Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 5A91
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 259 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.3 17.3 - - + -
49A ILE 3.3 4.9 - - - +
50A ASN* 3.7 34.8 - - + +
229A TRP* 4.3 15.0 - - + -
248A ALA 4.1 0.2 - - - +
249A VAL* 3.6 3.1 - - - +
250A ILE* 2.8 45.0 + - + +
252A PRO* 4.4 5.6 - - + -
257A ALA 4.0 2.7 - - - +
258A PRO* 1.3 77.4 - - - +
260A VAL* 1.3 63.0 + - - +
261A LEU 4.2 0.2 - - - -
286A VAL 5.7 0.2 - - - +
287A THR* 4.0 28.9 - - + -
290A PHE* 3.9 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.6 1.7 - - - +
48A LEU* 3.2 4.7 - - - +
49A ILE* 2.8 40.6 + - + +
51A THR* 4.6 5.8 - - + -
187A ALA* 3.5 31.8 - - + +
190A LEU* 4.0 13.9 - - + -
191A LYS* 3.9 30.5 - - + +
195A LEU* 3.9 22.2 - - + -
248A ALA 3.4 10.1 - - - +
249A VAL* 4.5 7.0 - - + -
259A LEU* 1.3 76.2 - - - +
261A LEU* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.9 8.3 - - + -
47A ALA 3.4 9.0 - - - +
48A LEU* 4.0 9.9 - - + -
221A ILE* 3.8 22.8 - - + +
247A ILE* 3.5 2.1 - - - -
248A ALA* 2.8 39.8 + - - +
250A ILE* 4.1 19.7 - - + -
259A LEU 4.2 0.2 - - - -
260A VAL* 1.3 76.1 - - - +
262A VAL* 1.3 77.6 + - - +
263A THR* 3.9 13.5 - - + -
283A ALA* 3.8 33.7 - - + -
286A VAL* 3.9 22.9 - - + -
287A THR* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.3 6.8 - - - -
47A ALA 2.8 34.0 + - - +
183A PRO* 3.8 28.3 - - + +
186A MET* 3.9 5.4 - - + +
187A ALA* 3.5 35.0 - - - +
190A LEU* 5.2 2.2 - - + -
246A ASP 3.7 2.7 - - - -
247A ILE* 3.8 19.3 - - + -
261A LEU* 1.3 78.1 - - - +
263A THR* 1.3 65.1 + - - +
264A TYR* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.3 1.1 - - - -
45A GLY 3.4 4.7 - - - -
46A VAL* 4.4 5.6 - - + -
221A ILE* 3.5 17.6 - - + +
245A ASN* 3.4 3.5 - - - -
246A ASP 2.9 33.2 + - - +
261A LEU* 3.9 27.6 - - + -
262A VAL* 1.3 78.1 - - - +
264A TYR* 1.3 62.0 + - - +
279A LEU* 3.6 29.3 - - - +
282A ALA* 4.1 23.8 - - + -
283A ALA 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.5 5.7 - - - +
45A GLY 2.8 34.2 + - - +
66A PHE* 3.7 45.8 - + + -
68A MET* 3.7 4.8 - - + +
71A THR* 2.9 23.5 + - - -
181A THR* 3.6 23.7 - - + +
182A THR 4.5 3.8 - - - -
183A PRO* 4.1 6.5 - - + -
186A MET* 3.6 23.7 - - + +
245A ASN* 3.2 34.5 - - + +
247A ILE* 3.7 9.4 - - + -
262A VAL* 3.7 25.6 - - + -
263A THR* 1.3 80.5 - - - +
265A PHE* 1.3 65.0 + - - +
279A LEU* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 3.3 42.0 - - - -
42A GLY* 3.6 27.1 - - - -
43A ARG 3.3 16.2 - - - -
44A LEU* 4.0 8.1 - - + -
66A PHE* 4.3 2.2 - - - -
242A GLY 4.2 2.9 - - - -
243A THR* 3.2 5.8 - - - +
244A THR* 2.8 42.2 + - - +
245A ASN* 3.2 2.8 + - - -
264A TYR* 1.3 75.5 - - - +
266A THR* 1.3 62.1 + - - +
267A GLN* 3.5 31.6 - - + -
275A ARG* 3.8 25.4 - - + -
278A ILE* 4.0 18.4 - - + -
279A LEU* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY* 3.3 2.4 - - - -
43A ARG* 2.8 70.0 + - + +
66A PHE* 3.9 13.7 - - + -
67A ALA 6.2 0.9 - - - +
172A ALA 4.4 3.6 + - - -
174A PRO* 5.5 5.7 - - + +
241A TYR* 3.5 13.0 + - - +
242A GLY 4.3 1.3 - - - -
243A THR* 2.7 27.4 + - - +
265A PHE* 1.3 77.3 - - - +
267A GLN* 1.3 70.0 + - - +
----------------------------------------------------------
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