Contacts of the helix formed by residues 253 - 268 (chain A) 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 SER 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 5.8 2.8 + - - -
202A ARG* 4.6 4.5 - - - -
251A THR* 3.4 2.0 + - - -
252A SER* 1.3 78.8 + - - +
254A HIS* 1.3 56.6 + - - +
255A ARG* 3.6 8.2 + - - +
256A ILE* 3.2 27.0 + - - +
257A THR* 2.8 34.3 + - - -
279A SER* 3.7 1.6 - - - -
280A PHE* 3.7 10.3 - - - -
281A ASP* 3.3 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 2.8 29.5 + - - -
80A VAL* 4.3 15.3 + - + +
81A PHE* 4.4 5.6 + - + -
253A SER* 1.3 76.6 - - - +
255A ARG* 1.3 92.5 + - - +
257A THR* 3.3 3.3 + - - -
258A GLU* 2.9 39.4 + - - +
280A PHE 3.4 1.6 + - - -
281A ASP* 3.0 34.2 + - + -
283A LEU* 3.8 27.5 - - + +
285A TRP* 4.4 3.5 + - + -
286A MET* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 3.7 12.1 + - - -
78A GLU* 3.9 10.7 + - - +
79A ASN* 3.7 42.7 - - - +
80A VAL* 4.6 0.8 - - - +
231A ASN* 2.7 42.7 + - - +
253A SER* 3.2 7.0 + - - +
254A HIS* 1.3 107.4 - - + +
256A ILE* 1.3 63.5 + - + +
258A GLU* 3.4 24.5 + - - +
259A GLY 3.3 6.9 + - - -
80B VAL* 5.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ILE* 3.5 40.4 - - + +
191A VAL 3.5 1.6 - - - +
192A GLY* 3.2 28.9 - - - +
231A ASN* 3.0 21.8 - - - +
232A GLY* 4.9 0.4 - - - +
251A THR* 3.9 9.4 - - + -
252A SER* 3.0 27.4 - - - +
253A SER* 3.2 20.7 + - - +
255A ARG* 1.3 76.7 - - + +
257A THR* 1.3 59.9 + - - +
259A GLY 3.0 2.1 + - - -
260A ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 2.6 19.4 + - - -
253A SER 2.8 9.4 + - - -
254A HIS* 3.3 11.0 + - - -
256A ILE* 1.3 76.5 - - - +
258A GLU* 1.3 62.3 + - - +
260A ALA* 3.4 1.6 + - - +
261A MET* 2.9 26.0 + - + +
277A ILE* 4.2 12.6 - - + -
279A SER* 2.5 28.9 + - - +
285A TRP* 4.0 14.1 - - + -
286A MET* 4.4 4.3 - - + -
293A LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 4.2 5.2 + - - +
254A HIS* 2.9 30.3 + - - +
255A ARG* 3.4 35.7 + - - +
256A ILE 3.2 0.4 - - - -
257A THR* 1.3 75.1 - - - +
259A GLY* 1.3 57.2 + - - +
261A MET* 3.1 4.7 + - - +
262A GLN* 2.8 37.4 + - - +
285A TRP* 4.3 19.4 + - + -
283B LEU* 6.1 0.2 - - - +
284B PRO* 3.8 33.0 - - + +
285B TRP* 4.8 3.8 + - - +
288B PHE* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 3.6 17.6 + - - -
233A ARG* 3.3 23.0 - - - +
255A ARG 3.3 5.1 + - - -
256A ILE 3.0 7.1 + - - -
258A GLU* 1.3 77.5 - - - +
260A ALA* 1.3 51.0 + - - +
262A GLN* 3.2 16.2 + - - -
263A ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ILE* 5.0 2.0 - - + -
232A GLY 4.6 1.2 + - - -
236A ALA* 3.9 22.0 - - + +
240A LEU* 5.1 0.3 - - - +
249A LEU* 4.7 10.1 - - + -
