Contacts of the helix formed by residues 361 - 378 (chain A) in PDB entry 4OE4
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 GLU 361 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU 3.6 0.4 + - - -
360A PRO* 1.3 70.3 - - - +
362A SER* 1.3 62.6 + - - +
363A LYS 3.1 1.0 + - - -
364A SER* 3.3 20.6 + - - -
365A GLU 4.7 1.4 + - - -
468A GLU* 4.0 16.5 - - + +
469A TYR 2.8 28.8 + - - +
470A PRO* 3.8 32.2 - - + +
471A ASP* 3.3 5.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
328A PRO* 4.4 0.2 - - - +
361A GLU* 1.3 76.0 - - - +
363A LYS* 1.3 83.7 + - - +
364A SER 3.5 0.2 - - - -
365A GLU* 5.3 1.3 + - - +
366A GLU* 5.6 1.4 + - - +
471A ASP* 2.5 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 5.6 0.2 - - + -
328A PRO* 3.3 27.6 - - + +
332A ILE* 3.9 31.1 - - + +
359A LEU* 5.5 0.7 - - + -
360A PRO* 3.1 28.9 + - + -
362A SER* 1.3 96.7 + - - +
364A SER* 1.3 59.6 + - - +
365A GLU 3.5 1.6 - - - -
366A GLU* 3.4 21.5 + - - +
367A PHE* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 3.8 12.8 - - - +
360A PRO 2.7 21.7 + - - -
361A GLU* 3.3 17.8 + - - -
362A SER 3.5 0.2 - - - -
363A LYS* 1.3 76.6 - - - +
365A GLU* 1.3 59.1 + - - +
367A PHE* 3.8 0.3 - - - +
368A LEU* 2.9 38.1 + - - +
468A GLU* 3.5 37.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
361A GLU 4.7 1.2 + - - -
362A SER 5.3 1.3 + - - +
363A LYS 3.5 0.2 - - - -
364A SER* 1.3 78.1 - - - +
366A GLU* 1.3 58.1 + - - +
368A LEU* 4.2 3.5 - - - +
369A SER* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.7 30.3 - - + +
362A SER 5.6 1.3 + - - +
363A LYS* 3.4 22.3 + - - +
364A SER 3.2 0.6 - - - -
365A GLU* 1.3 81.4 - - - +
367A PHE* 1.3 62.7 + - - +
369A SER* 3.8 3.7 - - - -
370A ASP* 3.1 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 4.0 10.1 - - + -
332A ILE* 3.8 21.7 - - + +
335A ALA* 3.7 18.2 - - + -
336A VAL* 3.5 34.6 - - + +
339A THR* 3.6 22.7 - - - -
357A LEU* 3.6 21.1 - - + -
359A LEU* 3.6 33.0 - - + -
363A LYS* 2.9 19.0 + - + +
364A SER 3.8 2.9 - - - +
366A GLU* 1.3 77.2 - - - +
368A LEU* 1.3 65.0 + - + +
370A ASP 3.3 0.2 + - - -
371A MET* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 4.9 2.0 - - + -
359A LEU* 3.9 19.7 - - + -
364A SER* 2.9 21.9 + - - +
365A GLU* 4.2 3.8 - - - +
367A PHE* 1.3 85.7 - - + +
369A SER* 1.3 57.9 + - - +
371A MET* 3.1 5.9 + - - -
372A PHE* 2.8 65.9 + - + -
427A LEU* 4.0 18.6 - - + -
444A VAL* 4.6 12.3 - - + -
466A VAL* 4.8 5.2 - - + -
468A GLU* 3.4 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 2.9 22.0 + - - +
366A GLU* 3.8 4.7 - - - -
368A LEU* 1.3 76.6 - - - +
370A ASP* 1.3 65.8 + - - +
372A PHE* 3.9 5.5 - - - +
373A GLY* 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 4.1 11.1 - - - +
333A SER* 4.8 9.1 - - - -
336A VAL* 4.0 14.8 - - + +
366A GLU* 3.1 34.8 + - - +
367A PHE 3.6 4.3 - - - +
369A SER* 1.3 77.3 - - - +
371A MET* 1.3 57.8 + - - +
373A GLY* 3.7 1.4 - - - -
374A ILE* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL* 3.6 14.8 - - + +
339A THR* 3.5 36.8 - - + -
340A ILE* 4.0 20.9 - - + +
344A PHE* 4.7 2.7 - - + -
367A PHE* 2.9 38.2 + - + +
368A LEU* 3.1 11.0 + - - +
370A ASP* 1.3 77.4 - - - +
372A PHE* 1.3 65.1 + - + +
374A ILE* 3.2 2.8 + - - +
375A LEU* 2.8 49.1 + - + +
444A VAL* 4.2 22.4 - - - -
464A LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 2.8 56.0 + - + +
369A SER* 4.0 5.6 - - - +
371A MET* 1.3 80.4 - - + +
373A GLY* 1.3 56.5 + - - +
375A LEU* 3.7 3.4 - - + +
376A GLN* 2.8 31.6 + - - +
427A LEU* 3.6 41.3 - - + -
428A TYR* 3.5 41.0 - + + -
444A VAL* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER 2.9 17.1 + - - -
370A ASP* 3.7 1.3 - - - -
372A PHE* 1.3 76.5 - - - +
374A ILE* 1.3 56.9 + - - +
376A GLN* 3.3 7.5 + - - +
377A SER* 2.9 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 5.7 1.8 - - - +
336A VAL* 3.9 18.2 - - + -
337A LEU* 3.7 33.4 - - + -
340A ILE* 3.6 19.7 - - + -
370A ASP* 2.8 28.5 + - + +
371A MET 3.7 2.7 - - - +
373A GLY* 1.3 75.5 - - - +
375A LEU* 1.3 64.0 + - - +
377A SER* 3.4 14.7 + - - +
378A GLN* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ILE* 3.9 21.5 - - + -
344A PHE* 4.0 25.1 - - + -
371A MET* 2.8 40.6 + - + +
372A PHE* 3.8 1.6 - - + +
374A ILE* 1.3 73.4 - - - +
376A GLN* 1.3 63.8 + - - +
378A GLN* 3.4 17.1 + - - +
399A MET* 3.9 26.9 - - + +
428A TYR* 3.4 46.6 + - + +
442A PRO* 4.3 8.1 - - + -
444A VAL* 4.5 3.8 - - + -
----------------------------------------------------------
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 PHE 2.8 16.9 + - - +
373A GLY* 3.3 8.5 - - - +
374A ILE 3.2 0.2 - - - -
375A LEU* 1.3 78.5 - - - +
377A SER* 1.3 63.2 + - - +
378A GLN 3.1 10.9 + - - +
428A TYR* 3.5 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 2.9 19.1 + - - -
374A ILE* 3.4 8.9 + - - -
376A GLN* 1.3 72.1 - - - +
378A GLN* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE 3.4 9.2 + - - +
375A LEU* 3.7 14.4 - - - +
376A GLN 3.1 14.1 + - - +
377A SER* 1.3 79.8 - - - +
399A MET* 5.1 14.4 - - + -
----------------------------------------------------------
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