Contacts of the strand formed by residues 375 - 382 (chain B) in PDB entry 1SNX
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 GLY 375 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLY 3.8 5.4 - - - +
371B SER 4.6 3.8 - - - -
372B GLY* 3.8 9.1 + - - +
374B PHE* 1.3 77.3 - - - +
376B LEU* 1.3 62.4 + - - +
377B VAL* 3.4 4.7 + - - +
391B LYS* 3.8 21.6 - - - +
392B THR 2.3 28.5 - - - -
393B ILE 3.7 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 3.4 26.0 - - - +
370B GLY 3.6 1.8 - - - -
371B SER* 3.7 28.9 - - - -
372B GLY 4.0 12.8 - - - +
375B GLY* 1.3 71.0 - - - +
377B VAL* 1.3 64.6 - - - +
378B HIS* 3.1 22.7 + - + +
390B ILE 3.3 4.9 - - - +
392B THR* 2.9 32.2 + - - +
393B ILE 4.6 4.6 + - - +
394B ARG* 4.9 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 3.3 7.6 - - - +
369B ILE* 2.9 66.5 + - + +
370B GLY* 3.0 17.4 + - - +
375B GLY 3.4 6.2 + - - +
376B LEU* 1.3 69.1 - - - +
378B HIS* 1.3 61.2 + - - +
379B LEU 4.1 0.2 - - - -
389B ALA* 4.3 17.9 - - + -
390B ILE 3.2 8.3 - - - +
391B LYS* 4.5 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.3 40.1 - + + +
367B GLN 2.6 24.5 + - - -
368B GLU* 3.5 21.1 + - + +
376B LEU* 3.2 35.9 - - + +
377B VAL* 1.3 65.0 - - - +
379B LEU* 1.3 67.0 + - - +
380B GLY 3.0 2.1 + - - -
389B ALA* 4.5 0.9 - - - -
390B ILE* 2.3 53.0 + - + +
392B THR* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.7 0.6 - - - -
366B VAL* 2.6 60.6 + - + +
367B GLN* 3.4 21.7 + - + +
369B ILE* 3.9 22.8 - - + +
377B VAL 4.1 1.8 + - - -
378B HIS* 1.3 70.5 - - - +
380B GLY* 1.3 55.6 + - - +
381B TYR* 4.8 5.2 - - + -
387B LYS* 3.8 24.0 - - + -
388B VAL 3.3 22.7 - - - +
389B ALA* 4.5 0.2 - - - +
437B PHE* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR 3.3 15.0 - - - -
365B PHE* 4.2 2.5 - - - -
366B VAL* 4.0 2.2 - - - -
378B HIS 3.0 7.8 + - - -
379B LEU* 1.3 77.3 - - - +
381B TYR* 1.3 68.1 + - - -
388B VAL* 2.8 42.6 + - - +
390B ILE* 4.2 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU 3.6 0.9 - - - +
363B LEU* 3.0 4.2 - - - -
364B THR* 2.5 49.4 + - - +
366B VAL* 4.1 19.5 - - + -
379B LEU* 4.8 5.2 - - + -
380B GLY* 1.3 81.1 - - - -
382B TRP* 1.3 60.1 + - - +
383B LEU 3.9 0.3 + - - -
384B ASN* 3.0 41.7 + - - +
385B LYS 5.6 0.4 - - - -
386B ASP 3.2 15.0 - - - +
387B LYS* 4.2 33.8 - - + +
388B VAL* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL* 6.1 5.2 - - + -
359B ASP* 2.8 37.8 + - - -
362B GLU* 3.0 19.8 + - + -
363B LEU* 3.5 28.9 - - + +
380B GLY 4.2 0.6 + - - -
381B TYR* 1.3 69.8 - - - +
383B LEU* 1.3 98.1 + - + +
384B ASN 2.5 14.9 + - - -
385B LYS 3.2 7.6 + - - -
386B ASP* 3.2 32.8 + - + +
388B VAL* 4.7 14.0 - - + +
422B TYR* 3.9 33.0 - + + -
434B VAL* 5.4 2.7 - - + -
----------------------------------------------------------
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