Contacts of the strand formed by residues 311 - 318 (chain D) in PDB entry 3VI4
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 ILE 311 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 5.4 1.1 - - + -
239D ALA* 4.5 13.9 - - + -
247D TRP* 3.7 39.5 - - + +
252D ARG* 3.9 17.7 - - + +
253D LEU 4.9 0.4 - - - -
254D LEU* 3.6 34.3 - - + +
306D LEU* 3.0 50.4 + - + +
309D ASN* 4.0 19.7 - - + -
310D ASN* 1.3 70.6 - - - +
312D GLN* 1.3 64.3 + - - +
313D THR* 3.9 3.2 + - - +
332D ILE* 6.1 0.2 - - - +
334D LYS* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D THR* 4.4 11.6 - - - +
252D ARG 3.1 14.1 + - - +
253D LEU* 3.4 24.7 - - + +
254D LEU 2.9 23.7 + - - -
310D ASN 3.5 1.3 + - - +
311D ILE* 1.3 74.1 - - - +
313D THR* 1.3 61.9 + - - +
314D ILE* 3.9 1.0 + - - +
334D LYS* 3.4 47.8 - - + +
355D TYR* 5.9 3.6 - - - -
358D LEU* 3.9 26.3 + - + +
359D SER* 5.7 1.4 - - - +
429D GLY* 3.6 32.7 - - - +
430D PHE* 5.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 5.4 4.3 - - + -
254D LEU* 3.5 21.8 - - + +
256D PHE* 4.6 4.0 - - + -
306D LEU* 3.7 33.2 - - + +
311D ILE* 4.1 3.8 + - - +
312D GLN* 1.3 72.7 - - - +
314D ILE* 1.3 67.3 - - - +
315D PHE* 3.7 34.3 - - + -
332D ILE* 4.4 3.0 - - - +
334D LYS 3.2 7.5 + - - -
335D SER* 3.1 14.5 - - - -
336D ALA 2.9 26.0 + - - +
358D LEU* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 4.3 24.9 - - + -
254D LEU 2.6 14.3 + - - +
255D VAL* 3.4 25.9 - - + -
256D PHE* 2.7 33.8 + - - +
312D GLN 4.8 1.3 - - - +
313D THR* 1.3 76.9 - - - +
315D PHE* 1.3 60.3 + - - +
316D ALA 3.5 0.9 + - - -
336D ALA* 3.6 6.1 - - + +
338D GLY 5.6 0.4 - - - +
350D LEU* 4.0 19.7 - - + -
351D ILE* 4.3 16.4 - - + +
354D ALA* 3.7 33.7 - - + -
355D TYR* 4.5 2.2 - - - +
358D LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 4.7 7.9 - - + -
256D PHE* 3.5 32.3 - + + -
313D THR* 3.7 26.2 - - + -
314D ILE* 1.3 71.6 - - - +
316D ALA* 1.3 61.0 + - - +
317D VAL* 3.5 12.5 + - + -
325D TYR* 3.9 21.5 - + + -
328D LEU* 3.7 30.7 - - + -
329D LYS* 4.3 7.2 - - + -
332D ILE* 3.7 22.7 - - + -
335D SER* 4.2 14.8 - - - -
336D ALA 2.8 28.3 + - - +
337D VAL* 3.6 12.3 - - + +
338D GLY 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL* 4.3 12.6 - - + -
256D PHE 2.8 8.1 + - - +
257D SER* 2.9 42.9 - - - -
258D THR 3.2 3.8 + - - -
314D ILE 3.5 1.8 + - - -
315D PHE* 1.3 71.3 - - - +
317D VAL* 1.3 57.6 + - - +
338D GLY 3.8 5.2 - - - -
340D LEU* 3.4 16.0 - - + +
347D VAL* 5.1 5.4 - - + -
350D LEU* 3.7 25.8 - - + -
351D ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D PHE 4.5 1.3 - - - +
258D THR* 3.3 18.8 - - + +
259D ASP* 5.6 0.2 - - - -
315D PHE* 3.5 13.7 + - + -
316D ALA* 1.3 80.2 - - - +
318D THR* 1.3 69.5 + - - +
321D PHE* 3.9 7.0 - - + +
322D GLN* 3.4 24.8 + - - +
325D TYR* 3.7 55.6 - - + -
337D VAL* 4.7 1.3 - - + -
338D GLY 3.4 5.4 + - - +
339D THR* 3.5 0.2 - - - -
340D LEU* 2.8 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D MET* 5.8 0.7 - - - -
138D ASP* 5.7 2.2 - - - +
258D THR 3.6 2.9 + - - +
259D ASP* 3.4 37.9 + - + +
317D VAL* 1.3 77.9 - - - +
319D GLU* 1.3 65.7 + - - +
320D GLU* 3.8 17.7 - - - +
321D PHE* 2.9 17.7 + - - -
322D GLN* 3.5 7.2 + - - +
340D LEU* 3.6 20.9 - - + +
341D SER 4.4 11.0 - - - +
342D ALA* 5.4 5.6 - - - +
----------------------------------------------------------
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