Contacts of the helix formed by residues 366 - 384 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F PRO* 5.0 4.5 - - + -
203F PRO 3.4 20.6 - - - +
204F GLY* 3.0 22.9 - - - +
205F THR* 4.4 10.8 - - + +
330F PRO* 4.5 17.5 - - + -
331F PRO* 4.6 7.0 - - + -
364F GLY 3.7 10.1 - - - +
365F PHE* 1.3 77.9 - - - +
367F GLY* 1.3 67.3 + - - +
368F ALA* 3.8 4.5 - - + +
369F ASP* 2.7 33.0 + - - +
370F LEU* 3.0 11.7 + - - +
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Residues in contact with GLY 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLY 2.8 12.1 + - - -
205F THR* 4.5 3.0 - - - +
331F PRO* 4.8 3.2 - - - +
339F ILE* 3.5 33.8 - - - +
366F VAL* 1.3 68.7 - - - +
368F ALA* 1.3 63.4 + - - -
370F LEU* 2.7 16.6 + - - +
371F GLU* 2.9 12.6 + - - +
1607F ADP 3.6 17.0 + - - -
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Residues in contact with ALA 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F GLY* 2.8 33.8 + - - -
366F VAL* 4.1 3.6 - - + -
367F GLY* 1.3 71.0 - - - +
369F ASP* 1.3 61.7 + - - +
371F GLU* 3.2 5.4 + - - +
372F ASN* 3.0 27.9 + - - +
1607F ADP 3.1 30.1 + - + +
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Residues in contact with ASP 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F GLY 4.9 0.9 - - - +
365F PHE* 3.3 33.7 - - + -
366F VAL* 2.7 37.8 + - - +
368F ALA* 1.3 77.4 - - - +
370F LEU* 1.3 55.0 + - - +
372F ASN* 3.8 6.9 - - - +
373F LEU* 3.1 27.4 + - - +
401F VAL* 4.9 12.2 - - + +
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Residues in contact with LEU 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F ARG* 3.2 41.3 - - + +
339F ILE* 3.3 34.3 - - + -
340F LEU* 4.0 29.2 - - + +
343F HIS* 5.5 0.7 - - - -
358F ILE* 5.6 0.2 - - + -
362F THR* 4.3 18.8 - - + +
365F PHE* 4.2 20.6 - - + -
366F VAL 3.0 12.3 + - - +
367F GLY* 2.7 9.4 + - - +
369F ASP* 1.3 76.5 - - - +
371F GLU* 1.3 59.7 + - - +
373F LEU* 3.2 7.5 + - + +
374F VAL* 2.9 27.9 + - - +
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Residues in contact with GLU 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F HIS* 3.3 40.0 - - + +
367F GLY 2.9 9.4 + - - +
368F ALA* 3.6 7.6 - - - +
370F LEU* 1.3 76.5 - - - +
372F ASN* 1.3 59.2 + - - +
374F VAL* 2.6 32.3 - - + +
375F ASN* 3.1 7.6 + - + +
1607F ADP 3.1 39.0 + - - +
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Residues in contact with ASN 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F ALA 3.0 16.6 + - - +
369F ASP* 3.8 8.7 - - - +
371F GLU* 1.3 78.8 - - - +
373F LEU* 1.3 54.2 + - - +
375F ASN* 2.9 14.0 + - - +
376F GLU* 2.8 61.2 + - - +
401F VAL* 4.5 18.0 - - - +
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Residues in contact with LEU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F LEU* 5.4 3.6 - - + -
358F ILE* 4.4 17.3 - - + -
362F THR* 4.8 3.1 - - + -
365F PHE* 3.2 36.1 - - + -
369F ASP 3.1 11.8 + - - +
370F LEU* 3.5 9.4 - - + +
372F ASN* 1.3 77.0 - - - +
374F VAL* 1.3 63.0 + - - +
376F GLU* 3.3 7.5 + - - -
377F ALA* 3.0 21.7 + - - +
394F PHE* 4.3 11.9 - - + +
397F ALA* 3.6 12.7 - - + +
398F ILE* 3.4 42.6 - - + +
401F VAL* 3.4 19.1 - - + -
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Residues in contact with VAL 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F LEU* 4.8 8.7 - - + +
343F HIS* 3.6 35.4 - - + +
344F THR* 4.8 7.9 - - - +
347F LYS* 5.3 13.2 - - + -
370F LEU 2.9 12.7 + - - +
371F GLU* 2.6 26.5 - - + +
373F LEU* 1.3 77.8 - - - +
375F ASN* 1.3 79.3 + - + +
377F ALA* 3.0 14.7 + - - +
378F ALA* 3.1 12.5 + - - +
389F ILE* 5.0 4.1 - - + +
