Contacts of the strand formed by residues 401 - 410 (chain A) in PDB entry 2XVS
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 LYS 401 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 4.5 18.2 - - - -
268A LEU* 4.3 13.9 - - + -
272A ASP* 4.4 13.6 + - - +
397A GLN* 3.3 5.4 - - - +
398A HIS 3.0 37.9 + - - +
399A LYS 3.8 7.2 - - - +
400A GLY* 1.3 82.1 - - - +
402A ASP* 1.3 62.9 + - - +
403A TYR* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ARG* 5.5 0.7 - - - +
396A ILE 3.3 8.6 + - - +
397A GLN* 3.1 34.0 + - + +
400A GLY 4.4 0.4 + - - +
401A LYS* 1.3 76.5 - - - +
403A TYR* 1.3 84.8 + - - +
404A SER* 5.2 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.4 27.1 + - + +
271A LEU* 3.7 31.2 - - + -
272A ASP* 2.6 35.8 + - - -
275A THR* 3.7 23.6 - - + -
394A HIS 3.8 0.6 - - - +
395A ARG* 3.5 3.1 - - - -
396A ILE* 2.9 49.6 + - + +
398A HIS 5.4 0.4 - - - -
401A LYS* 3.5 38.6 - - + +
402A ASP* 1.3 82.8 + - - +
404A SER* 1.3 62.3 + - - +
405A PHE* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 5.4 2.5 - - - +
394A HIS 3.3 8.9 + - - -
395A ARG* 4.6 11.8 - - - +
402A ASP* 5.2 3.1 - - - -
403A TYR* 1.3 75.6 - - - +
405A PHE* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.7 27.1 - - + -
274A LEU* 3.9 21.8 - - + -
275A THR* 4.2 14.8 - - + -
278A LEU* 4.2 19.7 - - + -
368A MET* 3.9 12.8 - - + -
393A LEU* 3.9 0.4 - - - -
394A HIS* 2.8 63.7 + + + +
396A ILE* 4.0 21.3 - - + -
403A TYR* 4.0 18.6 - - + -
404A SER* 1.3 78.1 + - - +
406A SER* 1.3 73.6 + - - +
407A SER* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 5.0 1.4 - - - +
365A TYR* 4.5 18.5 - - - -
366A ALA* 3.6 17.1 + - - +
391A LEU* 3.9 20.9 - - - +
392A ARG 3.2 9.9 - - - -
393A LEU* 3.9 18.7 - - - +
405A PHE* 1.3 87.8 - - - +
407A SER* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ALA* 3.4 11.2 - - - -
368A MET* 4.0 26.2 - - - -
390A ASN 3.7 0.2 - - - +
391A LEU* 3.5 3.9 - - - -
392A ARG* 2.8 54.5 + - - +
394A HIS* 2.7 29.3 + - - -
405A PHE* 4.4 0.7 - - - -
406A SER* 1.3 76.8 - - - +
408A VAL* 1.3 61.9 + - - +
409A ARG 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.9 10.1 - - + -
327A LEU* 4.3 16.8 - - + -
337A ILE* 5.8 0.2 - - + -
365A TYR* 5.4 3.1 - - + -
366A ALA 2.9 17.0 + - - +
367A VAL* 3.5 12.4 - - + +
368A MET 2.9 26.3 + - - +
386A ILE* 3.9 21.5 - - + -
389A PRO* 3.8 23.6 - - + -
390A ASN 3.3 11.7 - - - +
391A LEU* 3.9 20.2 - - + -
407A SER* 1.3 71.5 - - - +
409A ARG* 1.3 62.4 + - - +
410A VAL* 3.6 9.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A MET 3.7 3.1 - - - -
370A TYR* 3.8 32.7 - - + +
371A ASN* 5.4 2.2 - - - +
390A ASN* 2.8 50.9 + - - +
392A ARG* 3.7 37.9 - - - +
407A SER 3.8 1.4 + - - -
408A VAL* 1.3 72.7 - - - +
410A VAL* 1.3 63.2 + - - +
411A GLU* 2.7 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 3.5 30.3 - - + -
368A MET 2.9 13.6 + - - +
369A VAL* 4.0 8.1 - - + -
370A TYR* 2.9 33.6 + - - -
386A ILE* 4.2 6.3 - - + -
408A VAL* 4.1 12.1 - - + +
409A ARG* 1.3 76.3 - - - +
411A GLU* 1.3 59.8 + - - +
412A THR 3.3 26.9 + - - +
415A LEU* 4.7 7.6 - - + -
416A LEU* 3.9 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