Contacts of the helix formed by residues 365 - 379 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B GLU* 1.3 70.7 - - - +
366B PRO* 1.3 80.5 - - - +
367B GLN* 3.3 12.3 + - - +
368B ASP* 3.0 32.8 + - - +
369B LEU* 3.0 12.1 + - - +
5C ARG* 3.3 37.4 + - + +
7C GLY* 3.0 19.2 + - - -
8C THR* 2.8 11.2 + - - +
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Residues in contact with PRO 366 (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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253B ARG* 3.8 29.2 - - - +
257B THR* 3.8 29.4 - - + +
260B VAL* 4.3 15.7 - - + -
261B LEU* 4.4 2.4 - - - +
364B GLU 3.3 5.1 - - - +
365B ASP* 1.3 93.0 - - - +
367B GLN* 1.3 74.9 + - - +
369B LEU* 2.9 6.4 + - - +
370B ALA* 2.8 28.7 + - - +
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Residues in contact with GLN 367 (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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260B VAL* 4.0 22.4 - - - +
264B ARG* 4.1 18.1 - - - +
365B ASP* 3.3 10.7 + - - +
366B PRO* 1.3 95.3 - - - +
368B ASP* 1.3 61.3 + - - +
370B ALA* 3.8 2.5 - - - +
371B GLU* 3.1 44.6 + - - +
5C ARG* 4.0 17.7 - - - +
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Residues in contact with ASP 368 (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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317B LEU* 3.6 19.6 - - + +
365B ASP* 3.0 21.3 + - - +
367B GLN* 1.3 78.3 - - - +
369B LEU* 1.3 61.0 + - - +
371B GLU* 3.5 4.6 + - - +
372B ASP* 3.2 18.2 + - - +
375B ARG* 5.3 0.9 + - - -
3C GLY 3.2 19.0 + - - +
4C MSE 3.4 9.6 + - - -
5C ARG* 2.6 44.2 + - - +
8C THR* 2.7 22.7 + - - +
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Residues in contact with LEU 369 (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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257B THR* 3.7 22.9 - - + -
261B LEU* 4.2 9.9 - - + -
317B LEU* 3.8 22.2 - - + -
318B PHE* 3.5 29.4 - - + +
329B SER* 3.4 37.7 - - - +
361B VAL* 4.5 4.9 - - + -
362B GLY 4.6 0.4 - - - +
364B GLU* 3.6 32.5 - - + +
365B ASP 3.0 8.0 + - - +
366B PRO 2.9 6.5 + - - +
368B ASP* 1.3 75.7 - - - +
370B ALA* 1.3 65.0 + - - +
372B ASP* 3.4 1.3 + - - -
373B LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 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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260B VAL* 4.4 4.5 - - + -
261B LEU* 3.7 19.3 - - + +
264B ARG* 3.6 34.1 - - + +
366B PRO 2.8 18.7 + - - +
367B GLN* 3.8 14.8 - - - +
369B LEU* 1.3 74.1 - - - +
371B GLU* 1.3 56.5 + - - +
373B LEU* 3.5 4.8 + - - +
374B SER* 3.0 32.6 + - - -
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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
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264B ARG* 4.3 17.4 + - - +
367B GLN* 3.1 31.4 + - - +
368B ASP* 4.1 5.1 - - - +
369B LEU 3.2 0.2 - - - -
370B ALA* 1.3 74.1 - - - +
372B ASP* 1.3 65.3 + - - +
374B SER* 3.9 2.0 - - - -
375B ARG* 3.0 44.7 + - + +
3C GLY 5.9 0.7 + - - -
5C ARG* 3.7 29.1 + - - -
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Residues in contact with ASP 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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314B ARG 4.2 1.4 - - - +
315B PHE* 3.6 7.0 - - - +
316B THR* 2.7 23.8 + - - -
317B LEU* 2.7 36.0 + - + -
318B PHE* 2.9 23.5 + - + -
368B ASP 3.2 16.4 + - - +
369B LEU 3.8 4.0 - - - +
371B GLU* 1.3 76.4 - - - +
373B LEU* 1.3 62.9 + - - +
375B ARG* 2.7 29.7 + - - +
376B ALA* 3.2 23.4 + - - +
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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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261B LEU* 4.4 18.8 - - + +
264B ARG* 4.7 11.7 - - + -
265B LEU* 3.8 27.1 - - + +
301B PHE* 4.4 18.8 - - + -
315B PHE* 4.0 24.2 - - + -
318B PHE* 4.4 6.2 - - + -
359B LEU* 4.4 18.4 - - + -
369B LEU 3.0 17.6 + - - +
370B ALA 3.7 4.0 - - - +
372B ASP* 1.3 77.9 - - - +
374B SER* 1.3 58.3 + - - +
376B ALA* 3.4 1.9 + - - +
377B LEU* 2.9 51.7 + - + +
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Residues in contact with SER 374 (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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264B ARG* 2.8 43.3 + - - +
370B ALA 3.0 11.3 + - - -
371B GLU* 3.3 4.7 + - - -
373B LEU* 1.3 75.0 - - - +
375B ARG* 1.3 59.7 + - - +
377B LEU* 3.3 8.4 + - - +
378B ALA* 2.8 31.7 + - - +
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Residues in contact with ARG 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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314B ARG* 4.9 3.9 + - - +
316B THR* 2.8 21.7 + - - +
317B LEU* 5.1 1.0 - - - +
368B ASP 5.3 1.2 + - - -
371B GLU* 3.0 36.7 + - + +
372B ASP* 2.7 40.6 + - - +
374B SER* 1.3 75.3 - - - +
376B ALA* 1.3 54.0 + - - +
378B ALA* 3.6 4.8 - - - +
379B GLY* 2.7 37.5 + - - +
3C GLY 4.1 21.9 + - - +
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Residues in contact with ALA 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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311B LEU* 3.3 20.0 - - + +
314B ARG* 3.3 45.3 + - + -
315B PHE* 3.9 26.0 - - + -
372B ASP 3.2 17.8 + - - +
373B LEU 3.5 4.3 - - - +
374B SER 3.2 0.2 - - - -
375B ARG* 1.3 82.0 - - - +
377B LEU* 1.3 64.2 + - + +
379B GLY 3.4 0.2 + - - -
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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
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264B ARG* 5.8 2.2 - - + +
265B LEU* 4.0 15.7 - - + -
268B SER* 4.0 12.8 - - - +
270B VAL* 4.0 21.0 - - + +
271B VAL* 3.9 22.2 - - + -
301B PHE* 4.0 18.6 - - + -
303B TYR* 3.8 40.7 + - + -
311B LEU* 3.9 12.1 - - + -
314B ARG* 4.0 1.7 + - - -
373B LEU* 2.9 33.5 + - + +
374B SER* 3.8 7.9 - - - +
376B ALA* 1.3 77.2 - - - +
378B ALA* 1.3 63.8 + - - +
379B GLY 3.4 0.2 + - - -
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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
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270B VAL* 5.7 0.9 - - - -
314B ARG* 4.7 0.2 - - - -
374B SER 2.8 19.0 + - - +
375B ARG* 3.8 5.6 - - - +
377B LEU* 1.3 77.8 - - - +
379B GLY* 1.3 67.5 + - - +
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Residues in contact with GLY 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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314B ARG* 3.7 30.3 - - - -
375B ARG* 2.7 20.9 + - - +
376B ALA 3.4 0.4 + - - -
377B LEU 3.3 3.4 - - - -
378B ALA* 1.3 81.9 - - - +
380B GLY* 1.3 62.5 + - - -
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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