Contacts of the helix formed by residues 284 - 294 (chain A) in PDB entry 1VCN
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 LEU 284 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 5.3 0.2 - - - +
37A LEU* 4.1 19.3 - - + -
40A ALA* 3.4 26.9 - - + -
260A LEU* 3.8 28.3 - - + +
263A GLU* 3.7 34.1 - - + -
282A PRO* 3.5 20.8 + - + +
283A ASN* 1.3 72.8 - - - +
285A SER* 1.3 63.1 + - - +
286A PHE 3.3 3.0 + - - -
287A TRP* 3.4 17.3 + - + -
288A GLN* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN* 2.8 22.7 + - - -
284A LEU* 1.3 75.8 - - - +
286A PHE* 1.3 71.7 + - - +
288A GLN* 3.2 6.7 + - - +
289A GLU* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN 5.3 0.4 + - - -
284A LEU* 3.3 1.0 - - - +
285A SER* 1.3 84.0 + - - +
287A TRP* 1.3 84.8 + + + +
289A GLU* 3.0 5.7 + - + +
290A ALA* 2.6 49.2 + - + +
328A ILE* 6.3 2.0 - - + -
529A PRO* 3.3 51.6 - - + -
530A MET* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.1 17.8 + - + +
37A LEU* 6.0 0.2 - - + -
40A ALA* 5.9 1.9 - - + +
87A ARG 4.9 0.4 - - - -
88A PHE* 3.7 53.4 - + - -
256A TYR* 3.8 48.0 - + + -
259A PRO* 4.3 11.2 - - + -
260A LEU* 3.2 25.6 - - + -
283A ASN 5.5 0.9 - - - -
284A LEU* 3.4 25.7 + - + +
285A SER 3.4 0.4 - - - -
286A PHE* 1.3 104.2 - + + +
288A GLN* 1.3 61.1 + - - +
290A ALA* 3.5 2.4 - - + +
291A VAL* 3.0 30.7 + - - +
529A PRO* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.3 13.2 - - + +
284A LEU 3.0 19.1 + - - +
285A SER* 3.5 7.2 - - - +
287A TRP* 1.3 78.8 - - - +
289A GLU* 1.3 58.6 + - - +
291A VAL* 3.3 4.2 + - - +
292A ARG* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER 2.8 21.2 + - - +
286A PHE* 3.6 5.8 - - + +
288A GLN* 1.3 73.1 - - - +
290A ALA* 1.3 59.9 + - - +
292A ARG* 2.9 24.9 - - - +
293A VAL* 3.1 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 4.2 20.6 - - + -
286A PHE* 2.6 38.5 + - + +
287A TRP* 3.5 11.4 - - + +
288A GLN 3.2 0.2 - - - -
289A GLU* 1.3 72.3 - - - +
291A VAL* 1.3 62.1 + - - +
293A VAL* 3.2 9.8 + - - +
294A LEU* 3.0 26.2 + - - +
328A ILE* 4.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 4.7 9.6 - - + -
256A TYR* 3.7 27.6 - - + +
257A GLU* 3.5 43.5 - - + +
260A LEU* 4.8 4.0 - - + -
287A TRP 3.0 21.0 + - - +
288A GLN* 3.9 4.9 - - - +
290A ALA* 1.3 73.2 - - - +
292A ARG* 1.3 67.2 + - - +
294A LEU* 3.1 23.8 + - + +
296A HIS 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLN 2.9 15.0 + - - +
289A GLU* 2.9 21.1 - - - +
291A VAL* 1.3 79.5 - - - +
293A VAL* 1.3 60.6 + - + +
296A HIS* 3.6 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLU* 3.1 16.7 + - + +
290A ALA* 3.6 6.1 - - - +
292A ARG* 1.3 76.8 - - + +
294A LEU* 1.3 63.9 + - + +
296A HIS 3.1 18.5 - - - +
297A PRO* 3.4 9.9 - - + +
327A GLY 5.6 0.2 - - - -
328A ILE* 4.0 25.1 - - + +
331A ARG* 3.5 58.1 - - + +
332A ALA 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 3.8 53.9 + - + +
255A LEU* 5.8 0.7 - - + -
256A TYR* 3.5 33.0 - - + -
290A ALA 3.0 16.4 + - - +
291A VAL* 3.1 18.7 + - - +
293A VAL* 1.3 83.3 - - + +
296A HIS* 3.0 29.6 + - - -
297A PRO* 4.2 2.3 - - - +
324A ARG* 4.6 19.3 - - + +
328A ILE* 3.8 26.0 - - + -
333A ARG* 4.0 14.4 + - - -
----------------------------------------------------------
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