Contacts of the helix formed by residues 253 - 268 (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 SER 253 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASN* 5.9 2.2 + - - -
202E ARG* 4.5 4.9 - - - -
251E THR 3.4 1.0 - - - -
252E SER* 1.3 82.1 + - - +
254E HIS* 1.3 62.6 + - - +
255E ARG* 3.6 13.5 + - - +
256E ILE* 3.2 20.3 + - - +
257E THR* 2.9 28.8 + - - -
279E SER* 3.8 1.8 - - - -
280E PHE 3.7 8.5 - - - -
281E ASP* 3.3 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASN* 2.8 33.5 + - - -
80E VAL* 4.3 15.7 + - + +
81E PHE* 4.5 5.8 + - + -
253E SER* 1.3 73.9 - - - +
255E ARG* 1.3 88.3 + - - +
256E ILE 3.3 0.2 - - - -
257E THR* 3.5 3.7 - - - -
258E GLU* 3.0 40.0 + - - +
280E PHE 3.5 1.4 + - - -
281E ASP* 2.9 37.0 + - + -
283E LEU* 3.7 34.1 - - + +
285E TRP* 4.3 4.5 + - + -
286E MET* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ASP* 3.7 21.6 + - - -
78E GLU* 3.9 18.8 + - - +
79E ASN* 3.9 24.1 - - - +
80E VAL 4.7 0.6 - - - +
231E ASN* 2.7 43.4 + - - +
253E SER* 3.2 7.7 + - - +
254E HIS* 1.3 104.3 - - + +
256E ILE* 1.3 62.9 + - + +
257E THR 3.2 0.2 - - - -
258E GLU* 3.3 22.8 + - - +
259E GLY 3.2 7.3 + - - -
80F VAL* 5.7 3.2 - - - +
284F PRO* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ILE* 3.5 39.9 - - + +
191E VAL 3.6 3.4 - - - +
192E GLY* 3.4 24.7 - - - +
231E ASN* 2.9 23.0 - - - +
232E GLY* 4.9 0.8 - - - +
251E THR* 4.0 7.0 - - - -
252E SER* 2.9 30.1 - - - +
253E SER* 3.2 22.2 + - - +
255E ARG* 1.3 75.6 - - + +
257E THR* 1.3 61.2 + - - +
259E GLY 3.3 0.3 + - - -
260E ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E THR* 2.6 29.6 + - - +
253E SER 2.9 8.4 + - - -
254E HIS* 3.5 11.4 - - - -
255E ARG 3.2 0.4 - - - -
256E ILE* 1.3 77.6 - - - +
258E GLU* 1.3 56.9 + - - +
260E ALA* 3.3 1.4 + - - +
261E MET* 3.0 31.4 + - + +
277E ILE* 4.4 6.1 - - + -
279E SER* 2.7 21.6 + - - -
285E TRP* 3.9 20.0 - - + -
286E MET* 4.3 3.4 - - + -
293E LEU* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ASN* 4.4 4.8 + - - +
254E HIS* 3.0 31.8 + - - +
255E ARG* 3.4 31.7 + - - +
256E ILE 3.2 0.4 - - - -
257E THR* 1.3 74.1 - - - +
259E GLY* 1.3 63.6 + - - +
261E MET 3.5 0.5 + - - -
262E GLN* 3.1 32.8 + - - +
285E TRP* 4.3 16.8 + - + -
284F PRO* 3.5 35.7 - - + +
285F TRP* 4.9 1.9 + - - -
288F PHE* 3.6 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ASN* 3.3 24.8 + - - -
232E GLY 4.6 0.2 - - - -
233E ARG* 3.4 30.5 - - - +
255E ARG 3.2 8.5 + - - -
256E ILE 3.3 4.1 + - - -
258E GLU* 1.3 77.7 - - - +
260E ALA* 1.3 57.1 + - - +
262E GLN* 3.1 2.9 + - - -
263E ALA* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ILE* 5.2 1.8 - - + -
232E GLY 4.9 0.4 + - - +
236E ALA* 3.9 20.1 - - + +
240E LEU* 5.0 1.2 - - - +
249E LEU* 5.0 8.6 - - + +
251E THR* 3.9 20.4 - - + -
