Contacts of the strand formed by residues 276 - 280 (chain E) in PDB entry 3EGC
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 GLU 276 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E LEU* 4.2 10.5 - - + +
182E ARG* 2.7 44.9 + - - -
184E HIS* 2.8 34.7 + - + +
247E THR 2.8 9.5 + - - +
248E ALA* 3.2 3.0 - - + -
249E LEU 2.8 26.5 + - - -
271E TYR* 4.7 3.1 - - + +
272E GLY* 3.6 25.0 - - - +
275E VAL* 1.3 73.9 - - - +
277E ILE* 1.3 65.1 + - - +
291E PRO* 4.5 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E LEU* 5.1 1.8 - - - -
249E LEU* 3.4 15.5 - - + +
251E THR* 3.6 28.5 - - + +
257E THR* 4.4 4.5 - - + -
260E ALA* 4.4 18.2 - - + -
261E MET* 3.9 18.4 - - + -
264E LEU* 4.2 13.2 - - + -
271E TYR* 3.9 27.6 + - + -
275E VAL* 4.4 9.0 - - + -
276E GLU* 1.3 82.7 - - - +
278E VAL* 1.3 67.1 + - - +
293E LEU* 3.3 28.4 - - + +
294E PRO* 3.3 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ALA* 3.8 41.5 - - + +
178E TYR* 4.2 4.9 - - + -
179E LEU* 3.4 36.1 - - + -
249E LEU 3.1 6.2 + - - +
250E LEU* 3.5 13.9 - - + +
251E THR* 2.9 25.1 + - - +
277E ILE* 1.3 77.5 - - - +
279E SER* 1.3 62.4 + - - +
294E PRO* 3.2 30.5 - - + +
330E PHE* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E LEU* 5.4 0.2 - - - -
251E THR* 3.2 9.0 + - - -
253E SER 3.7 3.6 + - - -
257E THR* 2.7 30.0 + - - -
278E VAL* 1.3 73.9 - - - +
280E PHE* 1.3 76.0 + - - +
286E MET* 3.5 8.0 - - - +
293E LEU* 3.5 19.0 - - - +
294E PRO 2.9 7.3 + - - -
295E VAL* 3.0 9.7 - - - -
296E VAL* 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E ASN* 3.7 17.5 - - - -
171E GLY* 4.2 0.7 - - - -
172E ALA* 3.7 32.1 - - + -
202E ARG* 3.5 55.0 - - + +
250E LEU* 4.5 7.6 - - + -
251E THR 3.4 13.8 + - - -
252E SER* 3.3 23.1 - - - +
253E SER* 4.1 1.5 - - - +
254E HIS* 3.5 3.5 + - - -
279E SER* 1.3 87.3 + - - +
281E ASP* 1.3 79.6 + - - +
296E VAL* 3.5 40.6 - - + -
298E GLN* 4.3 9.4 - - + -
328E THR* 5.0 4.0 - - + -
----------------------------------------------------------
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