251A THR* 3.9 23.3 - - + -
256A ILE* 2.9 19.3 + - + +
257A THR 3.9 2.7 - - - +
259A GLY* 1.3 69.7 - - - +
261A MET* 1.3 65.1 + - - +
263A ALA* 3.3 2.6 + - - +
264A LEU* 3.0 28.6 + - + +
277A ILE* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 2.9 29.1 + - + +
258A GLU 3.5 7.2 - - - +
260A ALA* 1.3 71.4 - - - +
262A GLN* 1.3 63.8 + - - +
264A LEU* 3.3 18.2 + - + +
265A ASN* 3.6 14.2 + - - +
271A TYR* 3.8 35.9 - - + -
277A ILE* 3.8 23.3 - - + -
285A TRP* 4.6 4.7 - - + -
289A LEU* 4.3 22.4 - - + -
293A LEU* 4.7 1.8 - - - -
288B PHE* 3.7 46.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 2.8 29.1 + - - +
233A ARG* 3.5 24.3 - - - +
258A GLU* 2.8 23.4 + - - +
259A GLY* 3.2 10.5 + - - +
261A MET* 1.3 74.0 - - - +
263A ALA* 1.3 63.7 + - - +
265A ASN* 3.5 7.3 + - - +
266A VAL* 3.1 24.6 + - + +
284B PRO* 4.7 9.0 - - - +
288B PHE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.7 4.2 - - - +
236A ALA* 3.5 31.0 - - + -
237A ILE* 3.5 32.8 - - + +
240A LEU* 4.6 4.3 - - + -
259A GLY 2.8 14.4 + - - +
260A ALA 3.3 2.9 + - - +
262A GLN* 1.3 70.9 - - - +
264A LEU* 1.3 66.9 + - - +
266A VAL* 3.0 3.9 + - - +
267A LEU* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.8 24.7 - - + -
260A ALA* 3.0 19.5 + - + +
261A MET* 3.6 21.5 - - + +
262A GLN 3.3 0.4 - - - -
263A ALA* 1.3 77.2 - - - +
265A ASN* 1.3 60.0 + - + +
267A LEU* 3.1 3.5 + - - +
268A GLY 2.8 7.8 + - - -
269A LEU* 2.7 53.9 + - + +
270A ARG 5.1 0.2 - - - +
271A TYR* 3.7 36.1 - - + +
275A VAL* 3.8 21.3 - - + -
277A ILE* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A MET 3.6 8.3 + - - +
262A GLN* 3.5 9.7 + - - +
263A ALA 3.3 0.2 - - - -
264A LEU* 1.3 76.3 - - + +
266A VAL* 1.3 69.0 + - - +
268A GLY* 3.5 12.2 + - - +
269A LEU 4.5 5.6 - - - +
287B ALA 4.8 9.0 - - - +
288B PHE* 5.0 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.4 26.0 - - - +
237A ILE* 3.6 24.5 - - + -
262A GLN* 3.1 19.9 + - + +
263A ALA 3.0 8.6 + - - +
265A ASN* 1.3 79.6 - - - +
267A LEU* 1.3 66.7 + - + +
268A GLY 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.8 26.7 - - + +
240A LEU* 3.7 30.5 - - + +
241A THR* 3.2 37.5 - - + -
263A ALA 2.9 17.5 + - - +
264A LEU 3.6 3.8 - - - +
266A VAL* 1.3 81.7 - - + +
268A GLY* 1.3 62.2 + - - +
269A LEU* 3.6 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 2.8 3.9 + - - -
265A ASN* 3.5 10.1 + - - -
266A VAL 3.3 4.6 + - - -
267A LEU* 1.3 78.5 - - - +
269A LEU* 1.3 66.6 + - - +
270A ARG* 4.2 4.7 + - - +
274A ASP* 4.5 2.6 - - - +
----------------------------------------------------------
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