Contacts of the helix formed by residues 371 - 387 (chain B) in PDB entry 2CX9
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 THR 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLN* 4.0 7.9 - - - +
345A GLY* 5.0 10.5 - - - -
134B SER* 4.2 15.4 + - - +
366B ARG 3.4 7.9 - - - -
367B ILE* 3.2 25.0 + - + +
370B GLY* 1.3 77.2 - - - +
372B SER* 1.3 65.2 + - - +
373B GLU* 3.4 18.2 + - - +
374B ILE* 3.0 30.5 + - - +
375B LEU* 3.0 18.7 + - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 4.2 1.5 + - - -
326B LYS* 4.7 0.5 + - - +
327B LEU* 3.4 21.9 - - - +
330B SER* 4.1 3.6 + - - -
331B GLU* 2.7 30.7 + - - +
366B ARG* 3.2 22.2 + - - +
371B THR* 1.3 73.4 - - - +
373B GLU* 1.3 74.2 + - - +
375B LEU* 3.7 7.5 - - - +
376B LYS* 3.0 33.9 + - - +
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY* 4.9 5.8 - - - +
287A VAL* 6.1 2.7 - - + -
290A LYS* 2.7 36.7 + - - +
342A GLN* 2.9 32.1 + - - +
331B GLU* 5.3 0.3 - - - +
366B ARG* 5.6 1.0 + - - -
371B THR* 3.1 11.2 - - - +
372B SER* 1.3 84.0 - - - +
374B ILE* 1.3 64.1 + - + +
376B LYS* 3.3 12.1 + - - +
377B LEU* 3.3 25.9 + - + +
285D GLU* 5.9 0.2 - - - +
289D PHE* 3.7 31.9 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 4.4 19.1 - - + -
134B SER* 3.5 39.7 - - - +
249B ARG* 4.8 9.0 - - - +
370B GLY* 4.6 11.2 - - - -
371B THR* 3.0 29.8 + - - +
373B GLU* 1.3 77.1 - - + +
375B LEU* 1.3 58.2 + - - +
377B LEU* 3.1 20.6 + - + +
378B VAL* 3.0 37.5 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 3.6 44.4 - - - +
323B ALA* 3.7 18.6 - - + +
326B LYS* 3.4 34.8 - - + +
327B LEU* 3.6 27.4 - - + +
369B GLU 4.4 0.4 - - - +
370B GLY* 3.7 11.9 - - - +
371B THR 3.0 16.6 + - - +
372B SER* 3.7 9.2 - - - +
373B GLU 3.3 0.2 - - - -
374B ILE* 1.3 74.9 - - + +
376B LYS* 1.3 60.4 + - - +
378B VAL* 3.1 5.5 + - + +
379B ILE* 2.8 35.8 + - - +
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.0 28.9 - - + -
331B GLU* 6.2 2.3 - - - -
372B SER* 3.0 23.1 + - - +
373B GLU* 3.6 11.5 + - - +
374B ILE 3.3 0.2 - - - -
375B LEU* 1.3 76.5 - - - +
377B LEU* 1.3 58.8 + - - +
379B ILE* 4.4 2.0 - - - -
380B ALA* 2.8 30.7 + - - +
288D SER 4.3 0.2 - - - +
289D PHE* 3.7 42.1 - - + -
292D ALA* 3.3 21.8 - - + +
293D GLU* 2.7 38.3 + - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 6.2 2.0 - - + -
284A PHE* 6.2 0.7 - - + -
373B GLU* 3.3 15.0 + - + +
374B ILE* 3.1 22.8 + - + +
376B LYS* 1.3 73.8 - - - +
378B VAL* 1.3 68.1 + - + +
380B ALA* 3.8 2.6 - - - +
381B ARG* 2.9 57.4 + - - +
285D GLU* 3.0 32.5 - - + +
288D SER* 3.9 17.0 - - - +
289D PHE* 3.5 15.9 - - + -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 4.3 16.4 - - - +
319B THR* 3.9 28.3 - - + +
320B LEU* 5.4 0.4 - - - -
323B ALA* 4.2 14.8 - - + -
374B ILE* 3.0 31.4 + - + +
375B LEU* 3.1 11.2 + - - +
377B LEU* 1.3 77.8 - - + +
379B ILE* 1.3 61.3 + - - +
381B ARG* 3.6 6.9 + - - +
382B ARG* 3.2 28.9 + - + +
