Contacts of the helix formed by residues 382 - 393 (chain B) in PDB entry 6XWQ
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 PRO 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.7 22.8 - - + +
118B GLY 4.9 0.4 - - - +
119B SER* 4.1 33.2 - - - +
332B ILE* 3.9 22.2 - - + -
380B GLY 4.4 1.8 - - - +
381B SER* 1.3 88.2 - - - +
383B VAL* 1.3 55.9 + - - +
384B ALA 3.1 0.4 - - - -
385B LEU* 2.8 26.7 + - + +
386B ALA* 2.9 11.6 + - - +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 4.8 9.2 - - + -
332B ILE* 3.8 13.5 - - + -
370B LEU* 5.8 2.9 - - + -
375B LEU* 3.6 32.8 - - + -
376B ASP* 3.2 33.9 - - - +
377B LEU* 4.0 11.0 - - + -
378B THR 4.1 2.9 - - - +
381B SER* 3.6 19.5 - - - -
382B PRO* 1.3 77.4 - - - +
384B ALA* 1.3 59.2 + - - +
386B ALA* 4.3 8.1 - - - +
387B TYR* 2.8 39.4 + - + +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU 5.6 1.1 - - - +
378B THR 3.9 1.8 - - - +
379B PRO* 3.3 41.5 - - + +
381B SER 3.0 10.6 + - - +
383B VAL* 1.3 81.5 - - - +
385B LEU* 1.3 55.7 + - - +
387B TYR* 4.8 2.0 - - - -
388B ALA* 3.3 20.1 + - - +
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Residues in contact with LEU 385 (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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117B LEU* 3.7 28.5 - - + -
225B ARG* 6.1 2.5 - - - +
381B SER 4.3 0.4 + - - +
382B PRO* 2.8 14.8 + - + +
384B ALA* 1.3 78.2 - - - +
386B ALA* 1.3 64.6 + - - +
388B ALA* 3.2 8.3 + - + +
389B MET* 3.1 28.9 + - + +
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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
----------------------------------------------------------
117B LEU* 3.7 21.4 - - + +
327B PHE* 4.7 11.4 - - + -
328B VAL* 3.7 25.4 - - + -
331B ALA* 4.8 7.0 - - + -
332B ILE* 4.9 2.0 - - + -
382B PRO 2.9 10.7 + - - +
383B VAL* 4.4 2.0 - - - +
385B LEU* 1.3 73.2 - - - +
387B TYR* 1.3 66.6 + - - +
389B MET* 2.9 31.4 + - + +
390B ILE* 3.2 7.4 + - - +
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Residues in contact with TYR 387 (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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328B VAL* 4.7 4.1 - - + +
363B ALA* 2.6 27.4 + - + -
364B ILE* 3.9 10.6 + - - -
366B LEU* 3.9 23.6 - - + -
367B ALA* 4.0 14.7 + - + +
370B LEU* 3.6 28.7 - - + -
377B LEU* 4.5 10.5 - - + -
383B VAL* 2.8 26.6 + - + +
384B ALA* 4.8 2.0 - - - -
386B ALA* 1.3 73.8 - - - +
388B ALA* 1.3 60.9 + - - +
390B ILE* 3.6 7.5 + - - +
391B LEU* 3.2 42.6 + - + +
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Residues in contact with ALA 388 (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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225B ARG* 4.5 10.5 + - - +
384B ALA 3.3 22.2 + - - +
385B LEU* 3.2 14.2 + - + +
386B ALA 3.0 1.0 - - - -
387B TYR* 1.3 82.2 - - - +
389B MET* 1.3 57.6 + - - +
391B LEU* 3.5 7.1 + - - +
392B GLY* 2.9 23.9 + - - -
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Residues in contact with MET 389 (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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115B VAL* 4.1 29.2 - - + -
117B LEU* 5.5 0.4 - - + -
225B ARG* 4.5 14.6 - - - +
229B PRO* 5.9 4.7 - - + -
230B LEU* 3.2 47.7 - - + +
327B PHE* 3.6 28.5 - - + -
385B LEU* 3.1 21.1 + - + +
386B ALA* 2.9 24.1 + - - +
388B ALA* 1.3 74.5 - - - +
390B ILE* 1.3 66.0 + - - +
392B GLY* 3.4 7.1 + - - +
393B ILE* 3.7 3.5 + - - +
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Residues in contact with ILE 390 (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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230B LEU* 4.6 6.3 - - + -
233B VAL* 4.1 23.3 - - + -
320B TYR* 3.2 28.0 + - + +
324B THR* 3.6 28.9 - - + +
327B PHE* 3.4 39.7 - - + -
328B VAL* 6.0 0.9 - - + -
363B ALA* 5.8 0.9 - - + -
366B LEU* 4.2 9.0 - - + -
386B ALA 3.2 7.4 + - - +
387B TYR* 3.9 10.3 - - - +
389B MET* 1.3 73.0 - - - +
391B LEU* 1.3 63.5 + - - +
392B GLY 3.0 4.8 + - - -
393B ILE* 3.1 19.4 + - + +
394B ASP* 3.2 9.9 + - - -
397B LEU* 4.8 3.1 - - + +
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Residues in contact with LEU 391 (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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363B ALA* 4.4 21.3 - - + -
364B ILE* 6.4 1.6 - - + -
387B TYR* 3.2 37.7 + - + +
388B ALA* 3.9 6.3 - - - +
390B ILE* 1.3 80.2 - - - +
392B GLY* 1.3 62.6 - - - +
393B ILE 3.3 0.2 - - - -
394B ASP* 3.4 23.2 + - + +
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Residues in contact with GLY 392 (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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218B VAL* 5.2 2.4 - - - +
222B GLN* 3.2 29.0 + - - +
225B ARG* 4.0 20.4 - - - -
388B ALA 2.9 16.7 + - - -
389B MET 3.4 4.5 + - - -
390B ILE 3.0 1.8 - - - -
391B LEU* 1.3 81.5 - - - +
393B ILE* 1.3 60.7 + - - +
394B ASP 3.7 1.4 + - - -
395B ALA 5.1 0.7 + - - -
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Residues in contact with ILE 393 (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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218B VAL* 5.9 1.1 - - - -
222B GLN* 4.7 7.4 - - + -
225B ARG* 4.3 11.4 - - + +
226B VAL* 4.3 7.6 - - + -
230B LEU* 3.7 54.7 - - + +
233B VAL* 4.8 5.6 - - + -
234B VAL* 4.7 10.3 - - + -
389B MET 3.7 6.5 + - - +
390B ILE* 3.5 12.6 - - + +
392B GLY* 1.3 76.8 - - - +
394B ASP* 1.3 64.4 + - - +
395B ALA* 3.0 5.5 + - - +
396B ILE* 3.3 32.9 + - + -
397B LEU* 3.6 27.8 - - + +
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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
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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