Contacts of the helix formed by residues 366 - 384 (chain E) in PDB entry 2CEA
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 VAL 366 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E PRO* 5.4 4.7 - - + -
203E PRO 3.4 16.8 - - - +
204E GLY* 3.3 20.2 - - - +
205E THR* 3.8 20.6 - - + -
330E PRO* 4.1 14.8 - - + -
331E PRO* 4.0 5.4 - - + -
364E GLY 3.9 8.7 - - - +
365E PHE* 1.3 78.4 - - - +
367E GLY* 1.3 70.8 + - - +
368E ALA 4.0 1.3 - - - +
369E ASP* 2.7 37.8 + - - +
370E LEU* 2.9 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E GLY 2.9 12.3 + - - -
205E THR* 4.5 2.2 - - - +
331E PRO* 4.7 2.0 - - - +
339E ILE* 4.1 21.0 - - - +
366E VAL* 1.3 68.2 - - - +
368E ALA* 1.3 53.7 + - - -
370E LEU* 2.7 25.1 + - - +
371E GLU* 3.0 12.0 + - - +
1604E ADP 3.3 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E GLY* 2.8 33.0 + - - -
366E VAL* 4.5 0.7 - - + -
367E GLY* 1.3 72.2 - - - +
369E ASP* 1.3 68.4 + - - +
371E GLU* 3.4 4.6 + - - +
372E ASN* 3.0 31.0 + - - +
1604E ADP 3.4 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 369 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E GLY 4.5 1.6 - - - +
365E PHE* 3.6 30.8 - - + -
366E VAL* 2.7 42.6 + - - +
368E ALA* 1.3 77.4 - - - +
370E LEU* 1.3 56.8 + - - +
372E ASN* 3.5 10.4 + - - +
373E LEU* 3.1 25.8 + - - +
401E VAL* 4.3 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E PRO* 4.8 0.9 - - + -
336E ARG* 3.8 34.5 - - + +
339E ILE* 3.7 37.2 - - + -
340E LEU* 4.2 23.4 - - + +
343E HIS* 5.2 0.9 - - - -
362E THR* 4.3 13.0 - - - +
365E PHE* 4.0 24.7 - - + -
366E VAL 2.9 15.5 + - - +
367E GLY 2.7 7.6 + - - +
369E ASP* 1.3 76.2 - - - +
371E GLU* 1.3 64.2 + - - +
373E LEU* 3.5 13.0 + - + +
374E VAL* 3.2 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E HIS* 3.8 32.9 + - + +
367E GLY 3.0 9.6 + - - +
368E ALA* 3.4 9.6 + - - +
370E LEU* 1.3 76.0 - - - +
372E ASN* 1.3 66.9 + - - +
374E VAL* 3.2 8.5 + - - +
375E ASN* 3.0 36.6 + - - +
1604E ADP 2.5 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 372 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E ALA* 3.0 18.5 + - - +
369E ASP* 3.7 12.2 - - - +
371E GLU* 1.3 81.6 - - - +
373E LEU* 1.3 52.7 + - - +
375E ASN* 2.7 17.2 + - - +
376E GLU* 2.6 38.5 + - + +
401E VAL* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E LEU* 4.0 14.1 - - + -
358E ILE* 3.9 28.7 - - + -
362E THR* 4.3 14.6 - - + -
365E PHE* 5.0 4.9 - - + -
369E ASP 3.1 12.1 + - - +
370E LEU* 3.5 13.9 - - + +
372E ASN* 1.3 76.4 - - - +
374E VAL* 1.3 58.6 + - - +
376E GLU* 3.2 2.8 + - - +
377E ALA* 2.8 29.1 + - - +
394E PHE* 4.0 10.3 - - + +
397E ALA* 3.5 14.9 - - + +
398E ILE* 3.4 41.3 - - + +
401E VAL* 3.6 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E LEU* 3.8 24.7 - - + +
343E HIS* 3.6 33.2 - - + +
344E THR* 4.1 15.9 - - + -
347E LYS* 4.1 20.0 - - + -
370E LEU 3.4 12.3 - - - +
