Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 1UEC
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 TRP 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 6.4 0.2 - - - -
237A TYR* 3.3 36.1 - + - -
244A GLU* 4.1 7.6 - - + -
259A LEU* 3.6 10.6 - - - +
261A ASP* 3.1 33.4 + - - +
262A GLY* 1.3 79.0 - - - +
264A TRP* 1.3 64.4 + - - +
274A TYR* 3.4 26.5 - - + -
275A PHE* 3.6 24.0 - - - -
276A PRO* 3.4 34.3 - - + -
298A ALA* 4.2 8.3 - - + -
299A PRO* 2.8 33.4 + - + +
300A PRO* 4.8 0.9 - - + -
301A ARG* 3.3 46.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.8 34.3 - + - -
255A VAL* 3.6 22.7 - - + -
257A HIS 3.4 6.5 - - - +
258A LYS* 3.4 37.9 + - + -
259A LEU 3.2 36.5 + - - -
262A GLY* 4.3 2.1 - - - -
263A TRP* 1.3 74.1 - - - +
265A VAL* 1.3 67.0 + - - +
266A ILE* 3.6 7.6 + - + +
273A GLY 3.5 0.3 - - - +
274A TYR* 3.2 4.7 - - - -
275A PHE 2.9 35.4 + - - +
277A SER* 3.2 37.5 + - - -
280A LEU* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 3.8 1.7 - - - +
256A ILE* 2.9 50.0 + - + -
257A HIS* 3.0 16.4 + - + +
259A LEU* 4.0 4.0 - - + -
264A TRP* 1.3 72.9 - - - +
266A ILE* 1.3 64.3 + - - +
272A THR* 4.1 8.3 - - - -
273A GLY 3.4 6.5 - - - +
274A TYR* 3.6 26.0 - - + -
321A GLN* 3.9 20.6 - - - +
324A TYR* 3.7 35.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
245A VAL* 3.4 36.3 - - + -
247A LEU* 5.4 0.4 - - + -
253A VAL* 4.4 16.8 - - + -
254A GLU 3.2 9.6 - - - +
255A VAL* 4.0 23.3 - - + -
256A ILE* 4.6 3.8 - - - -
264A TRP* 4.0 9.6 - - + +
265A VAL* 1.3 79.9 - - - +
267A ARG* 1.3 72.8 + - - +
268A LYS* 4.2 6.3 - - + +
271A VAL 5.1 0.7 - - - +
272A THR* 3.1 7.1 - - - -
273A GLY 2.8 37.9 + - - +
275A PHE* 4.1 14.8 - - + -
280A LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR 3.5 12.1 + - - -
227A ALA 3.4 15.8 + - - -
228A GLY* 4.0 2.0 - - - -
253A VAL* 3.8 4.0 - - - +
254A GLU* 2.3 88.6 + - + +
256A ILE* 4.4 9.2 - - + +
266A ILE* 1.3 75.6 - - - +
268A LYS* 1.3 66.2 + - - +
270A ASP* 4.6 19.3 - - - +
271A VAL 3.4 11.0 - - - +
272A THR* 4.3 4.5 - - + -
328A SER* 2.9 30.7 + - - +
329A VAL* 6.0 1.3 - - - +
332A LEU* 3.7 25.9 - - - +
333A GLN 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 4.7 8.5 - - + -
246A SER 5.4 0.6 + - - -
247A LEU* 4.0 10.5 - - + +
251A GLU* 2.9 33.4 + - - -
252A ALA 3.2 28.3 - - - +
253A VAL* 3.8 9.4 - - + -
266A ILE* 4.2 15.2 - - + +
267A ARG* 1.3 75.9 - - - +
269A ASP* 1.3 78.8 + - + +
270A ASP 3.4 0.9 - - - -
271A VAL* 3.0 25.8 + - + +
----------------------------------------------------------
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