - -
662A VAL* 2.6 46.2 + - + +
673A LYS* 4.4 1.1 - - - +
676A ALA* 3.5 35.7 - - + +
677A SER* 3.7 24.5 - - - +
680A ILE* 4.0 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ASP 3.8 4.3 - - - +
637A THR* 3.2 2.9 - - - +
638A SER* 2.7 50.5 + - - +
654A VAL* 4.0 4.6 + - + -
655A MET* 1.3 75.7 - - - +
657A CYS* 1.3 61.5 + - - +
658A GLY 5.4 2.5 - - - +
660A HIS 3.2 7.9 - - - +
661A THR* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 4.6 1.3 - - - -
628A LEU* 3.8 21.5 - - - -
634A MET 4.7 4.9 - - - -
636A ASP 3.1 7.0 - - - -
637A THR* 2.7 31.4 - - + +
655A MET* 5.2 0.4 - - + -
656A ALA* 1.3 76.4 - - - +
658A GLY* 1.3 66.1 + - - +
660A HIS* 2.7 28.6 + - - +
680A ILE* 3.9 33.7 - - + -
684A LEU* 4.6 8.8 - - - +
----------------------------------------------------------
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