Contacts of the strand formed by residues 411 - 414 (chain A) in PDB entry 1GVJ
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 411 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A THR* 4.3 6.3 - - + -
362A GLU* 3.3 39.7 - - + +
363A PHE 3.3 6.5 - - - +
364A LYS* 4.0 22.0 - - + -
404A LYS* 3.6 10.5 - - - +
405A THR* 2.9 34.1 + - - +
408A LYS* 4.0 24.4 - - + -
409A ARG* 3.2 13.3 - - - +
410A TYR* 1.3 79.6 - - - +
412A TYR* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.3 7.6 - - - +
363A PHE* 2.8 55.0 + + + -
365A LEU* 4.1 11.7 - - + -
386A TYR* 4.7 11.1 + + - -
390A SER* 4.9 6.4 + - - -
393A LEU* 3.5 40.8 - - + +
394A ARG* 5.2 4.5 + - - +
397A TYR* 3.3 23.7 + + - -
402A ILE* 3.8 14.1 - - + -
403A HIS 3.2 9.0 - - - +
404A LYS* 3.7 35.2 - - + +
405A THR* 4.3 1.6 - - - +
410A TYR* 3.7 29.6 - + - -
411A VAL* 1.3 75.1 - - - +
413A ARG* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASP* 2.6 52.9 + - - -
360A GLY* 4.4 1.8 - - - -
361A TRP* 3.4 18.8 - - + +
362A GLU* 3.5 26.3 + - + +
363A PHE* 3.9 4.2 - - - -
402A ILE* 3.3 3.4 - - - -
403A HIS* 2.7 41.0 + - + +
405A THR* 4.7 6.1 + - - +
412A TYR* 1.3 78.2 - - - +
414A PHE* 1.3 77.0 + - - +
415A VAL* 3.4 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TRP* 3.8 26.2 - + + -
341A LEU* 4.3 12.6 - - + -
342A LEU* 3.7 26.2 - - + -
345A LEU* 3.8 18.4 - - + -
356A TRP* 4.0 6.7 - + - -
361A TRP* 3.2 33.9 + - + +
363A PHE* 3.6 22.9 - + - -
401A ILE* 3.3 12.3 - - + +
402A ILE* 3.7 25.8 - - + +
413A ARG* 1.3 83.6 - - - +
415A VAL* 1.3 59.3 + - - +
416A CYS* 4.6 8.3 - - - -
418A LEU* 3.5 31.6 - - + -
----------------------------------------------------------
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