Contacts of the strand formed by residues 252 - 256 (chain A) in PDB entry 1EFP
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 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG 3.2 2.0 + - - -
195A ARG* 3.3 23.2 - - + +
196A VAL 2.9 26.6 + - - -
219A LEU* 4.6 23.1 - - + -
250A PRO* 3.3 6.1 - - - +
251A GLU* 1.3 82.4 - - + +
253A TYR* 1.3 69.8 + - - +
254A VAL* 3.9 20.6 - - + -
273A VAL* 3.6 17.7 - - + +
275A VAL* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.4 18.8 - - + -
198A SER* 2.9 31.2 + - - -
241A VAL* 3.4 8.5 - - + +
248A VAL* 3.8 20.9 - - + -
250A PRO* 4.3 1.6 - - + -
252A LEU* 1.3 74.8 - - - +
254A VAL* 1.3 64.7 + - - +
255A ALA* 3.9 16.6 - - + -
264A HIS* 2.9 25.1 + - - -
268A MET* 3.4 51.6 - - + -
271A SER* 3.7 25.1 - - - +
273A VAL 2.9 9.5 + - - +
274A ILE* 3.4 5.8 - - + +
275A VAL 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL 2.9 13.5 + - - +
197A VAL* 3.6 19.4 - - + +
198A SER* 3.0 28.1 + - - +
215A LEU* 4.8 11.0 - - + -
219A LEU* 4.8 7.2 - - + -
252A LEU* 3.9 27.1 - - + -
253A TYR* 1.3 74.3 - - - +
255A ALA* 1.3 59.5 + - - +
256A VAL* 3.7 16.1 + - + -
275A VAL* 3.3 22.9 - - + +
277A ILE* 4.4 12.6 - - + -
304A LEU* 5.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER 4.0 4.0 - - - -
253A TYR* 3.7 21.6 + - + -
254A VAL* 1.3 69.9 - - - +
256A VAL* 1.3 61.6 + - - +
257A GLY 4.0 0.5 + - - -
258A ILE* 4.4 22.8 + - + +
264A HIS* 5.4 0.2 - - - +
268A MET* 4.6 1.3 - - + -
274A ILE* 5.3 0.9 - - + -
275A VAL 2.7 12.9 + - - +
276A ALA* 3.3 4.3 - - - +
277A ILE* 3.1 22.6 + - - +
278A ASN* 5.7 0.5 - - - +
285A ILE* 4.3 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 4.3 5.4 - - + -
198A SER 3.3 14.7 + - - +
199A GLY* 3.8 1.7 - - - -
200A GLY 3.4 15.9 + - - -
203A LEU* 4.5 2.4 - - + +
212A ILE* 3.3 35.2 - - + -
215A LEU* 5.3 0.9 - - + -
254A VAL* 4.2 18.6 - - + +
255A ALA* 1.3 71.7 - - - +
257A GLY* 1.3 66.1 + - - +
258A ILE* 3.4 0.7 + - - +
277A ILE* 3.4 19.5 - - + -
297A LEU* 3.7 32.8 - - + -
301A VAL* 3.9 10.8 - - + -
----------------------------------------------------------
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