371E GLU 3.2 9.5 + - - +
372E ASN 3.1 0.6 - - - -
373E LEU* 1.3 78.9 - - - +
375E ASN* 1.3 64.2 + - - +
377E ALA* 3.0 9.6 + - - +
378E ALA* 2.9 20.1 + - - +
389E ILE* 4.8 2.9 - - + +
394E PHE* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E LYS* 3.5 22.3 + - - -
371E GLU* 3.0 35.7 + - - +
372E ASN* 2.7 21.6 + - - +
374E VAL* 1.3 73.9 - - - +
376E GLU* 1.3 52.6 + - + +
378E ALA* 2.8 8.7 + - - +
379E LEU* 2.8 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E ASN* 2.6 23.3 + - + +
373E LEU* 3.6 6.7 - - - +
375E ASN* 1.3 73.3 - - + +
377E ALA* 1.3 61.5 + - - +
379E LEU* 3.7 24.0 - - - +
380E LEU* 3.2 28.8 + - - +
383E ARG* 4.4 2.3 + - - -
397E ALA* 4.1 15.0 - - + +
400E ARG* 2.7 47.7 + - + -
401E VAL* 4.2 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373E LEU 2.8 13.1 + - - +
374E VAL 3.1 10.5 - - - +
376E GLU* 1.3 76.6 - - - +
378E ALA* 1.3 64.5 + - - +
380E LEU* 3.4 4.4 + - - +
381E ALA* 3.3 20.4 + - - +
389E ILE* 3.8 22.4 - - + +
393E ASP* 3.8 10.3 - - - +
394E PHE* 3.8 25.8 - - + +
397E ALA* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E LYS* 4.3 15.7 - - + +
374E VAL 2.9 11.1 + - - +
375E ASN* 2.8 12.8 + - - +
377E ALA* 1.3 73.6 - - - +
379E LEU* 1.3 62.4 + - + +
381E ALA* 3.2 2.9 + - - +
382E ALA* 2.8 32.1 + - - +
389E ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375E ASN* 2.8 17.8 + - + +
376E GLU* 3.7 33.4 - - - +
378E ALA* 1.3 78.2 - - - +
380E LEU* 1.3 56.8 + - - +
382E ALA* 3.7 8.8 - - + +
383E ARG* 2.8 51.9 + - - +
400E ARG* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E GLU* 3.2 15.8 + - - +
377E ALA 3.7 7.0 - - - +
378E ALA 3.2 0.2 - - - -
379E LEU* 1.3 78.9 - - - +
381E ALA* 1.3 61.7 + - - +
383E ARG* 3.2 46.1 - - - +
384E GLU* 3.2 13.5 + - - +
386E ARG* 4.6 1.2 + - - -
393E ASP* 3.5 37.7 - - - +
396E GLU* 3.7 31.6 - - + +
397E ALA* 4.0 8.3 - - - +
400E ARG* 4.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E ALA 3.3 7.4 + - - +
378E ALA 3.2 7.2 + - - +
380E LEU* 1.3 75.3 - - - +
382E ALA* 1.3 68.2 + - - +
384E GLU* 3.0 12.0 + - - -
386E ARG* 3.0 37.0 + - - +
388E LYS 3.8 17.9 - - - +
389E ILE* 4.2 10.5 - - + -
393E ASP* 3.6 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E ALA 2.8 21.2 + - - +
379E LEU* 3.7 11.2 - - + +
381E ALA* 1.3 70.7 - - - +
383E ARG* 1.3 55.5 + - - +
385E GLY* 2.6 26.0 + - - +
386E ARG 4.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E GLU* 4.4 3.0 + - - -
379E LEU* 2.8 32.5 + - - +
380E LEU* 3.2 40.5 - - + +
382E ALA* 1.3 77.5 - - - +
384E GLU* 1.3 61.7 + - + +
385E GLY 3.5 1.2 + - - -
400E ARG* 4.1 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E LEU 3.2 8.2 + - - +
381E ALA 3.0 7.8 + - - +
383E ARG* 1.3 81.9 - - + +
385E GLY* 1.3 63.0 + - - +
386E ARG* 2.8 44.6 + - - +
----------------------------------------------------------
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