Contacts of the helix formed by residues 330 - 336 (chain A) in PDB entry 1H8F
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 330 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.6 1.8 - - - -
328A ARG 4.8 3.6 - - - +
329A LEU* 1.3 76.8 - - - +
331A PRO* 1.3 76.6 - - + +
332A LEU* 3.6 7.3 + - - +
333A GLU* 2.9 55.2 + - - +
334A ALA* 3.0 11.5 + - - +
369A SER* 5.1 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.3 47.8 - - + +
169A LEU* 3.6 10.8 - - + -
170A ALA* 3.4 20.6 - - + +
173A HIS* 3.5 27.8 - - + +
240A VAL* 3.7 19.5 - - + -
330A THR* 1.3 85.9 - - + +
332A LEU* 1.3 60.0 + - + +
334A ALA* 3.4 0.9 + - - +
335A CYS* 3.3 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 4.0 15.0 - - + +
330A THR* 3.0 5.6 + - - +
331A PRO* 1.3 78.9 - - - +
333A GLU* 1.3 65.5 + - - +
334A ALA 3.4 0.5 + - - -
335A CYS* 3.4 15.0 + - + +
336A ALA* 3.4 12.3 + - - +
362A PHE* 4.0 15.9 - - + -
366A GLU 3.6 22.9 - - - +
367A LEU* 3.8 20.4 - - + +
369A SER* 3.4 26.9 - - - +
370A ASN* 4.2 12.8 - - + +
373A LEU* 4.1 11.4 - - + +
377A LEU* 3.5 27.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
328A ARG 4.6 0.7 - - - +
329A LEU* 3.4 24.8 - - + +
330A THR* 2.9 47.0 + - - +
332A LEU* 1.3 74.5 - - - +
334A ALA* 1.3 65.1 + - - +
336A ALA* 3.4 12.4 + - - +
337A HIS* 3.4 10.0 + - - +
370A ASN* 4.7 7.4 - - + +
373A LEU* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.6 37.5 - - + -
316A LEU* 4.3 10.8 - - + -
320A LEU* 4.4 6.7 - - + -
329A LEU* 4.1 9.6 - - + +
330A THR 3.0 11.7 + - - +
331A PRO 3.7 7.0 - - - +
333A GLU* 1.3 73.6 - - - +
335A CYS* 1.3 57.0 + - - +
336A ALA 3.0 2.2 - - - -
337A HIS* 2.8 31.6 + - - +
340A PHE* 3.2 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.5 36.0 - - + -
166A PHE* 3.5 26.9 - - - +
167A ARG* 3.8 21.3 - - - -
331A PRO 3.3 9.3 + - - -
332A LEU* 3.6 12.3 - - + +
333A GLU 3.4 0.2 - - - -
334A ALA* 1.3 79.2 - - - +
336A ALA* 1.3 56.8 + - - +
337A HIS 3.2 0.9 + - - -
340A PHE* 3.8 10.2 - - - -
344A ARG* 2.9 22.9 + - - -
362A PHE* 4.8 4.5 - - + -
377A LEU* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU 3.4 5.9 + - - +
333A GLU 3.4 10.5 + - - +
334A ALA 3.0 1.4 - - - -
335A CYS* 1.3 77.2 - - - +
337A HIS* 1.3 63.5 + - - +
338A SER* 3.7 1.4 + - - -
341A ASP* 4.9 0.3 - - - +
344A ARG* 3.7 12.0 + - - +
373A LEU* 4.6 13.2 - - + -
376A ILE* 4.2 29.9 - - + +
377A LEU* 3.6 21.5 - - + -
----------------------------------------------------------
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