Contacts of the helix formed by residues 361 - 368 (chain A) in PDB entry 1V9P
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 ASN 361 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 3.6 24.3 + - - +
193A GLY* 3.5 14.1 - - - -
194A GLU 2.7 29.8 + - - +
195A LYS* 5.1 0.5 - - - -
196A VAL* 5.2 0.6 + - - +
337A ARG* 4.2 4.0 - - - +
340A PRO* 4.0 4.9 - - - -
360A HIS* 1.3 89.9 - - - +
362A GLU* 1.3 76.9 + - - +
363A SER* 3.7 6.7 - - - +
364A TYR* 2.9 18.9 + - - +
365A ILE* 3.4 21.7 + - - +
405A TRP* 4.2 5.4 - - - -
422A VAL* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 4.9 2.3 + - - +
338A VAL 4.9 2.4 - - - +
361A ASN* 1.3 76.1 - - + +
363A SER* 1.3 65.0 + - - +
365A ILE* 3.9 3.3 - - - +
366A GLU* 3.0 40.9 + - - +
405A TRP* 2.9 48.2 + - + -
418A LYS* 4.8 7.0 - - - +
421A LYS 2.9 22.9 - - - +
422A VAL* 3.1 34.1 - - - +
423A HIS* 3.3 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY 2.6 28.2 + - - -
194A GLU* 4.5 0.3 - - - -
195A LYS* 4.4 15.7 - - - -
361A ASN* 3.2 8.1 + - - -
362A GLU* 1.3 76.0 - - - +
364A TYR* 1.3 54.6 + - - +
366A GLU* 2.6 34.2 + - - +
367A GLU* 2.7 25.0 + - - +
421A LYS* 3.8 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 4.2 20.0 - - + +
196A VAL* 3.9 15.3 - - + -
198A LYS* 2.9 33.8 - - + +
358A THR 5.9 0.4 - - - -
359A LEU* 5.4 3.1 - - - -
360A HIS* 3.3 41.7 - + + +
361A ASN* 2.9 18.7 + - - +
363A SER* 1.3 73.7 - - - +
365A ILE* 1.3 63.4 + - - +
367A GLU* 4.4 6.1 - - - -
368A LEU* 3.1 36.6 + - + +
370A ILE* 3.8 15.5 - - + -
387A GLU* 2.8 25.9 + - + -
388A VAL* 3.0 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PRO* 3.9 4.7 - - + -
359A LEU* 3.9 32.5 - - + -
361A ASN 3.4 8.0 + - - +
362A GLU* 3.9 8.3 - - - +
363A SER 3.2 0.6 - - - -
364A TYR* 1.3 80.7 - - + +
366A GLU* 1.3 61.2 + - + +
369A ASP* 3.2 5.5 + - - -
370A ILE* 2.9 41.2 + - + +
403A ILE* 3.4 59.9 - - + +
405A TRP* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.0 30.3 + - + +
363A SER* 2.6 22.0 + - - +
365A ILE* 1.3 73.6 - - + +
367A GLU* 1.3 68.3 + - - +
369A ASP* 2.9 15.6 + - - +
418A LYS* 4.8 9.5 + - - -
421A LYS* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 3.2 53.7 - - + +
363A SER* 2.7 19.9 + - - +
364A TYR 3.8 0.9 - - - +
366A GLU* 1.3 76.9 - - - +
368A LEU* 1.3 61.9 + - + +
369A ASP* 3.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 3.2 36.8 - - - +
198A LYS* 3.8 12.6 - - - +
364A TYR* 3.1 32.9 + - + +
367A GLU* 1.3 77.2 - - - +
369A ASP* 1.3 73.0 + - - +
370A ILE* 3.3 19.4 - - + +
388A VAL 4.3 1.3 - - - +
389A LEU 3.4 26.5 - - - +
390A ARG* 3.8 18.4 - - + -
391A VAL* 3.4 16.9 - - + +
393A LYS* 5.1 2.6 - - - -
----------------------------------------------------------
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