Contacts of the helix formed by residues 366 - 384 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO* 5.3 4.3 - - + -
203B PRO 3.7 15.7 - - - +
204B GLY* 3.3 19.7 - - - +
205B THR* 3.8 22.4 - - + -
330B PRO* 4.5 13.2 - - + -
331B PRO* 4.0 4.9 - - - -
364B GLY 4.1 7.9 - - - +
365B PHE* 1.3 78.0 - - - +
367B GLY* 1.3 65.8 + - - +
368B ALA* 4.3 1.3 - - + -
369B ASP* 2.8 39.2 + - - +
370B LEU* 2.9 15.5 + - - +
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Residues in contact with GLY 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY 3.1 3.4 + - - -
205B THR* 4.6 2.2 - - - +
331B PRO* 4.6 2.0 - - - +
339B ILE* 4.3 21.0 - - - +
366B VAL* 1.3 73.1 - - - +
368B ALA* 1.3 63.6 + - - +
370B LEU* 3.0 3.2 + - - +
371B GLU* 2.9 23.9 + - - +
1607B ADP 3.4 34.7 + - - -
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY* 2.9 33.8 + - - -
366B VAL* 4.3 2.9 - - + -
367B GLY* 1.3 70.9 - - - +
369B ASP* 1.3 63.2 + - - +
371B GLU* 3.4 3.2 + - - +
372B ASN* 3.1 23.2 + - - +
1607B ADP 3.3 23.8 + - - +
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLY 4.4 2.4 - - - +
365B PHE* 3.7 27.0 - - + -
366B VAL* 2.8 39.7 + - - +
368B ALA* 1.3 79.3 - - - +
370B LEU* 1.3 57.3 + - - +
372B ASN* 3.3 6.9 + - - +
373B LEU* 2.9 25.8 + - - +
401B VAL* 4.1 14.9 - - + +
405B PRO 3.8 19.2 - - - +
410B LEU 5.4 6.9 + - - +
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ARG* 3.8 28.3 - - + +
339B ILE* 3.8 41.1 - - + -
340B LEU* 4.1 23.9 - - + +
343B HIS* 5.1 0.9 - - - -
362B THR* 4.0 14.4 - - - +
365B PHE* 3.8 27.6 - - + +
366B VAL 2.9 18.0 + - - +
367B GLY 3.0 5.4 + - - +
369B ASP* 1.3 73.0 - - - +
371B GLU* 1.3 66.8 + - - +
373B LEU* 3.0 11.7 - - + +
374B VAL* 3.0 27.1 + - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 4.6 17.3 + - - +
343B HIS* 3.7 36.4 + - + +
367B GLY 2.9 15.1 + - - +
368B ALA* 3.9 4.7 - - - +
370B LEU* 1.3 76.6 - - - +
372B ASN* 1.3 65.4 + - - +
374B VAL* 3.2 4.9 + - - +
375B ASN* 3.1 19.7 + - + +
1607B ADP 2.5 38.6 + - - +
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Residues in contact with ASN 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.4 7.6 + - - +
368B ALA 3.1 11.9 + - - +
369B ASP* 3.5 10.3 - - - +
371B GLU* 1.3 79.9 - - - +
373B LEU* 1.3 65.8 + - - +
375B ASN* 3.1 11.2 + - - +
376B GLU* 2.8 50.1 + - - +
401B VAL* 3.8 16.4 - - + +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 4.3 6.5 - - + -
358B ILE* 4.0 26.2 - - + -
362B THR* 4.1 17.3 - - + -
365B PHE* 4.5 4.9 - - + -
369B ASP 2.9 15.3 + - - +
370B LEU* 3.0 23.3 - - + +
372B ASN* 1.3 75.7 - - - +
374B VAL* 1.3 57.2 + - + +
376B GLU* 3.2 4.0 + - - +
377B ALA* 2.9 26.9 + - - +
394B PHE* 4.3 8.7 - - + +
397B ALA* 3.5 16.8 - - + +
398B ILE* 3.4 37.7 - - + +
401B VAL* 3.6 13.2 - - + +
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 3.9 22.2 - - + +
343B HIS* 3.7 28.7 - - + +
344B THR* 4.5 11.0 - - - +
347B LYS* 3.7 30.1 - - + -
349B LEU* 6.5 0.2 - - + -
370B LEU 3.0 17.9 + - - +
371B GLU 3.6 7.4 - - - +
372B ASN 3.1 0.4 - - - -
373B LEU* 1.3 77.6 - - + +
375B ASN* 1.3 63.1 + - - +
377B ALA* 3.2 8.4 + - - +
378B ALA* 3.0 20.6 + - - +
389B ILE* 4.7 1.4 - - + +
394B PHE* 4.1 16.8 - - + -
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Residues in contact with ASN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY 3.9 5.4 - - - +
