Contacts of the helix formed by residues 290 - 303 (chain T) in PDB entry 6VVS
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 GLY 290 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P T 3.0 40.4 + - - -
18P T 4.4 2.9 - - - -
284T LEU* 3.6 17.2 - - - +
289T PHE* 1.3 74.8 - - - +
291T GLN* 1.3 64.4 + - - -
293T SER* 3.5 3.4 - - - -
294T ILE* 3.5 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P T 3.7 3.4 + - - +
284T LEU* 3.9 14.5 - - + +
290T GLY* 1.3 67.7 - - - -
292T LYS* 1.3 59.0 + - - +
293T SER 3.0 5.2 + - - -
294T ILE* 3.0 5.1 + - - +
295T ASP* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P T 3.3 49.5 + - + +
17P T 2.9 21.8 + - - +
291T GLN* 1.3 77.3 - - - +
293T SER* 1.3 59.8 + - - +
295T ASP* 3.9 12.8 - - + +
296T GLU* 3.6 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 293 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P T 2.7 21.8 + - - -
257T THR* 5.6 0.4 - - - -
259T ARG* 5.4 7.7 - - - -
260T SER* 3.5 28.6 + - - -
263T CYS* 5.6 2.9 - - - +
264T LEU* 6.2 0.3 - - - +
289T PHE* 4.5 11.6 - - - +
290T GLY 3.5 14.6 - - - -
291T GLN 3.0 0.6 - - - -
292T LYS* 1.3 74.0 - - - +
294T ILE* 1.3 64.7 + - - +
295T ASP 3.5 0.2 + - - -
296T GLU* 3.5 6.5 + - - +
297T VAL* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 294 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280T GLU* 3.6 35.0 - - + +
283T LEU* 3.7 22.2 - - + -
284T LEU* 4.0 22.2 - - + +
289T PHE* 6.2 1.8 - - + -
290T GLY 3.5 8.4 + - - +
291T GLN* 3.0 7.4 + - - +
293T SER* 1.3 77.9 - - - +
295T ASP* 1.3 65.6 + - - +
297T VAL* 3.7 13.5 - - + -
298T LYS* 3.2 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291T GLN 2.8 17.4 + - - +
292T LYS* 3.9 20.0 - - + +
293T SER 3.2 0.2 - - - -
294T ILE* 1.3 78.9 - - - +
296T GLU* 1.3 62.9 + - + +
298T LYS* 4.3 2.2 - - - +
299T ILE* 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 296 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256T LEU* 6.6 0.4 - - + -
257T THR* 4.5 26.5 - - + +
260T SER* 5.3 0.7 - - - +
292T LYS* 3.6 22.6 + - + +
293T SER* 3.5 7.9 + - - +
294T ILE 3.3 0.2 - - - -
295T ASP* 1.3 76.7 - - + +
297T VAL* 1.3 66.3 + - + +
299T ILE* 3.3 9.6 + - - +
300T LYS* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256T LEU* 5.8 4.9 - - + -
260T SER* 4.8 13.5 - - - +
264T LEU* 5.3 11.9 - - + -
293T SER* 3.2 19.5 - - - +
294T ILE* 3.3 19.2 + - + +
296T GLU* 1.3 79.9 - - + +
298T LYS* 1.3 63.7 + - - +
300T LYS* 3.4 11.3 + - - +
301T LEU* 3.4 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 298 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294T ILE* 3.2 16.7 + - + +
295T ASP* 4.5 2.5 - - - +
297T VAL* 1.3 81.9 - - - +
299T ILE* 1.3 62.5 + - - +
301T LEU* 3.5 6.4 + - - +
302T HIS* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295T ASP 3.4 17.1 + - - +
296T GLU* 3.3 13.9 + - - +
297T VAL 3.2 0.8 - - - -
298T LYS* 1.3 79.1 - - - +
300T LYS* 1.3 57.1 + - - +
302T HIS* 3.6 8.3 + - - +
303T GLN* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254T LEU* 5.5 11.7 - - + +
296T GLU 3.2 12.3 + - - +
297T VAL* 3.9 7.6 - - - +
298T LYS 3.3 0.4 - - - -
299T ILE* 1.3 74.4 - - - +
301T LEU* 1.3 65.1 + - - +
303T GLN* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297T VAL* 3.4 11.4 + - + +
298T LYS* 3.5 9.6 + - - +
300T LYS* 1.3 78.5 - - - +
302T HIS* 1.3 61.2 + - - +
303T GLN 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 302 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298T LYS 3.1 17.3 + - - +
299T ILE* 3.8 8.0 + - - +
300T LYS 3.1 0.2 - - - -
301T LEU* 1.3 78.5 - - - +
303T GLN* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 303 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299T ILE 3.1 16.8 + - - +
300T LYS* 3.0 18.1 + - - +
301T LEU 3.9 4.7 - - - +
302T HIS* 1.3 86.5 + - - +
----------------------------------------------------------
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