Contacts of the helix formed by residues 371 - 387 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLY 5.5 3.6 - - - +
134C SER* 4.5 14.4 - - - +
366C ARG 3.5 10.1 - - - -
367C ILE* 3.3 25.7 + - + +
370C GLY* 1.3 74.1 - - - +
372C SER* 1.3 65.3 + - - +
373C GLU* 3.5 18.6 + - - +
374C ILE* 2.8 37.5 + - + +
375C LEU* 2.9 10.4 + - - +
342D GLN* 4.3 5.4 - - - +
345D GLY* 5.2 8.5 - - - -
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Residues in contact with SER 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LYS* 4.5 1.0 + - - +
327C LEU* 3.5 20.3 - - - +
330C SER* 4.1 3.3 + - - -
331C GLU* 2.7 31.7 + - - +
366C ARG* 3.0 23.7 + - - +
370C GLY 3.7 0.6 + - - -
371C THR* 1.3 70.9 - - - +
373C GLU* 1.3 74.2 + - - +
375C LEU* 3.2 10.6 + - - +
376C LYS* 3.0 32.2 + - - +
342D GLN* 4.0 2.9 - - - -
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Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 6.0 0.7 - - - +
289A PHE* 3.8 38.3 - - + -
331C GLU* 5.1 0.9 - - - +
366C ARG* 5.7 0.5 + - - -
371C THR* 3.0 13.4 - - - +
372C SER* 1.3 83.0 - - - +
374C ILE* 1.3 63.6 + - + +
376C LYS* 3.4 16.4 + - - +
377C LEU* 3.4 13.9 + - - +
286D GLY* 5.0 4.0 - - - -
287D VAL* 6.3 1.6 - - + -
290D LYS* 3.2 34.2 + - - -
342D GLN* 2.8 37.7 + - - +
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Residues in contact with ILE 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER* 4.1 24.7 - - - +
249C ARG* 4.4 8.5 - - - +
370C GLY* 4.3 13.0 - - - -
371C THR* 2.8 40.5 + - + +
373C GLU* 1.3 73.0 - - + +
375C LEU* 1.3 60.9 + - - +
377C LEU* 3.2 15.9 + - + +
378C VAL* 3.0 31.9 + - + +
277D PHE* 3.9 29.4 - - + -
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 3.4 47.3 - - - +
323C ALA* 3.9 17.9 - - + +
326C LYS* 3.3 35.2 - - + +
327C LEU* 3.7 24.0 - - + +
369C GLU 4.2 0.2 - - - +
370C GLY* 3.6 13.9 - - - +
371C THR 2.9 15.0 + - - +
372C SER* 3.2 9.2 + - - +
374C ILE* 1.3 77.2 - - - +
376C LYS* 1.3 57.5 + - - +
378C VAL* 3.3 5.6 + - - +
379C ILE* 2.8 37.6 + - + +
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Residues in contact with LYS 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER 4.3 0.2 - - - +
289A PHE* 3.7 40.4 - - + -
292A ALA* 3.3 20.6 - - + +
293A GLU* 2.6 40.7 + - + +
327C LEU* 3.9 31.4 - - + -
331C GLU* 5.9 3.2 - - - +
372C SER* 3.0 20.9 + - - +
373C GLU* 3.7 11.6 + - - +
374C ILE 3.2 0.4 - - - -
375C LEU* 1.3 74.2 - - - +
377C LEU* 1.3 62.3 + - - +
379C ILE* 4.3 1.3 - - - -
380C ALA* 2.9 30.8 + - - +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU 5.3 3.6 - - - +
285A GLU* 3.0 42.0 - - + +
288A SER* 4.0 22.7 - - - +
289A PHE* 4.2 5.2 - - + -
373C GLU 3.4 12.0 + - - +
374C ILE* 3.2 20.2 + - + +
376C LYS* 1.3 76.2 - - - +
378C VAL* 1.3 60.0 + - + +
380C ALA* 3.7 1.6 - - + +
381C ARG* 2.8 67.4 + - + +
277D PHE* 6.0 4.7 - - + -
284D PHE* 6.3 0.7 - - + -
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 4.2 16.8 - - - +
319C THR* 4.1 17.9 - - + +
320C LEU* 5.6 0.2 - - - -
323C ALA* 4.2 14.8 - - + -
374C ILE* 3.0 26.3 + - + +
375C LEU* 3.4 11.0 - - - +
