Contacts of the helix formed by residues 315 - 323 (chain A) in PDB entry 1VCW
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 ALA 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLY 5.3 4.5 - - - +
263A GLY 5.1 2.7 - - - -
264A ARG* 4.5 23.1 - - - +
282A ILE* 3.2 26.4 - - + +
314A SER* 1.3 71.7 - - - +
316A LEU* 1.3 72.2 + - + +
318A THR* 3.3 2.9 + - - -
319A MET* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 3.8 33.4 - - - +
182A ASN* 5.5 2.7 - - - +
184A THR* 4.3 22.4 - - + -
188A ASN* 5.1 7.0 - - - +
314A SER* 3.5 3.9 - - - +
315A ALA* 1.3 80.3 - - + +
317A GLU* 1.3 56.7 + - - +
318A THR 2.7 15.4 + - - -
319A MET* 3.0 14.1 + - + +
320A ASP* 3.0 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 4.1 18.3 - - - +
311A PRO 5.8 0.3 - - - +
313A ILE* 4.8 17.0 + - - +
314A SER* 2.9 25.6 + - - +
316A LEU* 1.3 77.7 - - - +
318A THR* 1.3 58.1 - - - +
320A ASP* 3.9 11.2 - - + +
321A GLN* 3.5 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 5.7 3.1 - - + -
282A ILE* 4.0 16.8 - - + +
304A ILE* 6.5 0.7 - - + -
307A VAL* 3.1 41.7 - - + +
311A PRO 4.9 0.2 + - - -
312A ALA* 4.1 9.3 - - + +
313A ILE 4.9 0.2 + - - -
314A SER 2.6 23.8 + - - -
315A ALA 3.3 5.8 + - - +
316A LEU 2.7 5.9 + - - -
317A GLU* 1.3 73.2 - - - +
319A MET* 1.3 63.2 + - - +
320A ASP 3.1 1.1 - - - -
321A GLN* 2.8 35.9 + - - +
322A VAL* 3.2 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASN* 2.8 33.9 - - - +
258A TYR* 6.0 0.7 - - + -
259A ILE* 3.8 36.3 - - + +
261A ILE* 3.7 24.9 - - - +
262A GLY* 5.6 3.8 - - - +
282A ILE* 6.1 2.0 - - - -
315A ALA* 3.2 18.4 - - + +
316A LEU* 3.0 5.8 + - + +
318A THR* 1.3 83.3 - - - +
320A ASP* 1.3 57.5 + - - +
321A GLN 2.9 5.7 + - - -
322A VAL* 3.1 16.3 + - - +
323A ALA* 3.1 15.8 + - - +
351A TYR* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 2.8 34.2 + - - +
180A GLY* 2.9 22.4 - - - -
181A LEU* 4.9 4.7 + - - +
182A ASN* 3.1 31.2 - - - +
184A THR* 5.4 3.3 - - - +
316A LEU* 3.0 19.4 + - - +
317A GLU* 3.9 10.3 - - - +
318A THR 3.1 0.2 - - - -
319A MET* 1.3 74.8 - - - +
321A GLN* 1.3 59.6 + - - +
323A ALA* 4.4 4.0 - - - +
324A GLU* 4.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 3.2 36.6 + - + +
310A LYS* 4.9 14.4 - - - +
311A PRO 4.6 4.8 + - - +
317A GLU* 3.5 22.0 - - + +
318A THR* 2.8 7.8 + - - +
320A ASP* 1.3 78.7 - - + +
322A VAL* 1.3 66.9 + - - +
323A ALA 3.1 2.0 - - - -
324A GLU* 2.8 18.5 + - - +
325A ILE* 3.2 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLY* 3.1 32.3 - - - +
258A TYR 4.0 2.5 - - - +
259A ILE* 3.6 46.0 - - + +
307A VAL* 3.8 21.5 - - + -
318A THR* 3.6 14.1 - - + +
319A MET* 3.1 9.1 + - - +
321A GLN* 1.3 77.0 - - - +
323A ALA* 1.3 61.7 + - - +
325A ILE* 3.0 24.4 + - - +
331A ILE* 5.9 5.6 - - + -
348A ILE* 4.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.0 28.2 - - + +
182A ASN* 4.7 5.8 - - + +
255A ILE 3.7 6.8 - - - +
256A ARG* 3.5 20.5 - - + -
257A GLY 2.8 30.1 + - - +
319A MET 3.1 14.9 + - - +
320A ASP 4.5 5.2 - - - +
321A GLN 3.1 0.6 - - - -
322A VAL* 1.3 78.5 - - - +
324A GLU* 1.3 56.8 + - - +
325A ILE 3.1 4.0 + - - +
351A TYR* 6.4 0.4 - - + -
----------------------------------------------------------
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