Contacts of the strand formed by residues 495 - 504 (chain A) in PDB entry 2V5Y
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 LEU 495 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ILE* 3.5 10.9 - - - +
494A THR* 1.3 91.2 + - - +
496A TYR* 1.3 67.3 + - - +
497A GLU* 4.1 0.4 - - + -
520A SER* 4.3 22.9 - - - -
521A LYS* 3.4 19.1 - - - +
522A LEU* 4.6 8.5 - - + +
523A GLY 4.1 0.7 - - - +
546A SER* 3.1 32.3 + - - -
551A PHE* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 3.7 10.8 - - + -
483A TRP* 3.4 40.4 - + + -
485A GLU* 3.2 32.4 - - - +
486A PRO* 3.6 3.2 - - + +
493A ILE* 3.8 14.3 - - + +
495A LEU* 1.3 76.2 - - - +
497A GLU* 1.3 61.3 + - - +
498A ILE* 3.9 5.0 + - + +
519A VAL 3.9 0.2 - - - +
520A SER* 3.3 5.0 - - - -
521A LYS* 2.8 33.4 + - + +
522A LEU 4.3 1.8 - - - -
523A GLY* 3.6 21.2 + - - -
525A GLU 4.1 8.5 - - - -
526A THR* 3.4 20.4 - - + +
543A ILE* 3.9 14.6 - - + -
544A ARG 3.5 2.2 - - - +
545A ALA* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TYR* 1.3 73.2 - - - +
498A ILE* 1.3 67.3 + - - +
499A THR* 3.4 24.4 + - + +
518A ARG* 3.5 34.1 + - - +
519A VAL 3.6 5.8 - - - +
520A SER* 4.5 5.6 - - - +
542A THR 3.9 4.5 - - - +
543A ILE* 3.5 1.4 - - - +
544A ARG* 2.8 68.2 + - + +
551A PHE* 3.3 33.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 2.9 38.1 - - + -
483A TRP* 4.6 18.2 - - + -
496A TYR* 4.1 10.1 - - + +
497A GLU* 1.3 79.3 + - - +
499A THR* 1.3 67.5 + - - +
500A TYR* 4.7 1.4 - - - -
517A GLY 4.5 0.2 - - - +
518A ARG* 3.5 0.6 - - - -
519A VAL* 2.7 63.8 + - + +
520A SER* 5.0 0.7 - - - +
521A LYS* 5.6 0.9 - - + +
528A PHE* 4.8 6.1 - - + -
530A PHE* 3.4 21.5 - - + -
541A PHE* 4.3 4.0 - - + -
542A THR 3.6 4.7 - - - +
543A ILE* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLU* 3.4 24.0 - - - +
498A ILE* 1.3 79.5 - - - +
500A TYR* 1.3 64.6 + - - +
501A LYS* 4.2 20.2 - - - +
517A GLY 3.4 10.3 - - - -
518A ARG* 3.8 27.8 - - + +
540A SER 4.4 0.2 - - - -
541A PHE* 3.3 4.5 - - - -
542A THR* 3.0 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ILE 4.7 2.0 - - - -
499A THR* 1.3 77.9 - - - +
501A LYS* 1.3 63.7 + - - +
515A GLN* 4.1 8.0 + - - -
516A SER* 3.2 29.5 + - - -
517A GLY* 3.0 49.7 + - - +
518A ARG* 4.1 5.2 - - - -
519A VAL* 5.5 0.9 - - + -
530A PHE* 3.7 24.5 - + - -
531A PHE* 3.5 30.4 - + - -
533A LEU* 4.5 16.4 - - + -
539A TYR* 4.0 18.4 - + + -
540A SER 3.1 7.6 - - - +
541A PHE* 3.5 26.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A THR* 4.2 19.7 - - - +
500A TYR* 1.3 85.5 - - - +
502A ALA* 1.3 67.5 + - - +
503A VAL* 3.5 7.5 + - + +
515A GLN 4.1 0.4 - - - -
516A SER* 3.5 17.9 - - - +
517A GLY 5.9 0.2 - - - -
539A TYR* 3.2 6.9 - - - -
540A SER* 2.9 40.8 + - - +
542A THR* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LYS* 1.3 74.3 - - - +
503A VAL* 1.3 61.6 + - - +
513A SER* 4.1 25.7 - - - +
515A GLN* 3.2 32.2 + - + +
516A SER* 4.1 1.7 + - - -
534A TYR* 6.2 1.1 - - + -
537A THR* 4.0 15.3 - - + -
538A THR 3.9 1.8 - - - -
539A TYR* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LYS* 3.5 6.9 + - + +
502A ALA* 1.3 76.8 - - - +
504A SER* 1.3 70.6 + - - +
513A SER* 5.7 2.0 - - - -
538A THR* 2.8 27.9 + - - +
540A SER* 4.2 24.9 - - - +
558A GLN* 5.4 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA 3.8 0.4 - - - -
503A VAL* 1.3 86.0 - - - +
505A SER* 1.3 63.7 + - - +
513A SER* 5.1 5.3 + - - -
537A THR* 3.0 23.9 - - - +
538A THR* 3.1 32.0 + - - +
----------------------------------------------------------
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