Contacts of the strand formed by residues 570 - 577 (chain A) in PDB entry 2WIN
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 ARG 570 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 3.6 32.7 + - - +
164A LEU* 3.5 32.3 - - + +
166A VAL* 5.0 16.2 - - + +
568A GLY 3.9 1.2 + - - -
569A ALA* 1.3 72.9 - - - +
571A VAL* 1.3 64.8 + - - +
572A VAL* 4.9 5.1 - - + +
753B VAL* 3.7 25.0 - - + +
754B GLU 3.8 3.1 - - - -
755B ASP* 3.1 37.0 + - - +
785B VAL 3.6 1.6 - - - +
786B SER* 3.4 1.2 - - - -
787B MET* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 4.0 9.9 - - + -
563A ILE* 4.6 11.0 - - + -
569A ALA 4.5 1.1 - - - +
570A ARG* 1.3 78.1 - - - +
572A VAL* 1.3 67.1 + - - +
573A LEU* 3.7 28.2 + - + +
753B VAL* 3.6 1.0 - - - +
754B GLU* 2.7 47.5 + - + +
756B LEU* 3.9 28.9 - - + -
784B ALA* 4.1 11.4 - - + -
785B VAL 3.4 8.7 - - - +
786B SER* 4.0 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 4.4 0.6 + - - +
126A ARG* 3.4 41.2 + - - +
128A PHE* 4.1 13.0 - - + -
166A VAL* 4.2 16.2 - - + -
570A ARG* 4.2 6.0 + - + +
571A VAL* 1.3 75.5 - - - +
573A LEU* 1.3 60.7 - - - +
752B ASN 3.7 3.1 - - - +
753B VAL* 3.7 28.3 - - + -
783B LEU 3.8 1.7 - - - +
784B ALA* 3.7 4.3 - - - -
785B VAL* 3.1 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.4 9.6 + - - -
543A VAL* 5.1 2.0 - - + -
561A LEU* 4.7 6.3 - - + -
563A ILE* 3.8 14.4 - - + -
571A VAL* 3.7 28.9 - - + +
572A VAL* 1.3 74.3 - - - +
574A VAL* 1.3 68.1 + - - +
750B LEU* 3.0 32.9 - - + +
751B TRP* 3.6 9.9 - - - -
752B ASN* 3.0 15.2 + - + +
754B GLU* 4.6 5.4 - - + -
769B MET* 3.4 38.6 - - + -
782B ILE* 4.7 9.0 - - + -
783B LEU 3.7 2.7 - - - +
784B ALA* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 3.6 25.8 - - - +
113A ASP* 4.0 18.8 - - + +
126A ARG* 4.3 0.7 - - - +
573A LEU* 1.3 79.2 - - - +
575A ALA* 1.3 64.2 + - - +
576A VAL* 4.0 15.0 - - + +
748B SER* 5.1 1.3 - - - -
749B TRP 3.7 4.7 - - - +
750B LEU* 3.3 8.7 + - - +
751B TRP* 3.7 26.9 - - + -
781B GLU 3.6 1.9 - - - +
782B ILE* 3.4 5.5 - - - +
783B LEU* 3.0 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 1.3 73.4 - - - +
576A VAL* 1.3 63.7 + - - +
748B SER* 3.1 4.5 - - - -
749B TRP* 2.7 68.9 + - + +
750B LEU* 3.9 15.4 - - + +
780B TRP* 4.8 5.4 - - + -
781B GLU 3.7 3.8 - - - -
782B ILE* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 3.2 26.5 - - - +
114A LYS* 4.4 8.1 - - + -
574A VAL* 4.0 9.2 - - + +
575A ALA* 1.3 81.2 - - - +
577A ASP* 1.3 77.1 + - - +
578A LYS 3.4 0.5 + - - -
580A VAL* 3.9 17.5 - - + -
581A PHE* 4.1 20.6 - - + -
747B GLU 3.4 12.3 - - - +
748B SER* 3.8 12.8 - - - -
780B TRP* 3.7 4.7 - - - -
781B GLU* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.6 27.0 - - + +
238A LEU* 4.0 4.9 - - - +
576A VAL* 1.3 75.9 - - - +
578A LYS* 1.3 75.9 + - - +
579A GLY* 3.0 10.4 + - - -
580A VAL* 3.0 22.4 + - + +
581A PHE* 4.0 1.1 - - - -
746B PRO 4.8 1.2 - - - +
747B GLU* 3.2 11.5 + - - +
776B SER* 5.0 3.8 - - - -
778B THR* 2.8 42.7 + - - +
779B THR 4.1 1.3 - - - -
780B TRP* 3.5 22.9 - - + -
----------------------------------------------------------
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