Contacts of the helix formed by residues 316 - 329 (chain A) in PDB entry 5V6Y
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 ASP 316 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU 4.4 0.6 + - - -
313A LEU* 3.0 23.6 + - + +
314A ALA 3.8 3.6 - - - +
315A LYS* 1.3 78.0 - - - +
317A PRO* 1.3 71.5 - - - +
318A ARG* 2.9 63.7 + - - +
319A ILE* 3.1 23.1 + - + +
320A ALA* 3.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL 4.6 4.2 - - - +
315A LYS 3.4 9.2 - - - +
316A ASP* 1.3 91.6 - - - +
318A ARG* 1.3 58.4 + - + +
320A ALA* 3.2 10.0 + - + +
321A ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 3.3 52.6 - - + +
238A ASP* 3.7 13.3 + - - -
244A TYR* 3.0 30.3 + - - -
246A VAL* 3.6 24.4 - - + +
296A ASN* 6.1 1.0 - - - +
300A PRO* 5.0 8.5 - - - +
316A ASP* 2.9 28.6 + - - +
317A PRO* 1.3 78.1 - - + +
319A ILE* 1.3 58.2 + - - +
321A ALA* 3.5 2.8 + - - +
322A THR* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 3.7 19.1 - - + -
296A ASN* 6.1 0.2 - - - +
300A PRO* 6.1 0.4 - - + -
302A GLY* 3.4 36.6 - - - +
303A ALA* 4.4 15.0 - - + +
310A GLU* 3.9 19.3 - - - +
313A LEU* 3.3 36.3 - - + +
314A ALA* 4.5 4.0 - - - -
316A ASP* 3.1 16.0 + - + +
318A ARG* 1.3 73.4 - - - +
320A ALA* 1.3 62.4 + - - +
322A THR* 3.1 6.0 + - - +
323A MET* 2.8 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 4.9 7.1 + - - +
316A ASP 3.1 12.0 + - - +
317A PRO* 3.2 13.2 + - + +
319A ILE* 1.3 77.2 - - - +
321A ALA* 1.3 58.3 + - - +
323A MET* 3.2 7.8 + - - +
324A GLU* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.8 1.6 - - - -
246A VAL* 3.4 45.8 - - + +
247A THR* 3.9 12.3 - - - +
248A VAL 4.7 0.2 - - - +
317A PRO 3.0 12.2 + - - +
320A ALA* 1.3 76.1 - - - +
322A THR* 1.3 63.1 + - - +
324A GLU* 3.3 12.4 + - - +
325A ASN* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL 4.7 5.8 - - - +
114A ALA* 3.7 34.5 + - + +
116A SER* 3.6 12.3 + - - -
231A PRO* 4.2 11.4 - - + +
234A TRP* 3.2 21.4 - - - -
302A GLY* 5.4 0.2 - - - -
303A ALA 5.4 4.0 - - - +
318A ARG 2.9 15.4 + - - -
319A ILE* 3.1 13.7 + - + -
321A ALA* 1.3 76.4 - - - +
323A MET* 1.3 67.0 + - + +
325A ASN* 3.4 1.2 + - - -
326A ALA* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 4.1 17.3 - - + +
303A ALA* 3.6 27.6 - - + -
310A GLU* 5.3 3.8 - - - +
319A ILE* 2.8 32.4 + - + +
320A ALA* 3.7 7.4 - - - +
322A THR* 1.3 77.7 - - + +
324A GLU* 1.3 60.1 + - - +
326A ALA* 3.7 18.9 - - + +
327A GLN* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A THR* 5.5 0.5 + - - -
248A VAL* 3.5 33.1 + - + +
320A ALA 2.8 16.8 + - - +
321A ALA* 3.6 13.3 - - - +
322A THR 3.2 0.4 - - - -
323A MET* 1.3 78.0 - - - +
325A ASN* 1.3 61.2 + - - +
327A GLN* 3.6 4.0 + - - +
328A LYS* 3.3 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 4.8 0.7 - - + -
115A LEU 3.3 19.1 - - - +
116A SER* 3.0 36.0 + - - +
247A THR 3.4 12.1 + - - -
248A VAL* 3.3 12.0 - - - +
249A LEU* 2.9 30.9 + - - +
257A SER 5.2 2.3 - - - +
259A PRO* 3.3 18.8 - - + +
321A ALA 3.0 16.9 + - - +
322A THR 3.9 3.1 - - - +
324A GLU* 1.3 72.2 - - - +
326A ALA* 1.3 64.2 + - - +
328A LYS* 3.3 5.7 + - - +
329A GLY 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 5.0 0.7 - - + -
114A ALA* 3.7 15.0 - - + +
261A VAL* 3.3 36.6 - - + +
322A THR 2.8 18.7 + - - +
323A MET* 3.7 24.2 - - + +
324A GLU 3.3 0.2 - - - -
325A ASN* 1.3 77.3 - - - +
327A GLN* 1.3 62.4 + - + +
329A GLY 3.3 9.9 + - - +
330A GLU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A MET* 3.0 25.1 + - + +
324A GLU* 4.1 4.5 - - - +
325A ASN 3.3 0.2 - - - -
326A ALA* 1.3 78.4 - - + +
328A LYS* 1.3 62.4 + - + +
329A GLY 3.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.3 35.3 - - + +
251A THR* 5.8 3.8 - - - +
256A PRO* 3.9 32.5 - - + +
257A SER 4.0 12.8 - - - +
258A LYS* 3.4 22.7 - - - +
324A GLU* 3.3 36.2 + - - +
325A ASN* 3.3 6.7 + - - +
326A ALA 3.3 0.4 - - - -
327A GLN* 1.3 77.4 - - + +
329A GLY* 1.3 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 3.8 7.6 - - - -
259A PRO* 3.3 25.4 - - - -
325A ASN 3.0 9.1 + - - -
326A ALA 3.3 9.1 + - - +
327A GLN 3.2 10.2 - - - +
328A LYS* 1.3 81.3 - - - +
330A GLU* 1.3 70.1 + - - +
----------------------------------------------------------
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