Contacts of the strand formed by residues 362 - 366 (chain T) in PDB entry 1VYH
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 362 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T PRO 5.6 0.2 - - - +
354T LEU* 4.7 8.7 - - + -
355T SER 3.4 20.2 - - - +
356T CYS* 4.7 2.2 - - + +
360T LYS 4.3 0.8 + - - -
361T THR* 1.3 72.4 - - - +
363T ARG* 1.3 57.7 + - - +
364T VAL* 4.0 2.4 + - + -
375T THR* 3.5 1.4 - - - -
376T LEU* 2.7 70.5 + - + +
378T ALA* 4.2 14.7 - - + +
383T VAL* 6.2 1.1 - - + -
386T LEU* 3.8 24.0 - - + -
395T VAL* 4.9 19.7 - - + -
397T THR* 4.2 29.4 - - + +
407T TRP* 5.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318T LYS* 3.2 22.8 + - - +
320T ILE* 3.2 19.2 - - - +
336T GLY* 3.7 3.8 + - - -
337T HIS* 3.0 54.9 - - + +
338T ASP 3.4 6.9 - - - +
339T ASN 4.1 4.0 + - - -
341T VAL* 3.6 3.2 - - - +
355T SER* 2.9 52.0 + - - +
357T ALA* 3.8 15.8 - - - +
359T ASP* 2.9 31.3 + - - -
361T THR* 3.2 22.0 - - + +
362T LEU* 1.3 71.2 - - - +
364T VAL* 1.3 56.6 + - - +
365T TRP* 2.9 27.5 + - - +
372T CYS* 4.8 0.2 - - - -
374T LYS 4.2 0.2 - - - -
375T THR* 4.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T PRO* 4.3 24.5 - - + -
352T PHE* 4.5 11.0 - - + -
353T ILE 3.8 3.4 - - - +
354T LEU* 3.4 35.0 - - + -
362T LEU* 4.0 7.8 + - + +
363T ARG* 1.3 72.4 - - - +
365T TRP* 1.3 67.5 + - - +
372T CYS* 3.7 3.3 - - - -
373T MET* 3.3 34.9 + - + -
374T LYS* 3.2 34.9 + - + +
376T LEU* 4.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 365 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320T ILE* 4.0 7.2 - - + -
334T LEU* 2.8 54.1 - - + -
335T VAL 3.3 24.9 - - - -
336T GLY* 3.7 8.1 - - - -
337T HIS* 3.7 17.3 - + - -
352T PHE* 3.2 34.3 - - - -
353T ILE* 2.8 36.8 + - + +
355T SER* 4.0 6.4 + - - -
363T ARG* 2.9 49.7 + - - +
364T VAL* 1.3 76.4 - - - +
366T ASP* 1.3 63.1 + - - +
367T TYR 3.8 2.9 + - - +
370T LYS 4.7 14.6 - - - -
371T ARG 4.6 1.3 - - - -
372T CYS* 3.5 25.7 - - + -
373T MET* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 366 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351T LYS* 3.9 3.3 - - - +
352T PHE* 3.0 32.2 - - - -
365T TRP* 1.3 72.2 - - - +
367T TYR* 1.3 56.1 + - - +
368T LYS* 2.7 69.7 + - - +
370T LYS* 3.1 12.5 + - - -
371T ARG* 3.4 27.4 + - + +
373T MET* 3.9 17.5 - - + +
----------------------------------------------------------
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