191A ALA* 3.8 1.4 - - - -
192A ARG* 2.9 72.9 + - - +
347B LYS* 5.1 3.7 + - - +
371B GLU* 3.1 12.7 + - + +
372B ASN* 3.1 14.6 + - - +
374B VAL* 1.3 78.0 - - - +
376B GLU* 1.3 60.9 + - + +
378B ALA* 3.2 4.8 + - - +
379B LEU* 2.9 45.7 + - - +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ASN* 2.8 41.2 + - - +
373B LEU 3.6 4.7 - - - +
375B ASN* 1.3 76.8 + - - +
377B ALA* 1.3 63.5 + - - +
379B LEU* 3.5 23.2 + - - +
380B LEU* 3.2 27.7 + - - +
397B ALA* 4.0 16.8 - - + +
400B ARG* 3.6 34.5 + - + +
401B VAL* 3.9 14.8 - - + +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU 2.9 13.9 + - - +
374B VAL 3.2 9.2 + - - +
376B GLU* 1.3 75.8 - - - +
378B ALA* 1.3 63.5 + - - +
380B LEU* 3.3 5.5 + - - +
381B ALA* 3.2 16.5 + - - +
389B ILE* 3.6 24.6 - - + +
393B ASP* 3.8 25.3 - - - +
394B PHE* 3.7 24.5 - - + -
397B ALA* 3.8 0.8 - - + +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 3.1 14.1 - - + +
190A GLY 4.3 2.9 - - - +
191A ALA* 3.6 28.3 - - + +
347B LYS* 4.6 3.4 - - - -
374B VAL 3.0 13.4 + - - +
375B ASN* 3.2 11.0 + - - +
377B ALA* 1.3 77.4 - - - +
379B LEU* 1.3 56.4 + - - +
381B ALA 3.2 1.7 + - - -
382B ALA* 2.9 25.5 + - - +
389B ILE* 3.9 22.8 - - + +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 4.3 24.6 - - - +
186A PHE* 3.9 18.4 - - + -
191A ALA* 4.2 7.9 - - + -
192A ARG 4.2 8.3 - - - +
193A MET* 3.7 30.5 - - - -
375B ASN* 2.9 40.5 + - - +
376B GLU* 3.8 26.2 - - - +
377B ALA 3.3 0.2 - - - -
378B ALA* 1.3 74.6 - - - +
380B LEU* 1.3 58.4 + - + +
382B ALA* 3.7 1.9 - - - +
383B ARG* 2.8 33.4 + - - +
400B ARG* 6.0 2.0 - - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B GLU 3.2 17.5 + - - +
377B ALA 3.6 6.5 - - - +
379B LEU* 1.3 74.3 - - + +
381B ALA* 1.3 66.3 + - - +
383B ARG* 3.1 59.0 + - - +
384B GLU* 3.4 3.5 + - - +
386B ARG* 3.9 9.7 + - - +
393B ASP* 3.5 33.4 - - - +
396B GLU* 3.7 31.6 - - + +
397B ALA* 4.0 8.5 - - - +
400B ARG* 4.2 22.4 - - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 3.5 18.4 - - + -
377B ALA 3.2 6.8 + - - +
378B ALA 3.2 3.9 + - - +
380B LEU* 1.3 75.7 - - - +
382B ALA* 1.3 64.9 + - - +
384B GLU* 3.0 5.7 + - - +
385B GLY 2.9 16.8 + - - -
386B ARG* 3.0 28.2 + - - +
388B LYS 4.0 16.8 - - - +
389B ILE* 4.4 5.6 - - + -
393B ASP* 4.0 16.4 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 6.0 0.2 - - - +
185A LYS* 3.6 25.6 - - - +
186A PHE* 3.7 36.0 - - + -
189A ILE* 3.3 13.9 - - + +
191A ALA* 3.9 1.6 - - + -
378B ALA 2.9 15.6 + - - +
379B LEU 3.7 3.1 - - - +
381B ALA* 1.3 76.7 - - - +
383B ARG* 1.3 63.7 + - - +
385B GLY* 2.9 14.4 + - - +
386B ARG 4.7 1.6 - - - -
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 5.7 4.0 - - + +
178A GLU* 3.3 37.6 - - - +
186A PHE* 4.7 3.5 - - + -
379B LEU 2.8 14.5 + - - +
380B LEU* 3.1 49.6 + - - +
381B ALA 3.2 0.4 - - - -
382B ALA* 1.3 76.6 - - - +
384B GLU* 1.3 71.5 + - + +
385B GLY 3.6 0.3 + - - -
396B GLU* 5.6 3.4 + - - -
400B ARG* 4.7 13.9 - - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU 4.0 3.6 - - - +
381B ALA 3.0 7.2 + - - +
383B ARG* 1.3 97.6 + - + +
385B GLY* 1.3 62.9 + - - +
386B ARG* 2.8 42.0 + - + +
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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
------------------------------------------------------------
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