Contacts of the strand formed by residues 331 - 336 (chain A) in PDB entry 3CFV
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 331 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TRP* 3.6 8.7 - - - -
325A SER* 3.0 36.9 + - - -
328A ASN* 3.4 22.4 + - + +
330A THR* 1.3 82.7 - - - +
332A LEU* 1.3 62.8 + - - +
343A VAL* 3.6 24.5 - - + -
344A TRP 3.3 2.0 - - - +
345A ASP* 3.6 38.1 - - + +
366A LEU* 4.4 5.6 - - + -
381A TRP* 3.8 13.5 - - + -
387A TRP* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 3.8 19.7 - - + -
297A VAL* 4.0 18.6 - - + -
299A LEU* 5.1 0.2 - - + -
312A PHE* 4.4 15.5 - - + -
322A VAL* 3.8 14.4 - - + -
323A HIS 3.2 20.9 - - - +
324A TRP* 3.7 31.4 - - + +
330A THR 3.9 1.3 + - - +
331A ILE* 1.3 74.1 - - - +
333A ALA* 1.3 79.5 + - - +
343A VAL* 3.3 4.5 - - - +
344A TRP* 2.5 54.7 + - + +
346A LEU* 5.3 2.7 - - + -
381A TRP* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.5 3.3 - - - -
323A HIS 3.0 32.6 + - - -
332A LEU* 1.3 80.0 - - - +
334A SER* 1.3 61.8 + - - +
341A LEU* 3.9 12.1 - - + -
342A ASN 3.1 10.8 - - - +
343A VAL* 4.4 3.4 - - + -
344A TRP* 4.4 1.1 - - - -
379A PHE* 3.4 20.9 - - + -
381A TRP* 3.5 25.4 - - + +
389A ILE* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.8 21.7 - - - +
315A HIS* 2.7 29.5 + - - -
319A ILE* 4.1 3.6 - - - -
321A GLN 3.2 13.9 - - - -
322A VAL* 4.1 4.3 - - - -
332A LEU* 5.8 0.2 - - - -
333A ALA* 1.3 76.6 - - - +
335A SER* 1.3 61.2 + - - +
341A LEU* 3.3 5.0 - - - +
342A ASN 2.7 32.9 + - - -
344A TRP* 3.0 17.1 + - - -
379A PHE* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A HIS* 3.8 6.9 - - - -
319A ILE* 3.4 7.0 - - - +
320A PHE 2.9 20.4 + - - -
321A GLN* 3.2 17.4 + - - +
334A SER* 1.3 77.6 - - - +
336A GLY* 1.3 59.4 + - - +
338A ASP* 4.8 0.2 - - - -
340A ARG 3.4 15.9 - - - -
341A LEU* 4.0 11.7 - - - -
376A ILE* 3.6 25.3 + - - +
379A PHE* 3.3 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU 3.3 11.4 - - - -
320A PHE* 3.9 9.6 - - - -
335A SER* 1.3 77.7 - - - +
337A THR* 1.3 66.3 + - - -
338A ASP* 3.2 6.9 + - - -
339A ARG* 3.1 13.0 + - - -
340A ARG 3.7 5.1 + - - -
375A LYS* 4.1 6.5 - - - -
376A ILE* 3.4 25.2 + - - +
----------------------------------------------------------
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