Contacts of the strand formed by residues 292 - 301 (chain A) in PDB entry 4RQE
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 ILE 292 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 4.9 7.9 - - + -
280A HIS* 5.5 5.2 - - + +
285A LEU* 4.1 29.2 - - + -
286A ARG 5.8 0.2 - - - +
289A ASP* 3.1 29.4 - - + +
290A LEU* 2.5 18.7 + - - +
291A PRO* 1.3 71.0 - - - +
293A LYS* 1.3 64.9 + - - +
294A TYR* 3.5 33.1 - - + +
327A PHE 4.1 0.2 - - - +
328A VAL* 3.4 4.9 - - - +
329A TYR* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 3.5 22.6 + - - +
219A GLY* 3.6 23.1 + - - +
220A TYR* 3.5 42.5 - - + -
221A ILE* 3.6 21.8 - - + +
291A PRO* 3.7 10.2 + - - +
292A ILE* 1.3 77.5 - - - +
294A TYR* 1.3 73.6 + - - +
327A PHE 4.0 2.2 - - - -
328A VAL* 4.2 11.4 - - + -
340A MET* 5.2 13.0 - - - -
343A GLU* 4.6 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.4 11.6 - - - -
221A ILE* 3.7 24.2 - - + +
223A ILE* 4.1 23.8 - - + -
276A ILE* 4.0 19.7 - - + -
279A LEU* 4.2 14.8 - - + +
280A HIS* 2.6 30.7 + + - -
292A ILE* 3.5 26.6 - - + +
293A LYS* 1.3 83.7 - - - +
295A ALA* 1.3 60.3 + - - +
296A GLY 3.8 0.7 - - - -
325A GLU 3.5 0.9 - - - +
326A GLN* 3.7 0.2 - - - -
327A PHE* 2.8 42.9 + - + +
329A TYR* 3.7 35.7 - + - -
197C LYS* 5.5 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 4.5 9.9 - - + +
215A LEU* 3.6 30.1 - - + -
220A TYR* 3.7 16.6 - - + -
221A ILE 2.8 15.4 + - - +
222A PRO* 3.3 12.9 - - + +
223A ILE* 3.0 19.3 + - - -
294A TYR* 1.3 71.6 - - - +
296A GLY* 1.3 62.6 + - - +
297A LEU 3.3 1.6 + - - -
324A ILE* 4.8 2.2 - - - -
325A GLU 3.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.4 11.9 - - - -
225A THR* 4.9 0.2 - - - -
272A SER* 3.3 13.4 + - - -
276A ILE* 3.6 27.4 - - - +
294A TYR 3.8 2.0 - - - -
295A ALA* 1.3 69.9 - - - +
297A LEU* 1.3 60.4 + - - -
324A ILE* 3.4 3.6 - - - -
325A GLU 2.8 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.5 17.0 - - + -
212A LEU* 4.5 20.9 - - + -
223A ILE 3.0 19.2 + - - +
224A TYR* 3.5 24.9 - - + +
225A THR* 3.4 10.9 + - - -
295A ALA 3.3 3.4 + - - +
296A GLY* 1.3 69.9 - - - -
298A SER* 1.3 74.2 + - - +
322A GLU* 5.2 9.6 - - + -
323A LYS 4.4 1.8 - - - +
324A ILE* 4.1 21.3 - - + -
201C VAL* 4.2 21.5 - - + -
204C GLU* 5.8 2.0 - - - +
205C GLN* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 5.3 0.2 - - - -
225A THR* 3.2 21.1 - - - -
227A PHE* 3.7 14.4 - - - -
269A ILE* 3.9 3.7 - - - +
272A SER* 2.3 33.1 + - - -
297A LEU* 1.3 83.9 - - - +
299A THR* 1.3 68.7 + - - +
300A CYS* 3.6 4.0 - - - -
322A GLU* 4.5 4.0 - - - -
323A LYS 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 3.3 27.0 - - - -
269A ILE* 3.7 16.8 - - - +
298A SER* 1.3 80.3 + - - +
300A CYS* 1.3 58.4 + - - +
301A PHE* 3.6 23.8 - - + -
320A GLN* 5.2 0.2 - - + -
321A PHE 3.2 23.1 - - - +
322A GLU* 3.0 31.9 + - - +
224C TYR* 4.0 1.6 - - - +
227C PHE* 3.6 22.9 - - + -
299C THR* 4.1 3.8 + - - -
322C GLU* 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE 4.0 2.9 - - - -
270A ALA 3.2 20.4 - - - +
271A THR* 3.7 8.1 - - - +
272A SER 4.2 0.4 - - - -
298A SER* 3.6 22.4 - - - -
299A THR* 1.3 79.2 - - - +
301A PHE* 1.3 60.7 + - - +
320A GLN* 3.6 3.8 - - - -
321A PHE* 2.5 59.0 + - + -
323A LYS* 3.6 34.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 4.1 17.3 - + + -
246A GLU 4.0 4.9 - - - +
247A LEU* 4.9 1.0 - - - +
248A TYR* 4.5 9.2 + + + -
268A LEU* 4.0 42.5 - - + +
269A ILE* 2.8 31.0 + - + +
270A ALA* 3.2 12.0 - - - +
299A THR* 3.6 39.5 - - + -
300A CYS* 1.3 75.5 - - - +
302A ARG* 1.3 62.0 + - - +
319A HIS 3.3 5.6 - - - +
320A GLN* 4.3 14.1 - - + -
227C PHE* 3.6 32.3 - + + -
228C PHE* 4.5 14.1 - + - -
268C LEU* 5.6 1.1 - - + -
301C PHE* 4.7 11.0 - + - -
----------------------------------------------------------
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