Contacts of the strand formed by residues 361 - 365 (chain D) 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 THR 361 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D HIS* 4.1 0.9 - - - +
356D CYS* 3.3 4.0 - - - +
357D ALA 3.1 26.0 + - - -
359D ASP* 2.1 42.7 + - - +
360D LYS* 1.3 67.0 + - - +
362D LEU* 1.3 60.3 + - - +
363D ARG* 3.7 21.4 - - + -
375D THR* 3.7 18.5 - - + +
376D LEU 2.7 24.4 + - - -
377D ASN* 3.4 13.0 + - - -
378D ALA 4.4 1.3 - - - +
383D VAL* 3.4 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PRO 5.4 5.2 - - - +
354D LEU* 4.9 10.8 - - + -
355D SER 3.0 24.2 - - - +
356D CYS* 3.6 11.9 - - + -
361D THR* 1.3 72.8 - - - +
363D ARG* 1.3 63.7 + - - +
364D VAL* 4.3 1.5 + - + +
375D THR* 3.8 1.9 - - - -
376D LEU* 2.9 58.7 + - + +
378D ALA* 4.4 8.7 - - + -
383D VAL* 5.6 0.9 - - + -
386D LEU* 3.5 30.3 - - + -
395D VAL* 5.0 6.3 - - + -
397D THR* 4.0 18.4 - - - +
407D TRP* 4.6 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D LYS 4.9 1.2 + - - -
320D ILE* 4.6 1.2 - - - +
336D GLY* 4.0 0.6 - - - -
337D HIS* 2.9 86.8 + - + +
339D ASN 4.2 1.2 + - - -
341D VAL* 3.3 30.7 - - - +
353D ILE 3.9 0.2 - - - +
354D LEU* 3.3 4.2 - - - +
355D SER* 2.4 66.9 + - - +
356D CYS* 4.5 1.3 - - - +
357D ALA* 4.2 2.1 - - - +
359D ASP* 3.3 20.0 + - - -
361D THR* 3.7 16.6 - - + -
362D LEU* 1.3 74.0 - - - +
364D VAL* 1.3 62.4 + - - +
365D TRP* 3.4 30.2 - - + +
372D CYS* 4.4 2.0 - - - -
374D LYS 4.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PRO* 3.9 31.9 - - + +
97D ARG* 6.5 0.2 - - + -
352D PHE* 4.1 11.7 - - + -
353D ILE 3.4 4.3 - - - -
354D LEU* 3.4 32.5 - - + -
362D LEU* 5.4 2.7 - - + +
363D ARG* 1.3 73.3 - - - +
365D TRP* 1.3 68.6 + - - +
372D CYS* 3.8 1.6 - - - -
373D MET* 3.1 34.8 + - + -
374D LYS* 3.4 30.6 + - + +
376D LEU* 5.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D LYS 5.6 0.4 - - - -
320D ILE* 3.6 12.0 - - + +
334D LEU* 3.4 60.8 - - + -
335D VAL 3.8 9.4 - - - -
336D GLY* 3.1 28.5 - - - -
337D HIS* 4.0 10.1 - + - -
352D PHE* 3.2 30.6 - - - +
353D ILE* 2.6 29.5 + - + +
355D SER* 3.3 29.3 - - - -
363D ARG* 3.4 27.7 - - + +
364D VAL* 1.3 76.9 - - - +
366D ASP* 1.3 60.9 + - - +
367D TYR 3.7 2.9 - - - +
370D LYS 4.2 6.5 - - - -
371D ARG 3.8 4.0 - - - +
372D CYS* 3.5 28.9 - - + +
373D MET* 4.0 3.4 - - - +
----------------------------------------------------------
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