Contacts of the helix formed by residues 366 - 384 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO* 5.8 2.9 - - + -
203D PRO 3.9 13.9 - - - +
204D GLY* 3.5 17.0 - - - +
205D THR* 3.9 24.5 - - + +
330D PRO* 4.3 9.2 - - + -
331D PRO* 4.0 14.1 - - + -
364D GLY 4.3 5.8 - - - +
365D PHE* 1.3 78.0 - - - +
367D GLY* 1.3 67.9 + - - +
368D ALA* 4.5 1.6 - - + -
369D ASP* 2.9 28.9 + - - +
370D LEU* 2.9 24.4 + - - +
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Residues in contact with GLY 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLY 3.2 4.0 + - - -
205D THR* 4.8 2.4 + - - +
331D PRO* 4.5 2.0 - - - +
339D ILE* 4.1 21.1 - - - +
366D VAL* 1.3 73.2 - - - +
368D ALA* 1.3 64.9 + - - +
370D LEU* 3.0 2.1 + - - +
371D GLU* 2.8 24.8 + - - +
1608D ADP 3.4 35.5 + - - -
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLY* 3.0 30.8 + - - +
366D VAL* 3.3 3.8 - - + -
367D GLY* 1.3 74.7 - - - +
369D ASP* 1.3 64.3 + - - +
371D GLU* 3.4 3.6 + - - +
372D ASN* 3.1 22.7 + - - +
1608D ADP 3.1 23.2 + - - +
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Residues in contact with ASP 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D GLY 3.9 3.8 - - - +
365D PHE* 3.5 27.6 - - + -
366D VAL* 2.9 38.5 + - - +
368D ALA* 1.3 81.6 - - - +
370D LEU* 1.3 58.2 + - - +
372D ASN* 3.2 8.2 + - - +
373D LEU* 2.9 27.0 + - - +
401D VAL* 5.0 2.0 - - - +
408D LYS 3.9 6.2 - - - +
409D SER* 3.2 31.3 - - - +
410D LEU 5.0 1.6 + - - -
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Residues in contact with LEU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ARG* 3.6 40.2 - - + +
339D ILE* 3.7 37.0 - - + -
340D LEU* 4.4 15.4 - - + +
343D HIS* 5.1 0.2 - - - -
362D THR* 4.1 16.4 - - - +
365D PHE* 3.7 28.3 - - + +
366D VAL 2.9 17.6 + - - +
367D GLY 3.8 1.1 - - - +
369D ASP* 1.3 75.3 - - - +
371D GLU* 1.3 62.7 + - - +
373D LEU* 3.1 17.0 + - + +
374D VAL* 3.0 26.9 + - - +
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Residues in contact with GLU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D HIS* 4.0 32.5 + - + +
367D GLY 2.8 18.8 + - - +
368D ALA* 3.8 5.3 - - - +
370D LEU* 1.3 72.6 - - - +
372D ASN* 1.3 64.2 + - + +
374D VAL* 3.3 6.0 + - - +
375D ASN* 3.1 20.5 + - + +
1608D ADP 2.9 35.6 + - - +
192E ARG* 3.5 32.5 + - - +
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Residues in contact with ASN 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D ALA 3.1 11.4 + - - +
369D ASP* 3.5 9.9 - - - +
371D GLU* 1.3 78.8 - - + +
373D LEU* 1.3 61.5 + - - +
375D ASN* 3.2 7.8 + - - +
376D GLU* 2.8 50.3 + - - +
401D VAL* 3.0 30.7 - - - +
408D LYS* 6.2 1.6 - - - +
192E ARG* 4.7 11.1 + - - +
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D LEU* 4.1 15.0 - - + -
358D ILE* 3.7 30.3 - - + -
362D THR* 4.5 4.3 - - + -
365D PHE* 4.8 5.6 - - + -
369D ASP 2.9 13.4 + - - +
370D LEU* 3.3 19.7 - - + +
372D ASN* 1.3 78.6 - - - +
374D VAL* 1.3 62.1 + - - +
376D GLU* 3.2 2.4 + - - +
377D ALA* 3.0 19.6 + - - +
394D PHE* 4.1 7.9 - - + +
397D ALA* 3.4 15.5 - - + +
398D ILE* 3.2 47.3 - - + +
401D VAL* 4.0 14.5 - - + +
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Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D LEU* 3.5 26.9 - - + -
343D HIS* 3.5 36.3 - - + +
344D THR* 4.1 13.9 - - - +
347D LYS* 4.4 17.3 - - + -
370D LEU 3.0 14.7 + - - +
371D GLU 3.6 7.6 - - - +
372D ASN 3.2 0.2 - - - -
373D LEU* 1.3 76.6 - - - +
375D ASN* 1.3 57.4 + - + +
377D ALA* 3.3 3.6 + - - +
378D ALA* 3.0 25.1 + - - +
389D ILE* 4.7 3.0 - - + +
394D PHE* 4.2 18.6 - - + -
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Residues in contact with ASN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D LYS* 5.0 1.9 - - - +
371D GLU 3.1 16.1 + - - +
372D ASN* 3.2 10.0 + - - +
374D VAL* 1.3 76.9 - - - +
376D GLU* 1.3 61.5 + - - +
378D ALA* 3.4 3.6 + - - +
379D LEU* 3.0 41.7 + - - +
190E GLY 3.6 9.4 - - - +