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 3.5 26.6 - - + +
323B ALA* 3.7 18.2 - - + +
324B GLN* 3.8 26.9 - - + +
327B LEU* 4.0 16.8 - - + -
375B LEU 2.8 22.6 + - - +
376B LYS* 3.7 5.6 - - - +
378B VAL* 1.3 75.0 - - - +
380B ALA* 1.3 66.0 + - - +
382B ARG* 3.2 3.5 + - - +
383B LEU* 3.0 31.0 + - + +
292D ALA* 3.7 24.0 - - + +
296D THR* 3.7 17.3 - - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS 2.8 22.2 + - - +
377B LEU* 3.3 5.6 + - + +
379B ILE* 1.3 73.5 - - - +
381B ARG* 1.3 59.4 + - + +
383B LEU* 3.3 13.2 + - - +
384B LEU* 3.0 39.3 + - + +
288D SER* 3.5 41.5 - - - +
291D LEU* 5.0 4.4 - - + +
292D ALA* 4.2 1.3 - - - +
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 5.6 11.3 - - - -
377B LEU* 2.9 49.6 + - - +
378B VAL* 3.9 6.7 - - - +
380B ALA* 1.3 75.9 - - + +
382B ARG* 1.3 68.1 + - - +
384B LEU* 3.3 10.6 + - + +
385B GLU* 3.1 33.1 + - + +
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Residues in contact with ARG 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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319B THR* 3.2 42.0 + - + +
320B LEU* 4.0 36.7 - - + +
378B VAL* 3.2 24.0 + - - +
379B ILE 3.2 4.0 + - - +
381B ARG* 1.3 78.1 - - - +
383B LEU* 1.3 62.8 + - - +
385B GLU* 3.3 32.1 + - - +
386B ALA* 3.3 15.1 + - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.1 22.4 - - + -
324B GLN* 5.1 0.7 - - - +
379B ILE* 3.0 28.7 + - + +
380B ALA* 3.5 9.4 - - - +
381B ARG 3.2 0.2 - - - -
382B ARG* 1.3 79.7 - - - +
384B LEU* 1.3 61.4 + - + +
385B GLU 3.5 0.2 + - - -
386B ALA* 3.8 4.2 + - - +
387B VAL* 3.4 26.5 + - - +
264D LEU* 5.3 4.0 - - + -
268D LEU* 3.8 22.4 - - + +
291D LEU* 3.8 22.2 - - + +
292D ALA* 4.4 0.4 - - - -
295D ALA* 3.5 33.9 - - + -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 3.0 28.7 + - + +
381B ARG* 3.8 10.3 - - + +
382B ARG 3.3 0.4 - - - -
383B LEU* 1.3 74.1 - - + +
385B GLU* 1.3 60.3 + - - +
387B VAL* 2.6 20.0 - - - +
268D LEU* 3.4 31.0 - - + +
272D LYS* 2.9 32.0 + - + -
282D ALA* 4.0 31.4 - - + +
288D SER* 5.7 0.4 - - - -
291D LEU* 4.3 17.7 - - + -
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.1 18.0 + - + +
382B ARG* 3.3 37.9 + - - +
384B LEU* 1.3 75.1 - - + +
386B ALA* 1.3 59.1 + - - +
387B VAL* 2.9 12.0 + - - -
272D LYS* 4.1 6.8 + - - +
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG 3.3 12.4 + - - +
383B LEU* 4.1 6.3 - - - +
385B GLU* 1.3 78.5 - - - +
387B VAL* 1.3 62.3 + - + +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU 3.4 14.1 + - - +
384B LEU* 2.6 27.3 + - - +
385B GLU 2.9 1.9 + - - -
386B ALA* 1.3 84.1 - - + +
265D ASP 6.1 0.2 - - - +
268D LEU* 3.6 31.4 - - + +
269D ALA* 5.3 15.3 - - + -
272D LYS* 2.5 36.5 + - - +
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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
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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