Contacts of the helix formed by residues 367 - 382 (chain A) in PDB entry 2E3S
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 PHE 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 3.0 12.1 + - + -
366A ARG* 1.3 117.8 - - + +
368A VAL* 1.3 58.2 + - - +
369A GLN 3.3 2.9 - - - -
370A LYS* 3.1 21.4 + - + +
371A VAL* 2.8 29.3 + - - +
458A LEU* 3.9 12.3 - - + -
464A ILE* 3.8 11.9 - - + -
483A LEU* 3.4 30.5 - - + -
507A VAL* 3.8 30.7 - - + -
508A ASP 4.3 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 3.3 39.9 - - + +
366A ARG 3.4 2.1 - - - +
367A PHE* 1.3 77.6 - - - +
369A GLN* 1.3 69.2 + - + +
371A VAL* 3.4 6.1 + - + +
372A GLU* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ARG 5.0 2.4 + - - +
367A PHE 3.3 0.2 - - - -
368A VAL* 1.3 82.9 - - + +
370A LYS* 1.3 61.6 + - - +
372A GLU* 3.4 7.5 + - - +
373A GLU* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ARG 5.7 0.2 + - - -
367A PHE* 3.1 25.0 + - + +
369A GLN* 1.3 76.0 - - - +
371A VAL* 1.3 63.7 + - - +
373A GLU* 3.4 27.7 + - - +
374A MET* 3.0 51.0 + - + +
505A PHE* 3.4 29.4 - - + -
506A SER 5.5 2.9 - - - -
507A VAL* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 4.2 9.2 - - + +
367A PHE 2.8 25.3 + - - +
368A VAL* 3.7 7.4 - - + +
370A LYS* 1.3 71.9 - - - +
372A GLU* 1.3 59.0 + - - +
373A GLU 3.3 0.2 + - - -
374A MET* 3.3 1.6 + - - +
375A VAL* 2.9 38.2 + - + +
462A ALA* 5.6 0.2 - - + -
483A LEU* 3.8 33.2 - - + -
485A VAL* 3.8 30.5 - - + -
487A ARG* 4.6 9.4 - - - -
505A PHE* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 2.9 22.1 + - + +
369A GLN* 3.7 7.6 - - - +
370A LYS 3.3 0.2 - - - -
371A VAL* 1.3 78.5 - - - +
373A GLU* 1.3 56.5 + - - +
375A VAL* 3.9 8.6 - - - +
376A GLN* 2.9 39.9 + - + +
487A ARG* 4.5 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLN 3.1 17.4 + - - +
370A LYS* 3.5 34.7 + - - +
372A GLU* 1.3 73.8 - - - +
374A MET* 1.3 65.5 + - - +
376A GLN* 3.4 5.6 + - - +
377A ASN* 2.8 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LYS* 3.0 50.0 + - + +
371A VAL 3.9 2.5 - - - +
373A GLU* 1.3 80.1 - - - +
375A VAL* 1.3 64.5 + - - +
377A ASN* 3.4 9.4 + - - +
378A HIS* 3.0 31.3 + - - +
503A CYS* 4.0 14.6 - - - -
505A PHE* 3.8 32.5 - - + -
524A ASN* 3.4 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 2.9 35.0 + - + +
372A GLU* 3.9 10.1 - - - +
374A MET* 1.3 76.1 - - - +
376A GLN* 1.3 59.7 + - - +
378A HIS* 3.3 7.0 + - - +
379A MET* 3.0 31.4 + - + +
485A VAL* 4.8 2.9 - - + -
487A ARG* 4.7 12.6 - - + +
489A ILE* 3.8 31.2 - - + -
501A ILE* 4.2 21.0 - - + +
503A CYS* 4.5 17.5 - - + -
505A PHE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 2.9 30.0 + - + +
373A GLU* 3.7 6.3 - - - +
375A VAL* 1.3 75.9 - - - +
377A ASN* 1.3 59.9 + - - +
379A MET* 3.4 11.8 + - - +
380A THR* 3.0 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 2.8 24.4 + - + +
374A MET* 3.5 12.5 - - - +
376A GLN* 1.3 73.2 - - - +
378A HIS* 1.3 65.3 + - + +
380A THR* 3.9 5.6 - - - -
381A TYR* 2.9 54.6 + - - +
382A SER* 4.9 1.2 + - - -
524A ASN* 5.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.0 25.6 + - - -
375A VAL 3.3 6.9 + - - +
377A ASN* 1.3 81.0 + - - +
379A MET* 1.3 60.8 + - - +
382A SER* 2.8 53.9 + - - +
383A LEU* 3.7 4.7 + - - +
501A ILE* 3.8 17.7 - - + -
503A CYS* 3.6 19.2 - - - -
524A ASN* 2.9 39.9 + - - -
525A VAL 4.3 0.4 + - - -
526A ALA* 3.6 27.0 - - + +
528A ILE* 4.2 4.7 - - + +
554A VAL* 3.5 16.0 - - + +
556A ASN* 5.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.0 25.3 + - + +
376A GLN* 3.4 15.9 + - - +
378A HIS* 1.3 77.7 - - - +
380A THR* 1.3 61.2 + - - +
383A LEU* 3.9 37.8 - - + +
489A ILE* 4.2 31.9 - - + -
499A THR* 3.8 41.1 - - + +
501A ILE* 4.7 9.0 - - + -
528A ILE* 4.3 7.9 - - - -
530A GLN* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLN* 3.0 42.4 + - + +
377A ASN* 3.9 1.6 - - - -
379A MET* 1.3 79.2 - - - +
381A TYR* 1.3 85.6 + - - +
383A LEU 5.1 0.7 - - - -
384A GLN* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 2.9 46.3 + - - +
380A THR* 1.3 101.1 - - - +
382A SER* 1.3 64.4 + - - +
383A LEU 3.3 3.6 + - - -
384A GLN* 3.5 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 4.5 2.3 + - - -
378A HIS* 2.8 49.9 + - - -
381A TYR* 1.3 74.4 - - - +
383A LEU* 1.3 53.7 + - - +
384A GLN 3.4 0.4 - - - -
419A LYS* 2.7 29.1 + - - +
528A ILE* 3.9 13.7 - - - -
552A THR* 3.5 10.6 - - - +
554A VAL* 3.7 18.5 - - - +
----------------------------------------------------------
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