256E ILE 2.9 18.3 + - - +
257E THR 3.8 4.5 - - - +
258E GLU 3.3 0.2 - - - -
259E GLY* 1.3 74.1 - - - +
261E MET* 1.3 63.9 + - - +
263E ALA* 3.4 2.9 + - - +
264E LEU* 3.2 26.9 + - - +
277E ILE* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E THR* 3.0 29.4 + - + +
258E GLU 3.9 4.7 - - - +
259E GLY 3.3 0.2 - - - -
260E ALA* 1.3 74.6 - - - +
262E GLN* 1.3 65.1 + - - +
264E LEU* 3.4 14.6 + - + +
265E ASN* 3.6 15.9 + - - +
271E TYR* 3.9 44.0 - - + -
277E ILE* 3.9 11.9 - - + -
285E TRP* 4.7 2.7 - - + -
289E LEU* 4.4 20.0 - - + -
293E LEU* 4.7 1.6 - - - -
288F PHE* 4.0 48.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ASN* 2.8 26.1 + - - +
233E ARG* 3.6 22.8 - - - +
258E GLU* 3.1 24.2 + - - +
259E GLY* 3.1 9.0 + - - +
261E MET* 1.3 74.5 - - - +
263E ALA* 1.3 66.4 + - - +
265E ASN* 3.5 8.3 + - - +
266E VAL* 3.0 30.4 + - + +
284F PRO* 4.9 7.1 - - - +
288F PHE* 4.2 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ARG* 3.8 3.5 - - - +
236E ALA* 3.5 29.6 - - + -
237E ILE* 3.5 32.1 - - + +
240E LEU* 4.5 5.2 - - + -
259E GLY 2.9 9.5 + - - +
260E ALA 3.7 4.7 - - - +
261E MET 3.2 0.2 - - - -
262E GLN* 1.3 75.6 - - - +
264E LEU* 1.3 67.0 + - - +
266E VAL* 2.9 4.7 + - - +
267E LEU* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E LEU* 3.9 16.2 - - + -
249E LEU* 5.7 0.2 - - + -
260E ALA 3.2 17.2 + - - +
261E MET* 3.8 13.7 - - + +
262E GLN 3.3 0.8 - - - -
263E ALA* 1.3 77.0 - - - +
265E ASN* 1.3 56.3 - - + +
267E LEU* 3.2 2.2 + - - -
268E GLY 2.8 6.9 + - - -
269E LEU* 2.5 55.8 + - + +
270E ARG 5.0 0.2 - - - +
271E TYR* 3.5 37.5 - - + +
275E VAL* 3.5 36.3 - - + -
277E ILE* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET 3.6 11.2 + - - +
262E GLN* 3.5 8.3 + - - +
263E ALA 3.1 0.6 - - - -
264E LEU* 1.3 77.0 - - + +
266E VAL* 1.3 67.8 + - - +
267E LEU 3.3 0.2 - - - -
268E GLY* 3.8 10.7 + - - +
269E LEU 4.5 5.4 - - - +
287F ALA 4.9 8.0 - - - +
288F PHE* 5.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ARG* 3.5 25.4 - - - +
237E ILE* 3.7 22.2 - - + -
262E GLN* 3.0 20.9 + - + +
263E ALA 2.9 9.1 + - - +
265E ASN* 1.3 81.5 - - - +
267E LEU* 1.3 65.8 + - + +
268E GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E ILE* 3.9 24.5 - - + +
240E LEU* 3.7 30.7 - - + +
241E THR* 3.2 37.2 - - + -
263E ALA 2.8 16.3 + - - +
264E LEU 3.7 3.6 - - - +
266E VAL* 1.3 81.9 - - + +
268E GLY* 1.3 61.8 + - - +
269E LEU* 3.6 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E LEU 2.8 3.5 + - - -
265E ASN* 3.8 10.1 + - - -
266E VAL 3.4 3.6 - - - -
267E LEU* 1.3 80.0 - - - +
269E LEU* 1.3 64.7 + - - +
270E ARG* 4.7 5.0 - - - +
274E ASP* 4.6 2.4 - - - +
----------------------------------------------------------
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