Contacts of the strand formed by residues 291 - 298 (chain B) in PDB entry 3C7N
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 291 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 4.1 12.6 - - + -
249B HIS* 3.2 52.0 - - + +
251B LYS* 4.6 18.2 - - + +
286B SER* 2.9 1.9 - - - -
287B LEU* 2.6 35.4 + - - +
288B TYR 2.7 24.2 + - - +
289B GLU* 3.8 11.2 - - + +
290B GLY* 1.3 73.2 - - - +
292B ASP* 1.3 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 5.0 1.1 - - - -
249B HIS* 4.1 8.7 + - - -
284B ILE 4.4 0.2 - - - +
285B ASP* 3.4 3.7 - - - +
286B SER* 2.3 40.6 + - - +
290B GLY 3.8 4.2 + - - +
291B ILE* 1.3 85.6 - - - +
293B PHE* 1.3 60.9 + - - +
294B TYR* 3.5 37.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 4.1 21.8 - + + -
244B GLU* 3.8 23.8 - - + -
245B PHE* 3.7 26.5 - + + -
248B LYS* 5.8 1.6 - - + -
249B HIS* 4.9 8.3 - + - -
263B LEU* 3.8 31.0 - - + -
282B ILE* 3.8 6.0 - - + +
283B GLU* 3.3 0.9 - - - -
284B ILE* 2.9 45.5 + - + +
287B LEU* 3.8 26.9 - - + +
291B ILE 3.9 1.8 + - - -
292B ASP* 1.3 73.4 - - - +
294B TYR* 1.3 64.0 + - - +
295B THR* 3.3 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 4.8 2.7 + - - +
59A SER* 4.1 31.6 + - - -
282B ILE 3.2 5.2 - - - +
283B GLU* 3.4 39.0 - - + -
284B ILE 4.2 10.3 - - - -
285B ASP* 4.2 11.3 - - + +
292B ASP* 3.5 32.2 + - + -
293B PHE* 1.3 93.7 - - - +
295B THR* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 3.8 8.8 - - - -
244B GLU* 2.8 30.3 + - - +
248B LYS* 5.4 6.5 - - + -
281B SER* 3.6 4.9 - - - -
282B ILE* 2.7 43.5 + - - +
283B GLU* 4.9 0.5 - - - +
293B PHE* 3.3 32.6 - - + -
294B TYR* 1.3 80.4 - - - +
296B SER* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A PHE* 4.9 14.7 - - - -
241B PHE* 3.9 7.9 - - - -
244B GLU* 5.1 1.2 - - - +
279B GLN* 2.9 34.0 + - - -
280B ALA 3.5 10.3 - - - -
281B SER* 4.2 4.0 - - - +
282B ILE* 5.0 0.7 - - - -
295B THR* 1.3 87.6 + - - +
297B ILE* 1.3 69.0 + - - +
298B THR 4.8 0.2 + - - -
301B ARG* 5.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B MET* 4.3 22.0 - - + -
240B HIS* 4.4 14.1 - - + +
241B PHE* 3.7 27.1 - - + -
270B ALA* 4.5 11.4 - - + -
274B LEU* 4.0 7.5 - - + +
279B GLN* 3.7 4.1 - - - +
280B ALA* 3.1 41.4 + - + +
282B ILE* 4.6 2.7 - - + -
296B SER* 1.3 81.4 - - - +
298B THR* 1.3 77.2 + - - +
301B ARG* 4.3 12.1 - - + +
302B PHE* 4.3 16.8 - - + +
305B LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A GLU 5.0 1.6 + - - -
571A LYS* 4.9 12.9 + - - +
572A ASN* 3.2 21.1 + - - +
575A GLU* 3.0 31.2 + - - +
274B LEU* 4.2 1.6 - - - -
278B THR 3.4 9.6 + - - -
279B GLN* 4.6 6.5 - - - +
296B SER* 4.8 0.6 + - - -
297B ILE* 1.3 84.0 - - - +
299B ARG* 1.3 56.2 + - - +
300B ALA 3.5 3.8 - - - +
301B ARG* 3.1 37.9 - - + +
302B PHE* 2.9 22.9 + - - +
----------------------------------------------------------
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