Contacts of the strand formed by residues 371 - 377 (chain L) 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 ARG 371 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H SER* 2.7 24.0 + - - -
136H ASP* 2.6 27.5 + - - +
138H GLU* 3.3 22.8 + - - +
139H THR* 4.0 13.8 + - - -
143H GLU* 5.3 4.8 + - - -
365L TRP* 4.0 4.5 - - - -
366L ASP* 2.9 42.7 + - + +
369L ASN* 3.2 39.4 + - - +
370L LYS* 1.3 77.4 - - - +
372L CYS* 1.3 67.2 + - - +
373L MET* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 372 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335L VAL 5.8 0.4 - - - +
337L HIS* 3.3 34.5 - - + -
363L ARG* 4.2 8.1 - - - -
364L VAL 4.2 3.4 - - - -
365L TRP* 3.9 29.3 - - + -
370L LYS 4.0 1.2 + - - -
371L ARG* 1.3 73.9 - - - +
373L MET* 1.3 59.2 + - - +
374L LYS 3.4 17.5 + - - -
375L THR* 4.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 373 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L PRO* 6.3 1.6 - - - -
352L PHE* 4.2 24.9 - - - -
364L VAL* 3.0 23.9 + - - +
365L TRP 4.3 1.1 - - - -
366L ASP* 3.9 26.0 - - + +
371L ARG* 4.6 13.0 - - + +
372L CYS* 1.3 71.0 - - - +
374L LYS* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 374 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L PRO* 6.1 0.4 - - + -
97L ARG* 4.2 40.5 - - + +
98L PRO* 4.7 5.1 + - - +
363L ARG* 3.9 0.5 - - - -
364L VAL* 3.4 42.3 + - + -
372L CYS* 3.4 12.4 + - - -
373L MET* 1.3 79.2 - - - +
375L THR* 1.3 91.0 + - - +
376L LEU* 4.4 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337L HIS* 2.6 30.6 + - + +
361L THR* 3.7 23.1 - - + +
362L LEU 4.0 4.3 - - - -
372L CYS* 4.4 2.3 - - - -
374L LYS* 1.3 90.0 + - - +
376L LEU* 1.3 63.6 + - - +
377L ASN* 3.7 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L PRO 3.9 19.3 - - - +
97L ARG* 3.9 8.7 - - + +
98L PRO 3.2 26.9 - - - +
99L PRO* 5.3 0.2 - - + -
361L THR* 3.5 9.7 - - - +
362L LEU* 2.9 66.7 + - + +
364L VAL* 5.6 4.0 - - + -
374L LYS* 4.5 14.3 - - + +
375L THR* 1.3 76.9 - - - +
377L ASN* 1.3 65.3 + - - +
378L ALA* 3.6 3.1 - - + -
407L TRP* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 377 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360L LYS* 4.0 23.7 + - - +
361L THR* 4.4 11.3 + - - -
375L THR* 3.7 14.6 + - - +
376L LEU* 1.3 77.9 + - - +
378L ALA* 1.3 60.3 + - - +
379L HIS 5.4 0.7 - - - -
407L TRP* 4.5 6.2 - - - -
----------------------------------------------------------
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