Contacts of the strand formed by residues 296 - 305 (chain B) in PDB entry 5C5B
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 296 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG* 3.4 5.9 - - - +
288B ASN* 2.8 52.1 + - - +
294B THR* 5.0 8.7 - - + -
295B THR* 1.3 81.3 + - - +
297B TRP* 1.3 71.0 + - - +
298B GLU* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.7 39.0 - - + -
286B LEU 3.4 3.6 - - - -
287B ARG* 3.5 47.4 - - + +
295B THR* 4.3 2.9 + - + -
296B THR* 1.3 83.5 - - - +
298B GLU* 1.3 61.3 + - - +
299B ARG 4.4 0.2 + - - -
335B CYS* 3.9 13.2 - - + -
336B GLU* 2.8 25.8 + - - -
338B ARG* 3.2 47.9 - - - +
341B CYS* 3.9 18.8 - - - -
354B ILE* 3.9 14.1 - - + -
356B GLN* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 4.1 2.5 - - - -
286B LEU* 2.9 40.6 + - + +
288B ASN* 6.4 1.6 - - + -
296B THR* 5.8 1.8 - - - +
297B TRP* 1.3 76.8 - - - +
299B ARG* 1.3 65.2 + - - +
300B LEU* 3.3 40.2 + - + +
313B PRO* 4.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 4.2 19.4 - - - -
141A ASP* 4.5 5.3 + - - -
144A ILE* 4.0 36.6 - - - +
145A ASN* 5.0 8.7 - - - +
171A ARG* 5.0 7.1 - - - +
283B TYR* 3.3 53.0 - - + +
284B LEU 3.5 4.7 - - - +
285B ASN* 3.4 22.9 + - - +
297B TRP 4.4 0.2 + - - -
298B GLU* 1.3 72.4 - - - +
300B LEU* 1.3 70.9 + - - +
314B ARG* 3.9 26.7 + - - +
358B GLU* 5.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TYR* 3.4 9.8 - - - -
284B LEU 2.9 31.9 + - - +
286B LEU* 3.9 26.5 - - + -
298B GLU* 3.5 42.2 - - - +
299B ARG* 1.3 85.4 - - - +
301B TYR* 1.3 61.6 + - - +
302B PHE* 3.4 13.9 - - + -
311B CYS* 3.5 27.1 - - - -
312B GLN 4.3 2.2 - - - +
313B PRO* 3.6 28.0 - - + -
314B ARG 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 4.9 1.4 + - - -
14A GLU* 2.9 34.5 + - + +
16A SER* 3.9 26.8 - - - -
17A PRO* 3.4 28.0 - - + -
281B ALA* 3.6 18.7 - - + +
282B GLY* 3.8 22.9 - - - -
283B TYR* 3.8 23.0 - + + -
300B LEU* 1.3 72.1 - - - +
302B PHE* 1.3 61.5 + - - +
303B PHE* 3.8 27.3 - + + -
311B CYS* 3.3 5.2 - - - +
312B GLN* 2.9 48.2 + - + +
313B PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA* 3.2 2.4 - - - -
282B GLY 2.9 36.2 + - - +
284B LEU* 3.5 35.7 - - + -
286B LEU* 3.9 15.5 - - + -
300B LEU* 3.4 29.8 - - + -
301B TYR* 1.3 75.9 - - - +
303B PHE* 1.3 63.1 + - - +
309B LEU* 4.4 10.8 - - + -
310B MET 3.2 12.8 - - - -
311B CYS* 3.5 29.2 - - + -
322B ILE* 4.0 22.2 - - + -
353B ILE* 5.3 0.2 - - + -
355B LEU* 3.5 25.6 - - + -
366B TRP* 3.5 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LYS 3.3 4.7 - - - -
281B ALA* 3.7 18.8 - - + -
301B TYR* 3.8 20.2 - + + -
302B PHE* 1.3 75.8 - - - +
304B THR* 1.3 70.6 + - - +
305B GLN* 4.5 14.1 - - + -
309B LEU* 4.2 2.0 - - - -
310B MET* 2.9 69.3 + - + +
312B GLN* 4.2 30.7 - - + -
319B GLY* 4.7 13.2 - - - -
366B TRP* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE 4.0 0.5 + - - -
279B GLN* 3.2 24.3 + - - +
280B LYS* 2.8 42.1 + - + +
303B PHE* 1.3 78.6 - - - +
305B GLN* 1.3 62.2 + - - +
306B GLY 4.2 1.1 - - - -
308B ASN 3.3 5.4 - - - -
309B LEU* 4.0 9.0 - - + -
325B LEU* 4.4 7.0 - - + -
366B TRP* 3.9 20.4 - - + -
369B ALA* 5.4 3.8 - - + -
370B ILE* 5.5 1.1 - - + -
373B ILE* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 3.9 17.3 + - + -
304B THR* 1.3 74.7 - - - +
306B GLY* 1.3 65.8 + - - +
307B GLY 3.2 0.3 + - - -
308B ASN* 3.0 27.0 + - - +
310B MET* 3.8 33.3 - - + +
----------------------------------------------------------
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