Contacts of the helix formed by residues 365 - 377 (chain C) in PDB entry 4XQ2
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 ASP 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.0 32.8 + - + +
6B PHE 4.1 5.7 - - - +
7B GLY* 4.0 1.5 + - - -
8B THR* 2.8 24.4 + - - +
364C GLU* 1.3 72.1 - - - +
366C PRO* 1.3 77.8 - - - +
367C GLN* 2.7 36.6 + - - +
368C ASP* 3.1 15.0 + - - +
369C LEU* 3.0 22.0 + - - +
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Residues in contact with PRO 366 (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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253C ARG* 3.6 33.7 - - - +
257C THR* 3.5 34.9 - - + +
260C VAL* 4.6 17.2 - - + +
364C GLU 3.2 5.3 - - - +
365C ASP* 1.3 93.5 - - - +
367C GLN* 1.3 61.2 + - + +
369C LEU* 3.5 1.9 + - - +
370C ALA* 2.9 29.7 + - - +
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Residues in contact with GLN 367 (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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5B ARG* 3.6 15.7 - - - +
260C VAL* 5.5 5.8 - - + +
264C ARG* 3.5 22.5 + - - +
365C ASP* 2.7 20.3 + - - +
366C PRO* 1.3 75.8 - - + +
368C ASP* 1.3 57.3 + - - +
370C ALA* 3.9 4.8 - - - +
371C GLU* 2.7 51.2 + - - +
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Residues in contact with ASP 368 (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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3B GLY 5.3 0.2 - - - +
4B MSE 4.0 14.2 - - - +
5B ARG* 2.8 55.9 + - - +
8B THR* 2.6 31.0 + - - +
317C LEU* 3.8 14.4 - - + +
365C ASP* 3.1 8.1 + - - +
367C GLN* 1.3 78.0 - - - +
369C LEU* 1.3 62.2 - - - +
371C GLU* 3.2 10.1 + - - +
372C ASP* 3.0 22.7 + - - +
375C ARG* 4.4 2.6 + - - +
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Residues in contact with LEU 369 (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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257C THR* 3.7 23.3 - - + -
261C LEU* 4.0 9.9 - - + -
317C LEU* 3.8 21.3 - - + -
318C PHE* 3.6 23.4 - - + -
329C SER* 3.3 37.7 - - - +
361C VAL* 4.4 7.2 - - + -
362C GLY 4.8 1.3 - - - +
364C GLU* 3.6 34.3 - - + +
365C ASP 3.0 12.0 + - - +
366C PRO 3.8 3.4 - - - +
368C ASP* 1.3 77.4 - - - +
370C ALA* 1.3 61.3 + - - +
372C ASP* 3.2 2.3 + - - +
373C LEU* 3.0 23.9 + - - +
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Residues in contact with ALA 370 (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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260C VAL* 4.2 9.2 - - + -
261C LEU* 3.7 15.0 - - + +
264C ARG* 3.3 40.6 - - + +
366C PRO 2.9 19.1 + - - +
367C GLN* 3.9 4.9 - - - +
368C ASP 3.3 0.2 - - - -
369C LEU* 1.3 75.5 - - - +
371C GLU* 1.3 57.3 + - - +
373C LEU* 3.4 3.7 + - - +
374C SER* 2.9 32.2 + - - -
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Residues in contact with GLU 371 (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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5B ARG* 3.5 16.7 + - - -
264C ARG* 4.0 19.7 + - - +
367C GLN* 2.7 43.5 + - - +
368C ASP* 3.5 11.1 - - - +
369C LEU 3.2 0.2 - - - -
370C ALA* 1.3 75.6 - - - +
372C ASP* 1.3 64.3 + - - +
374C SER* 4.1 2.1 - - - -
375C ARG* 2.9 44.4 + - - +
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Residues in contact with ASP 372 (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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314C ARG 4.1 2.4 - - - +
315C PHE* 3.5 9.4 - - - -
316C THR* 2.7 31.5 + - - +
317C LEU* 2.9 34.3 + - + -
318C PHE* 3.0 24.1 + - + -
368C ASP 3.0 13.1 + - - +
369C LEU 3.6 8.1 - - - +
371C GLU* 1.3 76.6 - - - +
373C LEU* 1.3 62.7 + - - +
375C ARG* 3.2 16.7 + - - +
376C ALA* 3.0 21.8 + - - +
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Residues in contact with LEU 373 (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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261C LEU* 4.1 25.8 - - + +
264C ARG* 4.6 8.7 - - + -
265C LEU* 4.0 25.1 - - + -
301C PHE* 4.5 12.8 - - + -
315C PHE* 3.7 30.7 - - + -
318C PHE* 4.3 5.6 - - + -
359C LEU* 4.1 22.0 - - + -
369C LEU 3.0 12.6 + - - +
370C ALA* 3.5 8.7 - - - +
372C ASP* 1.3 77.1 - - - +
374C SER* 1.3 63.9 + - - +
376C ALA* 3.2 2.8 + - - +
377C LEU* 3.1 41.5 + - + +
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Residues in contact with SER 374 (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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264C ARG* 2.9 47.9 + - - +
370C ALA 2.9 8.5 + - - -
371C GLU* 4.1 4.3 - - - -
373C LEU* 1.3 75.7 - - - +
375C ARG* 1.3 59.7 + - - +
377C LEU* 3.7 14.9 + - - +
378C ALA* 3.6 19.4 + - - +
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Residues in contact with ARG 375 (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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4B MSE 5.3 12.3 - - - +
314C ARG* 4.5 13.5 - - - +
316C THR* 4.6 13.1 + - + -
368C ASP 4.4 2.2 + - - -
371C GLU* 2.9 48.6 + - - +
372C ASP* 3.2 20.9 + - - +
373C LEU 3.1 0.6 - - - -
374C SER* 1.3 76.1 - - - +
376C ALA* 1.3 61.8 + - - +
377C LEU 3.4 0.2 - - - -
378C ALA* 4.0 14.1 + - + +
379C GLY* 4.4 4.7 + - - -
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Residues in contact with ALA 376 (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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311C LEU* 3.5 26.4 - - + +
314C ARG* 3.0 42.3 + - + -
315C PHE* 3.9 26.0 - - + -
372C ASP 3.0 11.5 + - - +
373C LEU 3.7 7.2 - - - +
375C ARG* 1.3 74.8 - - - +
377C LEU* 1.3 63.1 + - - +
378C ALA 3.0 5.8 + - - -
379C GLY 3.3 1.6 + - - -
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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
----------------------------------------------------------
264C ARG* 5.2 4.3 - - + +
265C LEU* 4.2 6.7 - - + -
268C SER* 4.1 22.2 - - - +
270C VAL* 3.6 25.7 - - + +
271C VAL* 3.9 21.8 - - + -
301C PHE* 4.2 12.3 - - + -
303C TYR* 3.7 32.9 - - + -
305C GLY* 5.5 0.9 - - - -
311C LEU* 3.8 7.6 - - + +
373C LEU* 3.1 36.3 + - + +
374C SER* 3.8 11.9 - - - +
375C ARG 3.4 0.2 - - - -
376C ALA* 1.3 76.9 - - - +
378C ALA* 1.3 56.5 + - - +
379C GLY 3.4 3.5 + - - +
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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