Contacts of the strand formed by residues 325 - 331 (chain A) in PDB entry 3VF1
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 325 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 4.0 9.2 - - - +
239A GLY* 3.2 40.9 - - - +
240A SER* 4.4 1.3 - - - +
242A PHE* 5.1 0.4 - - + -
243A LEU* 4.0 26.4 - - + +
251A ILE* 3.7 28.9 - - + -
288A PHE* 5.1 7.9 - - + -
317A PHE* 4.0 16.2 - - + -
318A TYR 3.1 11.0 - - - +
319A LEU* 3.8 27.6 - - + -
323A ASP 3.9 2.4 + - - +
324A ASP* 1.3 73.2 - - - +
326A ILE* 1.3 64.7 + - - +
468A LEU* 5.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 4.1 14.4 - - + +
236A VAL* 4.0 20.6 - - + -
271A LEU* 4.4 19.7 - - + +
317A PHE* 3.1 7.5 - - - -
318A TYR* 2.8 43.0 + - + +
320A LYS* 3.6 35.7 - - + +
325A ILE* 1.3 79.4 - - - +
327A PRO* 1.3 70.6 - - + +
328A ILE* 3.6 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 3.3 36.0 - - + +
238A PHE* 3.6 32.5 - - + -
239A GLY 4.3 3.1 - - - +
271A LEU* 5.1 0.2 - - - +
316A LEU 3.5 9.0 - - - +
317A PHE* 3.7 13.6 - - + -
326A ILE* 1.3 90.0 - - + +
328A ILE* 1.3 61.5 + - - +
329A ALA 5.1 0.2 - - - +
330A ILE* 5.2 4.9 - - + -
345A PRO* 4.4 5.0 - - - +
353A TRP* 3.7 31.1 - - + -
357A LYS* 4.4 0.2 - - + -
360A LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.3 21.6 - - + +
271A LEU* 3.7 36.1 - - + +
272A LEU* 4.1 20.0 - - + -
278A LEU* 4.8 0.7 - - + -
287A ILE* 4.2 15.3 - - + -
316A LEU* 2.8 43.6 + - + +
317A PHE 4.3 1.6 - - - +
318A TYR* 3.8 16.6 - - + -
326A ILE* 3.8 18.2 - - + +
327A PRO* 1.3 79.1 - - - +
329A ALA* 1.3 62.1 + - - +
344A THR* 3.1 16.1 + - - -
345A PRO* 3.7 8.3 - - - +
353A TRP* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 4.4 2.0 - - + -
263A VAL* 4.1 27.1 - - + -
268A VAL* 4.2 8.7 - - + -
314A LEU 4.0 0.2 - - - +
316A LEU* 2.9 36.3 + - + +
327A PRO 3.8 0.4 - - - -
328A ILE* 1.3 85.9 + - + +
330A ILE* 1.3 69.6 + - - +
342A ILE* 4.1 4.5 - - + -
343A TRP 3.3 8.5 - - - +
344A THR* 3.9 8.3 - - - +
353A TRP* 4.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 5.1 2.0 - - + -
261A PHE* 4.4 3.6 - - - -
313A PRO* 4.9 0.9 - - + -
314A LEU 3.3 11.4 - - - +
315A GLY* 4.4 0.2 - - - -
327A PRO* 5.2 2.9 - - + -
329A ALA* 1.3 82.2 - - - +
331A GLN* 1.3 71.0 + - - +
332A LEU* 4.1 18.6 - - + -
342A ILE* 3.5 2.1 - - - -
343A TRP* 2.8 42.9 + - + +
353A TRP* 3.8 26.9 - - + -
356A ALA* 3.8 32.1 - - + +
357A LYS* 3.9 12.8 - - + -
360A LEU* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASN 2.9 22.7 + - - -
261A PHE* 3.6 22.0 - - + -
262A PRO* 3.6 23.6 - - - +
313A PRO* 3.0 3.3 - - - +
314A LEU* 2.8 45.6 + - + +
330A ILE* 1.3 76.7 - - - +
332A LEU* 1.3 60.8 + - - +
333A TYR 2.8 23.9 + - - +
334A GLN 3.0 9.3 + - - -
336A PRO* 4.1 6.8 - - - +
340A ASN* 3.7 21.1 - - - +
341A SER 4.0 11.0 - - - +
342A ILE* 3.8 10.5 - - + +
----------------------------------------------------------
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