Contacts of the helix formed by residues 325 - 335 (chain A) in PDB entry 3R2W
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 LEU 325 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 4.6 0.4 - - + -
219A PHE* 4.1 3.4 - - + -
225A LEU* 3.3 44.4 - - + +
228A PHE* 4.2 7.9 - - + -
229A ILE* 4.2 16.6 - - + +
233A LYS* 3.8 16.4 - - + -
234A GLU* 2.7 43.2 + - - +
235A TYR 3.7 5.8 - - - +
236A ILE* 3.6 33.4 - - + +
323A ILE* 3.5 2.6 + - - +
324A SER* 1.3 68.0 - - - +
326A ALA* 1.3 65.4 + - - +
328A VAL* 2.8 21.3 + - + +
329A LYS* 3.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 4.6 22.6 - - + +
234A GLU* 4.1 8.3 + - + +
324A SER* 3.3 7.8 + - - +
325A LEU* 1.3 78.3 - - - +
327A ALA* 1.3 61.3 + - - +
329A LYS* 3.7 7.1 + - - +
330A ARG* 3.4 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.3 35.9 - - - +
324A SER* 3.1 21.2 + - - +
325A LEU 3.0 0.4 - - - -
326A ALA* 1.3 75.5 - - - +
328A VAL* 1.3 65.8 + - - +
330A ARG* 3.2 14.0 + - - +
331A LEU* 3.0 30.8 + - + +
368A PHE* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.9 35.7 - - + +
219A PHE* 5.7 4.0 - - + -
225A LEU* 4.5 17.3 - - + -
323A ILE* 3.4 24.7 - - + -
324A SER 2.8 20.0 - - - +
325A LEU* 2.8 12.5 + - + +
327A ALA* 1.3 71.3 - - - +
329A LYS* 1.3 57.3 + - - +
331A LEU* 4.4 2.0 - - - +
332A GLN* 2.9 33.0 + - + +
337A ILE* 4.6 6.0 - - + +
368A PHE* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.5 5.3 - - + -
225A LEU* 4.1 23.3 - - + +
226A ASP* 5.7 4.9 - - - +
229A ILE* 5.8 6.3 - - + -
325A LEU 3.1 10.4 + - - +
326A ALA* 3.9 11.0 - - - +
327A ALA 3.2 0.4 - - - -
328A VAL* 1.3 75.1 - - - +
330A ARG* 1.3 64.2 + - + +
332A GLN 4.2 0.2 - - - -
333A GLU* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.0 34.8 + - - -
326A ALA* 3.4 17.8 + - - +
327A ALA* 3.2 12.9 + - - +
329A LYS* 1.3 79.7 - - + +
331A LEU* 1.3 75.4 + - - +
333A GLU* 3.7 6.9 + - - +
334A GLN* 3.3 29.5 + - - +
369A GLU* 4.9 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 4.7 1.8 - - - +
327A ALA* 3.0 31.3 + - + +
330A ARG* 1.3 93.3 - - - +
332A GLN* 1.3 56.8 + - - +
333A GLU 3.3 4.3 - - - -
334A GLN* 3.6 0.6 + - + -
335A ASN 3.1 2.9 + - - -
336A ALA* 2.8 52.4 + - + +
337A ILE* 3.8 22.2 + - + +
367A SER 3.7 24.9 - - - +
368A PHE* 4.2 24.9 - - + -
369A GLU 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 4.1 17.7 - - - +
217A ALA* 3.8 28.6 - - - +
220A TYR* 4.0 41.9 - - + -
328A VAL* 2.9 25.4 + - + +
329A LYS 4.2 0.4 - - - -
331A LEU* 1.3 75.5 - - - +
333A GLU* 1.3 61.8 + - - +
334A GLN 3.4 0.4 - - - -
335A ASN* 3.8 26.4 + - - +
337A ILE* 4.0 22.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
220A TYR* 3.2 28.5 + - + +
329A LYS* 3.0 31.9 + - - +
330A ARG* 3.9 8.0 + - - +
331A LEU 3.3 0.4 - - - -
332A GLN* 1.3 76.9 - - - +
334A GLN* 1.3 65.0 + - - +
335A ASN* 3.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 3.3 22.3 + - - +
331A LEU* 3.6 0.6 + - + -
332A GLN 3.4 0.2 - - - -
333A GLU* 1.3 80.6 + - - +
335A ASN* 1.3 68.6 + - - +
336A ALA* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU 3.1 5.1 + - - -
332A GLN* 3.8 29.1 + - - +
333A GLU 3.3 5.1 - - - +
334A GLN* 1.3 80.1 - - - +
336A ALA* 1.3 54.7 + - - +
337A ILE* 2.9 15.4 + - - +
338A ASP* 3.5 15.4 - - - +
----------------------------------------------------------
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