Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 3H60
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 THR 324 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 6.3 2.9 - - - -
319A VAL* 3.4 8.1 + - - +
320A LYS* 4.2 12.0 - - - -
323A TYR* 1.3 91.0 - - - +
325A ALA* 1.3 64.9 + - - +
326A GLN* 3.2 20.2 + - - +
327A MET* 3.3 12.3 + - - +
328A TYR* 3.2 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS* 4.1 31.5 - - + +
324A THR* 1.3 75.3 - - - +
326A GLN* 1.3 62.3 + - - +
328A TYR* 3.1 5.6 + - - +
329A GLU* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 3.1 12.0 + - - +
325A ALA* 1.3 78.3 - - - +
327A MET* 1.3 62.3 + - - +
329A GLU* 3.2 12.2 + - + +
330A LEU* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 3.7 31.0 - - + +
209A ALA* 4.0 9.4 - - + -
210A TYR* 4.2 12.6 - - + +
213A LEU* 3.8 23.1 - - - -
319A VAL* 3.9 1.8 - - + -
323A TYR* 3.5 46.9 - - + -
324A THR* 3.3 15.1 + - - +
326A GLN* 1.3 78.6 - - - +
328A TYR* 1.3 61.8 + - - +
330A LEU* 3.1 12.6 + - - +
331A PHE* 3.0 41.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASP* 3.4 15.9 + - - -
310A ASN* 3.0 34.0 + - + +
311A GLN* 3.0 32.5 + - - -
315A PHE* 3.9 15.7 - + - -
316A GLU* 3.7 49.6 - - + +
319A VAL* 3.4 24.1 - - + +
320A LYS* 5.0 1.6 - - + -
324A THR 3.2 6.4 + - - +
325A ALA* 3.1 12.8 + - - +
327A MET* 1.3 76.2 - - - +
329A GLU* 1.3 78.8 + - - +
331A PHE* 3.2 3.9 + - + +
332A SER* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLU* 4.8 3.8 - - - +
320A LYS* 5.6 0.3 - - - -
325A ALA* 3.0 30.9 + - - +
326A GLN* 3.6 10.5 - - + +
328A TYR* 1.3 93.3 - - - +
330A LEU* 1.3 63.1 + - - +
332A SER* 3.3 9.0 + - - -
333A GLU* 3.2 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.5 37.9 - - + +
213A LEU* 3.7 30.7 - - + -
214A VAL* 4.1 14.8 - - + +
217A LYS* 5.0 8.5 - - + +
326A GLN 3.0 12.7 + - - +
327A MET* 3.1 14.1 + - - +
329A GLU* 1.3 76.8 - - - +
331A PHE* 1.3 61.0 + - - +
333A GLU* 3.2 18.4 + - + +
334A VAL* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 6.0 0.2 - - + -
213A LEU* 3.6 28.0 - - + +
280A VAL* 5.2 3.4 - - + -
283A ILE* 3.4 31.6 - - + -
284A LEU* 3.9 27.6 - - + -
287A PHE* 4.2 7.6 - + - -
315A PHE* 3.7 29.8 - + + -
319A VAL* 3.9 21.3 - - + -
323A TYR* 5.1 4.3 - + - -
327A MET* 3.0 43.3 + - + -
328A TYR* 3.2 6.7 + - + +
330A LEU* 1.3 74.6 - - - +
332A SER* 1.3 63.7 + - - +
334A VAL* 3.3 4.7 + - - +
335A PHE* 3.0 33.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASP* 2.7 36.1 + - - -
310A ASN* 5.7 0.2 - - - -
328A TYR* 2.9 22.8 + - - -
329A GLU* 3.6 14.8 - - - -
330A LEU 3.3 0.4 - - - -
331A PHE* 1.3 75.9 - - - +
333A GLU* 1.3 63.6 + - - +
335A PHE* 3.3 13.9 + - - +
336A GLU* 3.2 27.0 + - - +
374A GLN* 3.8 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LYS* 3.1 29.5 + - + +
329A GLU* 3.2 22.3 + - + +
330A LEU* 3.7 16.7 - - + +
332A SER* 1.3 77.7 - - - +
334A VAL* 1.3 63.8 + - - +
336A GLU* 3.5 28.7 + - - +
337A TRP* 3.6 14.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 3.4 36.8 - - + +
216A VAL* 3.5 26.0 - - + -
217A LYS* 3.8 18.2 - - + +
220A LEU* 3.7 12.7 - - + +
287A PHE* 3.6 23.1 - - + -
330A LEU* 3.0 26.5 + - + +
331A PHE 3.8 4.5 - - - +
332A SER 3.3 0.2 - - - -
333A GLU* 1.3 77.3 - - - +
335A PHE* 1.3 61.9 + - - +
337A TRP* 3.0 18.4 + - - +
338A LEU 3.8 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.3 7.9 - - + -
283A ILE* 3.8 22.2 - - + -
287A PHE* 3.7 28.9 - + - -
301A ARG* 3.2 21.3 + - - +
305A GLU* 3.6 52.5 - - + +
306A THR* 4.5 0.7 - - - -
307A ASP* 6.1 0.2 - - - -
310A ASN* 3.6 22.0 - - - -
315A PHE* 3.6 28.5 - + - -
331A PHE* 3.0 24.5 + + + -
332A SER* 3.5 11.9 - - - +
334A VAL* 1.3 74.3 - - - +
336A GLU* 1.4 61.5 + - - +
338A LEU* 3.1 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 3.8 9.6 + - - +
307A ASP* 5.3 0.3 - - - +
332A SER* 3.2 17.7 + - - +
333A GLU* 3.6 21.8 - - - +
334A VAL 3.2 0.6 - - - -
335A PHE* 1.4 76.5 - - - +
337A TRP* 1.3 62.8 + - + +
338A LEU 3.8 0.9 + - - +
371A ARG* 3.1 25.3 - - - +
372A ASN* 3.2 18.8 + - + +
373A ARG* 3.6 33.5 - - - +
374A GLN* 3.1 26.6 + - - +
----------------------------------------------------------
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