Contacts of the strand formed by residues 361 - 370 (chain B) in PDB entry 3N9V
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 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.7 17.0 - - + -
353B VAL* 4.0 30.5 - - + -
357B HIS 3.7 13.5 - - - +
358B ALA* 3.2 14.1 + - - +
359B ALA 4.5 3.6 - - - +
360B TYR* 1.3 78.2 - - - +
362B SER* 1.3 63.7 + - - +
364B VAL* 3.5 27.4 - - + -
387B PHE* 3.6 34.8 - - + -
388B GLN 3.5 1.1 - - - -
389B PHE* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TYR 3.9 2.5 + - - -
361B ILE* 1.3 76.7 - - - +
363B GLU* 1.3 70.8 + - - +
364B VAL* 3.2 7.0 + - - +
387B PHE* 3.7 3.3 - - - +
388B GLN* 2.8 48.2 + - - +
390B HIS 5.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER* 1.3 83.4 - - - +
364B VAL* 1.3 65.4 + - - +
365B GLU* 3.5 9.6 + - + +
386B ARG* 2.9 42.3 + - - +
387B PHE* 3.5 2.6 - - - -
388B GLN* 3.0 27.0 - - - +
434B LEU* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.7 13.9 - - + +
340B LYS* 3.9 39.2 - - + -
361B ILE* 3.5 32.5 - - + -
362B SER* 4.0 4.0 - - - +
363B GLU* 1.3 75.1 - - - +
365B GLU* 1.3 78.0 + - - +
385B ILE* 4.0 13.0 - - + -
386B ARG 3.4 5.4 - - - +
387B PHE* 3.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LYS* 5.3 2.1 + - - -
340A LYS* 5.4 6.2 + - - -
340B LYS* 5.4 2.0 - - - +
363B GLU* 3.9 11.8 - - + +
364B VAL* 1.3 87.3 - - - +
366B ALA* 1.3 62.7 + - - +
385B ILE* 3.2 5.0 - - - -
386B ARG* 2.8 47.1 + - - +
424B PHE* 3.8 22.7 - - + -
425B CYS* 3.9 36.9 - - - +
434B LEU* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LYS* 4.1 28.4 - - + +
342B ILE* 3.8 35.4 - - + +
365B GLU* 1.3 76.8 + - - +
367B GLU* 1.3 70.5 + - - +
384B ALA 3.1 11.0 - - - +
385B ILE* 4.2 1.6 - - + -
424B PHE* 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 4.1 2.5 - - - +
366B ALA* 1.3 79.2 - - - +
368B THR* 1.3 84.7 + - - +
369B VAL* 5.8 0.2 - - + -
383B VAL* 3.5 1.0 - - - +
384B ALA 3.1 30.7 + - - +
422B MET* 3.6 21.5 - - - -
423B GLN 3.3 28.4 - - - +
424B PHE* 3.8 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.6 27.8 - - + -
343B ARG 4.1 5.4 - - - +
344B LEU* 3.9 33.2 - - + +
367B GLU* 1.3 95.5 + - - +
369B VAL* 1.3 69.0 + - - +
370B GLY 4.3 0.4 - - - -
382B GLY 3.7 4.3 - - - -
383B VAL* 3.6 13.9 - - + -
422B MET* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.8 4.6 - - - +
367B GLU* 5.8 0.4 - - + -
368B THR* 1.3 79.6 - - - +
370B GLY* 1.3 64.0 + - - +
371B THR* 3.8 19.3 - - + -
381B GLY* 3.3 2.3 - - - -
382B GLY 3.0 36.4 + - - +
417B ASP 4.1 6.5 - - - +
418B ILE* 4.1 7.0 - - + -
421B ARG* 3.7 30.5 - - + +
422B MET* 3.5 44.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.7 14.6 - - - +
368B THR 4.3 0.2 - - - -
369B VAL* 1.3 74.4 - - - +
371B THR* 1.3 60.5 + - - +
376B ARG* 3.2 26.0 + - - +
377B MET 3.8 3.6 - - - -
378B GLY* 4.2 0.4 - - - -
380B LYS 3.5 8.5 - - - -
421B ARG* 3.0 22.5 + - - -
----------------------------------------------------------
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