Contacts of the strand formed by residues 310 - 315 (chain H) 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 PHE 310 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H TRP* 3.5 9.5 - - - -
285H ALA* 2.7 52.4 + - + +
289H SER* 4.5 28.9 - - - -
291H SER* 5.3 8.3 - - - -
292H SER* 5.6 9.4 - - - -
308H GLY* 3.0 29.2 - - - -
309H PRO* 1.3 80.0 - - + +
311H LEU* 1.3 56.4 + - - +
322H MET* 4.0 24.0 - - + -
323H TRP 2.9 17.3 - - - +
324H ASP* 3.1 33.4 - - + -
325H VAL* 4.3 0.9 - - - +
331H LEU* 4.3 10.3 - - + -
346H PHE* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H ALA* 3.6 20.4 - - + -
258H VAL* 4.0 8.3 - - + -
260H VAL* 3.6 30.3 - - + -
272H LEU* 3.6 25.8 - - + -
282H ILE* 3.7 16.2 - - + -
283H SER 3.1 11.9 - - - +
284H TRP* 4.2 15.9 - - + -
285H ALA* 4.6 0.7 - - - +
310H PHE* 1.3 75.6 - - - +
312H LEU* 1.3 63.3 + - - +
313H SER* 5.9 0.2 - - - -
322H MET* 3.6 2.3 - - - -
323H TRP* 3.1 42.8 + - + +
325H VAL* 4.7 6.0 - - + +
346H PHE* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H CYS 4.1 0.3 - - - -
282H ILE* 2.9 12.1 - - - +
283H SER* 2.4 52.7 + - - +
311H LEU* 1.3 69.5 - - - +
313H SER* 1.3 59.9 + - - +
320H ILE* 4.0 10.8 - - + -
321H LYS 3.3 15.3 - - - +
322H MET* 3.6 25.8 - - + -
334H LEU* 6.2 0.7 - - + -
344H VAL* 3.8 17.5 - - + +
345H LEU 4.1 6.7 - - - +
346H PHE* 3.8 27.6 - - + -
353H ILE* 3.6 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H VAL* 4.0 13.9 - - - -
275H HIS* 2.8 29.7 + - - -
279H VAL* 4.0 10.3 - - - -
281H CYS 3.4 10.1 - - - -
282H ILE* 4.7 1.6 - - - -
311H LEU* 4.0 1.0 + - - -
312H LEU* 1.3 73.9 - - - +
314H GLY* 1.3 58.9 + - - +
320H ILE* 3.1 8.2 - - - +
321H LYS* 2.6 42.8 + - - +
323H TRP* 3.2 22.8 + - - -
344H VAL* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H VAL* 3.2 8.3 - - - +
280H GLU 2.9 19.5 + - - -
281H CYS* 3.2 25.4 + - - +
313H SER* 1.3 73.8 - - - +
315H SER* 1.3 61.9 + - - -
319H THR 4.0 3.8 - - - -
320H ILE* 4.3 2.5 - - - -
341H VAL* 3.8 18.8 - - - -
344H VAL* 3.8 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H HIS* 3.6 26.5 - - - -
277H HIS 3.1 9.7 + - - -
278H VAL 2.6 17.0 + - - -
279H VAL* 3.7 7.2 - - - -
280H GLU* 3.9 4.0 - - - +
314H GLY* 1.3 75.4 - - - -
316H ARG* 1.3 70.4 + - - +
317H ASP* 2.9 18.8 + - - +
318H LYS* 3.3 8.1 + - - -
319H THR 3.6 5.9 + - - -
341H VAL* 3.0 31.5 + - - +
----------------------------------------------------------
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