394F PHE* 4.2 26.0 - - + -
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Residues in contact with ASN 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F LYS* 6.3 1.6 - - - +
371F GLU* 3.6 10.1 - - + +
372F ASN* 2.9 16.2 + - - +
374F VAL* 1.3 85.5 - - + +
376F GLU* 1.3 63.1 + - - +
378F ALA* 3.1 12.4 + - - +
379F LEU* 2.9 45.6 + - - +
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Residues in contact with GLU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F ASN* 2.8 48.7 + - - +
373F LEU* 3.6 8.5 - - - +
374F VAL 3.2 0.2 - - - -
375F ASN* 1.3 73.0 - - - +
377F ALA* 1.3 65.4 + - - +
379F LEU* 3.3 28.5 + - - +
380F LEU* 3.2 27.4 + - - +
397F ALA* 4.0 15.0 - - + -
400F ARG* 3.4 32.4 + - + +
401F VAL* 5.0 6.7 - - + -
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Residues in contact with ALA 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F LEU 3.0 11.1 + - - +
374F VAL 3.0 11.4 + - - +
376F GLU* 1.3 78.0 - - - +
378F ALA* 1.3 61.3 + - - +
380F LEU* 3.1 7.0 + - - +
381F ALA* 3.1 18.9 + - - +
389F ILE* 3.7 21.8 - - + -
393F ASP* 3.8 11.2 - - - +
394F PHE* 3.9 31.0 - - + +
397F ALA* 3.9 6.2 - - - +
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Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F LYS* 5.5 12.8 - - + +
374F VAL 3.1 10.6 + - - +
375F ASN* 3.4 17.3 - - - +
377F ALA* 1.3 76.8 - - - +
379F LEU* 1.3 56.5 + - - +
381F ALA* 3.1 3.6 + - - +
382F ALA* 2.8 32.1 + - - +
389F ILE* 3.8 25.3 - - + +
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Residues in contact with LEU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375F ASN* 2.9 29.3 + - - +
376F GLU* 3.3 46.2 - - - +
378F ALA* 1.3 75.3 - - - +
380F LEU* 1.3 61.5 + - + +
382F ALA* 3.8 5.8 - - - +
383F ARG* 2.9 31.4 + - - +
400F ARG* 5.7 1.8 - - - +
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Residues in contact with LEU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F GLU 3.2 13.0 + - - +
377F ALA 3.1 6.5 + - - +
379F LEU* 1.3 78.6 - - + +
381F ALA* 1.3 67.3 + - - +
383F ARG* 3.5 29.0 + - - +
384F GLU* 3.4 25.6 + - - +
393F ASP* 3.4 36.9 - - - +
396F GLU* 3.8 31.0 - - + +
397F ALA* 4.5 5.6 - - - +
400F ARG* 4.2 26.5 - - - +
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Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F ALA 3.1 10.0 + - - +
378F ALA* 3.1 8.4 + - - +
380F LEU* 1.3 79.7 - - - +
382F ALA* 1.3 60.8 + - - +
384F GLU* 3.4 1.6 + - - -
385F GLY 3.2 3.5 + - - -
386F ARG* 2.9 59.6 + - - +
387F ASP 5.9 0.2 - - - -
388F LYS 4.1 8.1 - - - +
389F ILE* 4.0 22.9 - - + -
393F ASP* 3.6 1.4 + - - +
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F ALA 2.8 21.4 + - - +
379F LEU* 3.8 6.1 - - - +
381F ALA* 1.3 71.6 - - - +
383F ARG* 1.3 58.4 + - - +
385F GLY* 2.7 24.8 + - - +
386F ARG 4.7 5.4 - - - +
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Residues in contact with ARG 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F LEU 2.9 21.9 + - - +
380F LEU* 3.9 23.5 + - - +
381F ALA 3.4 0.2 - - - -
382F ALA* 1.3 73.4 - - - +
384F GLU* 1.3 65.7 + - + +
385F GLY 3.5 0.2 + - - -
400F ARG* 3.9 22.8 - - - +
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Residues in contact with GLU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F LEU 3.4 14.4 + - - +
381F ALA 3.4 4.4 + - - +
382F ALA 3.1 0.8 - - - -
383F ARG* 1.3 85.2 - - + +
385F GLY* 1.3 62.0 + - - +
386F ARG* 3.4 33.0 + - + +
392F LYS* 5.0 11.1 + - - -
393F ASP* 5.6 1.9 - - - +
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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