Contacts of the strand formed by residues 263 - 270 (chain A) in PDB entry 2W77
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 GLY 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.7 27.8 - - - +
210A ARG* 4.6 6.2 - - - -
212A PHE* 4.1 6.8 - - - +
214A ILE* 5.0 2.7 - - - -
250A LYS* 3.3 4.2 - - - +
251A GLY* 2.7 40.2 + - - -
262A LEU* 1.3 74.2 - - - +
264A ALA* 1.3 61.0 + - - +
638A ILE* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 4.1 7.2 - - + -
214A ILE* 3.6 39.7 - - + +
216A ASN* 3.2 20.7 + - - +
248A VAL* 4.4 10.8 - - + -
249A LEU 2.9 14.4 - - - +
250A LYS* 4.2 4.0 - - + +
251A GLY 4.0 1.7 + - - +
253A THR* 4.3 5.1 + - - -
261A SER 4.8 0.2 + - - -
262A LEU 3.4 4.8 + - - +
263A GLY* 1.3 78.4 - - - +
265A THR* 1.3 63.9 + - - +
266A ILE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 5.5 2.6 - - + +
216A ASN* 3.8 11.6 - - + +
218A GLN* 3.7 39.5 - - + +
247A GLU 3.8 0.7 - - - +
248A VAL* 3.3 9.0 - - - +
249A LEU* 2.8 37.1 + - - -
253A THR* 2.7 33.3 + - - -
257A THR* 2.9 14.7 + - - +
264A ALA* 1.3 73.0 + - - +
266A ILE* 1.3 71.7 + - - +
267A ASN* 4.4 3.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
185A ILE* 4.2 10.1 - - + -
189A MET* 3.6 27.6 - - + -
207A TYR* 3.8 17.5 - - + -
214A ILE* 3.7 30.3 - - + -
216A ASN 3.2 10.4 + - - +
217A PHE* 3.4 16.0 - - + -
218A GLN 2.7 28.2 + - - +
246A VAL* 3.9 19.3 - - + -
247A GLU 3.9 1.8 - - - -
248A VAL* 4.4 11.2 - - + -
264A ALA* 5.4 0.4 - - + -
265A THR* 1.3 80.3 - - - +
267A ASN* 1.3 58.6 + - - +
268A LEU* 3.6 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 5.8 1.6 - - - +
153A ALA 5.8 0.4 - - - -
154A THR* 3.8 16.2 - - + +
218A GLN* 3.5 27.5 + - - +
220A ASP 3.9 0.2 + - - -
221A GLY* 3.0 30.6 + - - +
246A VAL* 3.6 1.2 - - - -
247A GLU* 2.7 78.7 + - + +
265A THR* 4.6 1.6 - - + -
266A ILE* 1.3 73.0 - - - +
268A LEU* 1.3 66.4 + - - +
269A ILE* 3.5 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 4.4 9.4 - - + -
217A PHE* 4.8 5.6 - - + -
218A GLN 3.0 20.8 + - - +
219A TYR* 3.3 22.7 - - + +
220A ASP 2.7 32.2 + - - -
238A SER* 4.5 7.4 - - - +
240A MET* 4.0 17.5 - - + -
243A TYR* 3.8 41.6 - - + -
245A ARG 3.9 4.0 - - - -
246A VAL* 4.4 10.8 - - + -
266A ILE* 3.6 29.6 - - + +
267A ASN* 1.3 74.5 + - - +
269A ILE* 1.3 56.6 - - - +
270A ARG 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.4 23.1 - - + +
220A ASP* 3.5 14.1 - - - +
243A TYR* 3.1 13.4 - - - +
244A ASP* 3.1 20.8 + - + -
245A ARG* 3.3 49.3 + - + +
247A GLU* 3.6 24.5 - - - +
267A ASN* 3.5 31.4 - - - +
268A LEU* 1.3 78.0 - - - +
270A ARG* 1.3 70.2 + - - +
272A LYS* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 6.0 0.2 - - - +
219A TYR* 3.9 32.2 + - + +
220A ASP* 2.6 42.8 + - - +
222A ILE* 6.1 0.6 - - - +
242A ILE* 3.6 10.1 - - + +
243A TYR* 3.8 22.6 + - + -
244A ASP* 4.2 3.6 - - - +
268A LEU 3.9 0.8 + - - +
269A ILE* 1.3 83.0 - - - +
271A LYS* 1.3 63.7 + - - +
272A LYS* 3.5 8.7 + - - +
333A TYR* 3.4 39.5 - - + +
335A ILE* 5.9 0.9 - - + -
351A ASP* 2.6 34.5 + - - -
397A THR* 4.1 9.9 + - - +
399A PHE* 3.6 28.0 - - - -
417A ASP* 4.8 9.5 + - - -
----------------------------------------------------------
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