Contacts of the helix formed by residues 257 - 266 (chain A) in PDB entry 3IQS
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 HIS 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 4.1 8.7 - - + -
254A GLU 5.6 2.8 + - - -
255A GLY* 4.2 4.5 - - - -
256A ARG* 1.3 81.6 - - - +
258A ALA* 1.3 66.7 + - - +
259A GLU* 3.1 5.6 - - - +
260A LEU* 2.9 22.3 + - + +
261A CYS* 2.9 11.1 + - - -
288A CYS* 4.2 9.4 - - + -
291A CYS* 3.6 12.2 - - - -
400A ZN 2.2 38.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 3.4 44.6 - - + +
220A LEU* 4.2 7.8 - - + +
242A LEU* 3.3 21.1 - - + +
243A CYS 3.9 2.9 - - - -
244A ASN* 3.6 21.6 - - - +
257A HIS* 1.3 73.8 - - - +
259A GLU* 1.3 54.9 + - - +
261A CYS* 3.3 0.8 + - - -
262A PHE* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 3.9 23.0 + - - +
220A LEU* 4.4 9.4 - - + -
257A HIS* 3.1 10.8 - - - +
258A ALA* 1.3 86.6 + - - +
260A LEU* 1.3 61.6 + - - +
262A PHE* 3.5 9.2 + - - +
263A LEU* 3.2 27.6 + - - +
283A THR* 5.3 3.8 - - + +
285A TRP 4.1 1.4 - - - +
286A SER 4.0 3.8 - - - +
287A PRO* 3.3 42.9 - - + +
288A CYS 4.5 1.7 + - - -
291A CYS* 3.5 21.0 - - + -
295A MET* 4.0 21.3 - - + +
400A ZN 4.2 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 3.8 34.7 + - - +
257A HIS* 2.9 19.9 + - + +
259A GLU* 1.3 77.3 - - - +
261A CYS* 1.3 58.3 + - - +
263A LEU* 3.4 8.4 + - + +
264A ASP* 3.0 34.1 + - - +
290A SER* 5.5 4.9 - - - +
291A CYS* 3.8 22.7 - - - -
294A GLU* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.9 16.4 - - + -
243A CYS 4.3 6.7 - - - +
245A GLN* 3.7 23.3 - - - -
252A PHE* 5.5 0.9 - - - -
256A ARG* 3.3 32.1 - - - -
257A HIS 2.9 13.8 + - - -
258A ALA 3.6 7.0 - - - +
260A LEU* 1.3 73.8 - - - +
262A PHE* 1.3 66.0 + - - +
264A ASP* 3.1 25.3 + - - +
265A VAL* 3.3 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.8 26.2 - - + -
222A TYR* 3.7 23.6 - + + -
242A LEU* 3.8 8.9 - - + +
258A ALA 2.8 17.6 + - - +
259A GLU 3.5 5.4 - - - +
261A CYS* 1.3 77.1 - - - +
263A LEU* 1.3 69.3 + - + +
265A VAL* 3.1 22.5 + - + +
266A ILE* 3.5 19.6 + - + +
269A TRP* 3.4 28.5 - + - -
279A VAL* 3.6 19.5 - - + -
281A CYS* 3.4 25.8 - - - -
295A MET* 4.0 24.5 - - + -
298A PHE* 6.0 1.8 - + - -
307A LEU* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU 3.2 15.0 + - - +
260A LEU* 3.4 11.4 + - + +
262A PHE* 1.3 87.4 - - + +
264A ASP* 1.3 62.3 - - - +
266A ILE* 3.7 19.3 + - + +
267A PRO* 3.3 18.4 - - - +
294A GLU* 3.9 45.1 - - + +
295A MET* 4.2 12.8 - - + +
298A PHE* 3.7 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE* 5.0 4.7 - - - -
256A ARG* 2.8 45.9 + - - +
260A LEU 3.0 18.8 + - - +
261A CYS* 3.2 17.5 - - - +
262A PHE 3.1 0.4 - - - -
263A LEU* 1.3 79.2 - - - +
265A VAL* 1.3 58.1 + - + +
267A PRO* 3.3 14.9 - - - +
268A PHE* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 4.5 11.0 - - - +
242A LEU* 4.5 12.6 - - + -
261A CYS* 3.3 11.4 + - + +
262A PHE* 3.1 24.1 + - + +
264A ASP* 1.3 79.5 - - + +
266A ILE* 1.4 64.7 + - - +
267A PRO* 3.2 4.0 - - - -
268A PHE* 2.8 34.5 + - + +
269A TRP* 3.7 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.5 26.0 - - + +
263A LEU* 3.8 33.9 - - + +
264A ASP 3.6 0.2 - - - -
265A VAL* 1.4 75.2 - - - +
267A PRO* 1.3 69.9 - - + +
269A TRP* 2.9 56.4 + - + +
270A LYS 3.9 1.9 + - - -
271A LEU* 4.7 10.7 - - + +
279A VAL* 5.7 1.1 - - + -
298A PHE* 3.8 35.9 - - + -
----------------------------------------------------------
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