Contacts of the strand formed by residues 332 - 339 (chain A) in PDB entry 6N8P
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 332 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 3.8 31.4 + - - +
313A HIS* 3.9 18.7 + - + +
314A CYS 4.9 0.4 - - - +
315A ILE* 3.7 26.7 - - + -
328A PHE* 3.6 35.9 - - + -
331A ARG* 1.3 73.9 - - - +
333A ILE* 1.3 61.9 + - - +
334A GLY 3.3 23.1 + - - +
335A PHE* 4.5 0.2 - - + -
355A VAL* 3.9 7.4 - - + -
356A LEU 4.3 2.2 - - - -
357A ALA* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.2 47.8 - - + +
36A SER* 4.3 15.9 - - - +
37A ALA* 4.3 1.6 - - - -
38A LEU* 4.3 14.6 + - - +
52A ARG* 5.1 5.6 - - - +
331A ARG* 4.4 12.1 - - + -
332A VAL* 1.3 74.8 - - - +
334A GLY* 1.3 56.2 + - - +
356A LEU* 3.2 22.7 + - + +
357A ALA 3.8 3.4 - - - +
358A GLU* 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.6 16.6 - - - -
285A ARG* 5.7 0.4 - - - -
301A GLN* 5.8 0.6 + - - -
332A VAL* 3.3 10.8 + - - +
333A ILE* 1.3 79.4 - - - +
335A PHE* 1.3 66.6 + - - +
356A LEU 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.6 8.0 - - - +
285A ARG* 2.5 66.7 + - + +
287A LEU* 3.9 22.2 - - + -
299A ILE* 4.1 19.7 - - + -
301A GLN* 3.4 43.5 - - + -
315A ILE* 3.6 26.7 - - + -
332A VAL* 4.5 0.9 - - + -
334A GLY* 1.3 78.3 - - - +
336A THR* 1.3 63.3 + - - +
337A VAL* 4.8 2.2 - - + -
353A LEU* 3.8 17.5 - - + -
354A VAL 3.2 13.7 - - - +
355A VAL* 3.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.6 8.1 - - + -
40A TYR* 4.5 25.9 - - + +
47A LEU* 5.2 1.1 - - + -
285A ARG* 4.7 7.3 + - - +
287A LEU* 5.8 1.1 - - - -
335A PHE* 1.3 77.8 - - - +
337A VAL* 1.3 75.0 + - - +
338A LEU* 4.0 15.3 - - + -
353A LEU* 3.3 7.2 - - - +
354A VAL* 2.8 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 5.5 1.6 - - - -
287A LEU* 3.8 22.2 - - + +
289A LEU* 3.6 26.7 - - + -
299A ILE* 3.6 24.5 - - + -
335A PHE* 4.8 2.5 - - + -
336A THR* 1.3 86.0 + - - +
338A LEU* 1.3 64.8 + - - +
339A THR* 3.5 9.6 + - + +
350A PRO* 3.6 18.4 - - + -
352A ALA 3.2 14.8 - - - +
353A LEU* 3.8 13.5 - - + -
366A LEU* 3.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.4 45.8 - - + +
336A THR* 4.0 9.6 - - + -
337A VAL* 1.3 73.8 - - - +
339A THR* 1.3 59.8 + - - +
350A PRO* 3.3 3.5 - - - +
351A TYR* 3.0 43.8 + - + +
352A ALA* 2.8 21.4 + - + +
354A VAL* 3.7 24.9 - - + -
421A PRO* 3.6 39.0 - - + -
422A ILE* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 5.9 0.2 - - - -
42A PRO* 5.9 5.2 - - - +
240A ARG* 5.6 0.7 + - - -
289A LEU* 4.4 12.3 - - + -
337A VAL 3.5 11.4 + - - +
338A LEU* 1.3 77.9 - - - +
340A GLU* 1.3 59.5 + - - +
341A ALA* 3.0 22.4 + - - +
348A ASP* 3.4 33.4 + - + +
349A ASP 3.7 4.5 - - - -
350A PRO* 4.0 16.6 - - + -
351A TYR* 3.6 8.9 + - - -
----------------------------------------------------------
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