Contacts of the strand formed by residues 328 - 333 (chain A) in PDB entry 3F6K
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 VAL 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.4 32.5 - - + -
281A PHE* 3.6 18.6 - - + -
320A ILE* 4.9 3.4 - - + -
322A ALA 3.4 8.7 - - - +
323A ALA* 3.7 15.0 - - + -
327A MET* 1.3 85.4 - - - +
329A PHE* 1.3 65.3 + - - +
330A MET* 4.6 4.7 - - + -
344A PHE 3.8 0.2 - - - +
345A THR* 3.4 3.8 - - - -
346A SER* 3.0 37.8 + - - +
350A GLY* 5.4 0.2 - - - -
353A TYR* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.8 4.0 - - - -
321A LEU* 3.1 40.1 + - + -
322A ALA* 2.8 25.9 + - + +
327A MET* 3.4 26.9 - - + -
328A VAL* 1.3 74.5 - - - +
330A MET* 1.3 59.4 + - - +
343A ILE* 3.8 14.1 - - + -
344A PHE 3.4 4.9 - - - -
345A THR* 3.7 18.4 - - + -
356A SER* 5.0 0.2 - - - -
371A PHE* 3.8 19.7 - + - -
381A TYR* 3.7 43.7 - + - -
400A GLN* 3.8 22.7 - - + -
401A GLY* 4.4 6.1 - - - -
404A TRP* 4.5 8.7 - + - -
1B NAG 4.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.8 27.1 - - + -
294A ILE* 4.6 4.3 - - + -
309A LEU* 3.9 22.4 - - + -
318A TYR* 4.1 17.3 - - + -
319A SER 3.5 12.1 - - - +
320A ILE* 2.9 38.1 - - + -
321A LEU* 4.3 3.1 - - - -
328A VAL* 4.0 3.9 - - + -
329A PHE* 1.3 73.1 - - - +
331A HIS* 1.3 67.0 + - - +
332A VAL* 4.0 6.9 + - + -
342A THR 3.6 0.9 - - - +
343A ILE* 3.4 2.8 - - - -
344A PHE* 2.8 43.0 + - + +
353A TYR* 4.2 21.3 - - + +
13N LEU* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 3.6 19.8 - + - -
318A TYR* 3.2 8.3 - - - +
319A SER* 2.8 40.4 + - - +
321A LEU* 4.0 21.2 - - + +
330A MET* 1.3 74.4 - - - +
332A VAL* 1.3 62.0 + - - +
333A ASP* 3.7 11.4 + - - -
340A PHE 4.3 1.0 - - - -
341A GLY* 3.4 37.5 + - - -
342A THR 3.5 6.5 + - - -
343A ILE* 5.0 0.2 - - + -
360A HIS* 2.9 27.3 + - - +
362A TYR* 3.4 40.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.3 11.0 - - + -
310A PRO* 4.0 18.8 - - + -
312A VAL* 3.6 28.9 - - + -
316A GLN* 4.9 1.1 - - - +
317A PHE 3.7 2.7 - - - -
318A TYR* 3.9 18.8 - - + -
330A MET* 4.5 2.9 - - + -
331A HIS* 1.3 78.5 - - - +
333A ASP* 1.3 71.7 + - - +
334A GLU* 4.5 0.7 - - - +
341A GLY* 3.2 0.7 - - - -
342A THR* 3.0 30.2 + - - +
344A PHE* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU 3.7 6.2 - - - +
316A GLN* 2.8 46.3 + - + +
317A PHE* 3.0 57.1 + - + +
331A HIS* 3.7 9.8 - - - -
332A VAL* 1.3 80.0 - - - +
334A GLU* 1.3 64.2 + - - +
335A PRO* 4.3 0.3 - - - +
337A ASP* 4.8 10.4 + - - +
338A THR* 5.1 0.2 + - - -
339A GLY* 4.8 4.7 + - - -
340A PHE 3.2 23.2 + - - +
362A TYR 4.7 2.9 - - - +
364A THR* 5.7 3.4 - - - -
----------------------------------------------------------
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