Contacts of the strand formed by residues 357 - 360 (chain A) in PDB entry 3SRH
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 CYS 357 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 4.1 1.1 - - - -
45A GLY* 3.2 12.8 - - - +
47A ILE* 3.2 31.4 - - + -
70A VAL* 5.7 2.7 - - - -
323A VAL 3.2 1.6 + - - +
324A ILE* 3.5 15.0 - - + -
325A CYS 3.0 23.3 + - - -
355A ALA* 3.8 4.3 - - - +
356A ASP* 1.3 85.7 - - - +
358A ILE* 1.3 66.9 + - - +
463A HIS 3.3 26.5 - - - -
464A LEU* 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.5 23.3 - - + -
45A GLY 2.9 18.6 + - - +
46A ILE* 3.5 16.7 - - + -
47A ILE* 3.0 26.6 + - - +
325A CYS* 3.5 6.7 - - + -
329A MET* 3.1 19.5 - - + -
347A VAL* 4.8 7.6 - - + +
350A ALA* 4.1 24.0 - - + -
351A VAL* 4.6 6.1 - - + -
355A ALA* 4.6 3.4 - - + -
357A CYS* 1.3 79.1 - - - +
359A MET* 1.3 58.5 + - - +
377A GLN* 3.3 31.2 + - + +
381A ALA* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.4 27.6 - - + +
49A THR* 4.4 0.7 - - + -
72A ARG* 3.5 40.8 - - - +
240A PHE* 4.5 7.4 - - - -
290A MET* 4.0 14.6 - - + +
324A ILE* 4.4 7.4 - - + -
325A CYS 3.1 16.5 + - - +
326A ALA* 3.7 25.4 - - + -
327A THR* 4.6 5.8 + - + -
329A MET* 3.3 25.5 + - - +
358A ILE* 1.3 76.4 - - - +
360A LEU* 1.3 73.8 + - - +
361A SER* 3.2 23.8 - - - +
363A GLU* 4.6 0.9 - - - +
377A GLN* 3.7 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.6 0.9 - - + -
47A ILE 3.1 7.7 + - - +
48A CYS* 4.0 8.7 - - - -
49A THR* 2.8 35.9 + - - +
327A THR 6.0 0.2 - - - +
330A LEU* 3.7 26.0 - - + +
359A MET* 1.3 71.9 - - - +
361A SER* 1.3 56.0 + - - +
362A GLY 4.2 1.1 - - - -
363A GLU* 3.6 33.2 - - + +
364A THR* 3.7 29.1 + - + +
373A ALA* 4.0 13.0 - - + +
374A VAL* 4.0 14.4 - - + +
377A GLN* 3.2 37.0 - - + +
----------------------------------------------------------
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