377C LEU* 1.3 77.8 - - - +
379C ILE* 1.3 61.4 + - - +
381C ARG* 4.4 4.5 - - - +
382C ARG* 2.9 58.1 + - + +
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Residues in contact with ILE 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA* 3.8 24.7 - - + +
295A ALA* 4.8 0.2 - - + -
296A THR* 3.8 15.9 - - - +
320C LEU* 3.6 21.9 - - + +
323C ALA* 3.8 26.9 - - + +
324C GLN* 3.9 20.4 - - + +
327C LEU* 3.8 21.3 - - + -
375C LEU 2.8 26.5 + - - +
376C LYS* 3.7 5.6 - - - +
378C VAL* 1.3 77.9 - - - +
380C ALA* 1.3 57.3 + - - +
382C ARG* 3.3 4.0 + - - +
383C LEU* 3.0 40.0 + - + +
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER* 3.7 40.4 - - - +
291A LEU* 5.0 4.3 - - + -
292A ALA* 4.6 1.8 - - + +
376C LYS 2.9 19.6 + - - +
377C LEU* 3.8 4.3 - - + +
379C ILE* 1.3 73.3 - - - +
381C ARG* 1.3 67.1 + - + +
383C LEU* 3.3 12.0 + - - +
384C LEU* 2.9 35.6 + - + +
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Residues in contact with ARG 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 2.8 62.3 + - + +
378C VAL* 4.4 3.5 - - - +
379C ILE 3.3 0.2 - - - -
380C ALA* 1.3 74.1 - - + +
382C ARG* 1.3 79.6 + - - +
384C LEU* 3.4 7.1 + - + +
385C GLU* 2.8 43.9 + - + +
277D PHE* 6.1 2.8 - - - -
279D ARG* 6.0 2.0 - - - +
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 6.0 4.0 - - - +
319C THR* 4.1 19.3 - - - +
320C LEU* 4.3 34.1 - - + +
378C VAL* 2.9 56.4 + - + +
379C ILE 3.6 5.6 - - - +
380C ALA 3.2 0.2 - - - -
381C ARG* 1.3 100.9 - - - +
383C LEU* 1.3 65.4 + - - +
385C GLU* 3.5 17.6 + - - +
386C ALA* 3.2 23.6 + - - +
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 5.1 2.5 - - + -
268A LEU* 3.9 30.3 - - + +
291A LEU* 3.7 25.1 - - + +
292A ALA* 4.3 1.1 - - - +
295A ALA* 3.4 34.1 - - + -
320C LEU* 4.4 21.8 - - + -
324C GLN* 5.0 0.4 - - - +
379C ILE* 3.0 31.9 + - + +
380C ALA* 3.7 7.6 - - - +
382C ARG* 1.3 77.3 - - - +
384C LEU* 1.3 62.7 + - - +
386C ALA* 3.4 6.9 + - - +
387C VAL* 3.4 19.6 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU* 3.6 35.4 - - + +
272A LYS* 3.2 29.0 + - + -
282A ALA* 3.8 40.4 - - + +
283A GLU* 5.9 0.2 - - - -
288A SER* 4.6 5.2 - - - +
291A LEU* 4.4 6.7 - - + -
380C ALA* 2.9 26.5 + - + +
381C ARG* 3.8 6.3 - - + +
383C LEU* 1.3 73.4 - - - +
385C GLU* 1.3 61.4 + - + +
386C ALA 3.0 4.9 - - - -
387C VAL* 2.9 21.4 + - - +
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Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 4.7 7.0 + - - +
381C ARG* 2.8 35.5 + - - +
382C ARG* 3.8 27.7 + - - +
384C LEU* 1.3 71.9 - - + +
386C ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 5.4 0.4 - - - -
382C ARG 3.2 12.8 + - - +
383C LEU* 3.4 13.2 - - - +
384C LEU 3.0 0.6 - - - -
385C GLU* 1.3 81.7 - - - +
387C VAL* 1.3 72.2 + - + +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 5.3 1.3 - - - +
268A LEU* 4.4 22.8 - - + +
269A ALA* 4.6 10.7 + - + +
272A LYS* 3.4 25.6 - - - +
383C LEU 3.4 7.4 + - - +
384C LEU* 2.9 26.4 + - - +
386C ALA* 1.3 88.8 - - + +
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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