191E ALA* 3.6 1.2 - - - -
192E ARG* 2.8 76.7 + - - +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D ASN* 2.8 36.1 + - - +
373D LEU 3.6 4.0 - - - +
375D ASN* 1.3 72.8 + - - +
377D ALA* 1.3 62.8 + - - +
379D LEU* 3.4 24.5 + - - +
380D LEU* 3.1 27.5 + - - +
383D ARG* 4.8 2.6 + - - -
397D ALA* 4.1 15.5 - - + +
400D ARG* 3.7 26.4 + - + -
401D VAL* 3.7 22.2 - - + +
175E GLU* 5.1 1.7 - - - +
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Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D LEU 3.0 13.4 + - - +
374D VAL 3.5 8.5 - - - +
376D GLU* 1.3 74.3 - - - +
378D ALA* 1.3 65.1 + - - +
380D LEU* 3.2 5.0 + - - +
381D ALA* 3.2 18.4 + - - +
389D ILE* 3.8 18.8 - - + +
393D ASP* 3.8 13.0 - - - +
394D PHE* 3.9 34.5 - - + +
397D ALA* 3.9 6.0 - - + +
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Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D LYS* 4.4 6.5 - - - -
374D VAL 3.0 12.2 + - - +
375D ASN 3.7 8.7 - - - +
376D GLU 3.4 0.2 - - - -
377D ALA* 1.3 74.8 - - - +
379D LEU* 1.3 52.3 + - - +
381D ALA* 3.0 5.2 + - - +
382D ALA* 2.8 31.7 + - - +
389D ILE* 3.7 26.8 - - + +
189E ILE* 3.5 16.3 - - + +
191E ALA* 3.8 23.1 - - + -
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Residues in contact with LEU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D ASN* 3.0 38.6 + - - +
376D GLU* 3.5 30.7 - - - +
377D ALA 3.2 0.4 - - - -
378D ALA* 1.3 77.9 - - - +
380D LEU* 1.3 56.3 + - - +
382D ALA* 3.2 1.8 + - - +
383D ARG* 2.8 35.2 + - - +
175E GLU* 3.2 26.2 - - - +
186E PHE* 3.9 10.0 - - + -
191E ALA* 3.8 20.2 - - + -
192E ARG 4.1 9.0 - - - +
193E MET* 3.9 26.2 - - - -
194E PRO* 6.4 0.4 - - + -
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D GLU 3.1 20.0 + - - +
377D ALA 3.6 6.1 - - - +
378D ALA 3.2 0.4 - - - -
379D LEU* 1.3 75.5 - - - +
381D ALA* 1.3 64.6 + - - +
383D ARG* 2.8 43.5 + - - +
384D GLU* 3.2 25.5 + - - +
386D ARG* 4.3 2.9 - - - +
393D ASP* 3.6 34.3 - - - +
396D GLU* 3.8 28.7 - - + +
397D ALA* 4.1 5.6 - - - +
400D ARG* 4.1 23.1 - - - +
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ALA 3.2 6.7 + - - +
378D ALA 3.0 8.6 + - - +
380D LEU* 1.3 79.7 - - - +
382D ALA* 1.3 60.1 + - - +
384D GLU 3.3 2.9 + - - -
385D GLY 3.2 2.6 + - - -
386D ARG* 3.0 50.2 + - - +
388D LYS 4.3 2.9 - - - +
389D ILE* 4.2 12.1 - - + -
393D ASP* 3.5 16.7 + - - +
189E ILE* 3.6 15.0 - - + -
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Residues in contact with ALA 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D ALA 2.8 18.8 + - - +
379D LEU 3.2 3.6 + - - +
381D ALA* 1.3 69.2 - - - +
383D ARG* 1.3 58.8 + - - +
384D GLU 3.0 1.3 - - - -
385D GLY* 2.7 26.0 + - - +
386D ARG 4.8 1.1 - - - -
178E GLU* 5.6 0.5 - - - +
185E LYS* 3.9 21.9 - - - +
186E PHE* 3.7 43.5 - - + -
189E ILE* 3.7 7.8 - - + +
191E ALA* 4.2 3.1 - - + -
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Residues in contact with ARG 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D GLU* 4.8 1.8 + - - -
379D LEU* 2.8 15.2 + - - +
380D LEU* 2.8 60.9 - - - +
382D ALA* 1.3 72.8 - - - +
384D GLU* 1.3 62.7 + - + +
385D GLY 3.6 0.5 + - - -
400D ARG* 3.9 23.4 - - - +
174E LYS* 5.8 1.3 - - - -
175E GLU* 2.2 55.8 + - + +
178E GLU* 4.1 33.7 - - + +
186E PHE* 4.4 5.3 - - - -
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Residues in contact with GLU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D LEU 3.2 14.5 + - - +
381D ALA 3.3 1.8 + - - +
382D ALA 3.0 0.8 - - - -
383D ARG* 1.3 79.9 - - + +
385D GLY* 1.3 63.8 + - - +
386D ARG* 2.8 49.7 + - + +
392D LYS* 5.2 7.1 + - - -
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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
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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) + - + + + + + -
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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