Contacts of the strand formed by residues 279 - 284 (chain G) 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 VAL 279 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G ARG* 3.8 7.4 - - - +
252G CYS* 3.1 28.5 - - - -
253G SER 3.2 14.8 + - - +
256G GLN* 3.4 34.1 - - - +
257G THR 3.6 9.6 - - - +
258G VAL* 4.1 7.2 - - + -
275G HIS* 3.9 23.8 - - + -
277G HIS 4.2 0.9 - - - +
278G VAL* 1.3 81.2 - - - +
280G GLU* 1.3 58.9 + - - +
281G CYS 4.1 2.0 - - - +
313G SER* 3.9 14.8 - - - -
314G GLY 3.3 17.9 - - - +
315G SER* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G ARG* 3.9 24.1 + - - +
239G MET* 3.8 16.8 - - - +
252G CYS* 3.6 7.0 - - - -
278G VAL* 4.4 2.5 - - + +
279G VAL* 1.3 75.5 - - - +
281G CYS* 1.3 60.8 + - + +
314G GLY 3.2 6.2 + - - +
316G ARG* 2.4 55.4 + - + +
340G TRP* 3.9 6.1 - - - -
341G VAL 3.4 21.8 - - - +
342G ARG* 3.1 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 281 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G MET* 4.1 8.5 - - - -
252G CYS* 3.4 5.9 - - - -
279G VAL* 4.1 0.7 - - - +
280G GLU* 1.3 80.0 - - - +
282G ILE* 1.3 70.7 + - - +
313G SER* 3.4 19.5 - - - -
314G GLY* 3.4 11.6 + - - +
341G VAL 4.3 3.8 - - - -
342G ARG* 2.9 42.4 - - - -
343G GLY* 3.4 4.3 - - - -
344G VAL* 3.2 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G MET* 3.3 36.3 - - + +
241G ARG* 3.6 17.2 - - + +
250G ALA* 3.1 34.1 - - + +
251G SER 3.4 8.3 - - - +
252G CYS* 3.4 29.6 - - + -
258G VAL* 4.4 6.7 - - + -
281G CYS* 1.3 79.6 - - - +
283G SER* 1.3 65.7 + - - +
284G TRP* 6.0 0.2 - - - +
311G LEU* 3.1 31.9 - - + -
312G LEU 3.0 19.5 - - - +
313G SER* 4.8 0.9 - - - -
344G VAL* 4.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ARG* 5.3 0.9 - - - -
282G ILE* 1.3 75.5 + - - +
284G TRP* 1.3 68.6 + - - +
311G LEU* 3.1 6.8 - - - +
312G LEU* 2.9 37.1 + - - +
344G VAL 2.8 26.0 + - - -
345G LEU* 4.1 25.0 - - - +
346G PHE* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ARG* 3.4 25.5 + - + +
242G PRO 2.8 29.2 + - - -
243G ASN* 4.1 27.6 - - + -
244G GLN* 5.3 4.5 - - + +
248G LEU* 4.6 8.7 - - + -
249G ILE 4.3 3.6 - - - -
250G ALA* 3.5 30.8 - - + +
260G VAL* 4.0 27.1 - - + -
282G ILE* 6.2 0.2 - - + -
283G SER* 1.3 78.7 - - - +
285G ALA* 1.3 67.8 + - - +
286G PRO* 3.8 8.3 - - - +
309G PRO* 4.5 18.4 - - + -
310G PHE 3.5 19.7 - - - -
311G LEU* 4.2 15.7 - - + -
325G VAL* 4.6 4.3 - - + -
346G PHE* 4.0 8.6 - - - +
----------------------------------------------------------
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