Contacts of the strand formed by residues 361 - 370 (chain A) in PDB entry 3MTC
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 5.9 0.2 - - + -
339A VAL* 3.9 16.4 - - + -
353A VAL* 3.8 32.8 - - + -
357A HIS 4.0 8.5 - - - +
358A ALA* 3.1 16.9 + - - +
359A ALA 4.4 4.0 - - - +
360A TYR* 1.3 78.3 - - - +
362A SER* 1.3 64.0 + - - +
364A VAL* 3.7 26.2 - - + -
387A PHE* 3.7 27.6 - - + -
388A GLN 3.4 2.5 - - - +
389A PHE* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A TYR 5.0 1.0 + - - -
361A ILE* 1.3 77.0 - - - +
363A GLU* 1.3 71.2 + - - +
364A VAL* 3.3 5.9 + - - -
387A PHE* 3.7 2.9 - - - +
388A GLN* 2.8 52.9 + - - +
390A HIS 5.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 1.3 82.7 - - - +
364A VAL* 1.3 63.5 + - - +
365A GLU* 3.4 12.2 + - + +
386A ARG* 2.9 43.0 + - - +
387A PHE* 3.5 1.6 - - - -
388A GLN* 2.9 26.7 - - + +
427A PRO* 4.0 29.5 - - + +
434A LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 3.8 13.7 - - + +
340A LYS* 3.8 44.7 + - + +
361A ILE* 3.7 30.3 - - + -
362A SER* 4.2 3.4 - - - +
363A GLU* 1.3 74.1 - - - +
365A GLU* 1.3 72.2 + - - +
385A ILE* 4.3 7.0 - - + -
386A ARG 3.4 9.0 - - - +
387A PHE* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LYS* 5.3 1.1 - - - +
363A GLU* 4.0 14.6 - - + +
364A VAL* 1.3 86.4 - - - +
366A ALA* 1.3 61.8 + - - +
367A GLU* 5.5 3.3 - - + +
385A ILE* 3.4 3.6 - - - +
386A ARG* 2.8 51.1 + - + +
424A PHE* 4.1 12.5 - - + -
425A CYS* 3.8 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LYS* 3.8 24.5 - - + +
342A ILE* 3.8 31.7 - - + +
365A GLU* 1.3 77.4 + - - +
367A GLU* 1.3 75.5 + - - +
384A ALA 3.2 12.6 - - - +
385A ILE* 4.0 8.5 - - + -
424A PHE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 4.2 1.8 - - - +
365A GLU* 5.5 3.4 - - + +
366A ALA* 1.3 82.6 - - - +
368A THR* 1.3 73.1 + - - +
383A VAL* 3.5 0.5 - - - +
384A ALA 3.0 31.4 + - - +
422A MET* 3.6 20.9 - - - +
423A GLN 3.3 26.5 - - - +
424A PHE* 3.9 15.6 - - + -
425A CYS* 4.8 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.7 26.7 - - + -
343A ARG 4.2 4.7 - - - +
344A LEU* 3.9 32.1 - - + +
367A GLU* 1.3 87.4 + - - +
369A VAL* 1.3 70.5 + - - +
382A GLY 3.4 7.2 - - - -
383A VAL* 3.7 12.1 - - + -
422A MET* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.8 3.4 - - - +
368A THR* 1.3 81.1 - - - +
370A GLY* 1.3 57.7 + - - +
371A THR* 3.9 11.4 - - + -
381A GLY* 3.3 3.8 - - - -
382A GLY 2.9 35.7 + - - +
417A ASP 4.1 11.0 - - - +
418A ILE* 4.2 10.8 - - + +
421A ARG* 3.4 44.4 - - + +
422A MET* 3.7 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.7 16.0 - - - +
369A VAL* 1.3 72.5 - - - +
371A THR* 1.3 58.1 + - - -
375A GLY 3.3 4.9 - - - +
376A ARG 3.4 14.3 + - - +
377A MET 3.4 16.8 - - - -
378A GLY* 4.4 0.2 - - - -
380A LYS 3.7 4.5 - - - -
421A ARG* 2.9 29.8 + - - +
----------------------------------------------------------
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