Contacts of the helix formed by residues 314 - 332 (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 MET 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 4.7 5.1 + - - -
280B SER* 4.5 2.9 - - - +
309B GLY 5.1 0.4 - - - +
310B ALA 4.3 4.0 - - - +
311B THR* 3.4 21.8 - - - +
312B ILE 3.0 10.9 + - - +
313B ASN* 1.3 76.9 + - - +
315B ASP* 1.3 61.3 + - - +
317B THR* 4.0 13.0 - - - -
318B ALA* 3.3 23.5 + - - +
352B SER* 3.2 31.9 + - - +
355B THR* 3.2 29.6 - - - +
356B ALA 3.8 9.2 - - - +
357B GLY* 4.0 4.7 - - - +
405B ASN* 3.1 27.1 - - + +
501B ASP* 3.3 24.7 - - - +
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 5.1 0.2 + - - -
94B THR* 3.0 33.7 + - - +
95B SER* 3.2 19.6 + - - -
98B ALA* 3.6 16.1 - - + +
244B GLN* 4.4 4.0 - - - +
249B TYR* 2.4 37.1 + - - +
313B ASN* 3.4 15.1 + - - +
314B MET* 1.3 72.3 - - - +
316B GLY* 1.3 59.4 + - - +
318B ALA* 3.3 2.7 + - - +
319B LEU* 2.9 30.8 + - - +
404B VAL* 4.6 6.5 - - + +
405B ASN* 2.7 8.2 + - - +
408B GLY* 4.3 4.0 - - - -
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.7 20.1 - - - +
315B ASP* 1.3 73.4 - - - +
317B THR* 1.3 55.1 + - - -
319B LEU* 3.3 3.1 + - - +
320B TYR* 2.9 28.8 + - - +
401B ARG* 3.3 25.1 - - - +
404B VAL* 3.9 6.9 - - - +
405B ASN* 2.5 17.1 + - - -
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B MET* 4.0 10.7 - - + +
316B GLY* 1.3 75.1 - - - +
318B ALA* 1.3 59.3 + - - +
320B TYR* 3.3 1.8 + - + +
321B GLN* 2.9 37.3 + - + +
352B SER* 4.4 12.3 - - - -
355B THR* 4.7 10.3 - - + +
362B GLY* 4.0 26.2 - - - -
401B ARG* 3.7 16.5 - - - +
405B ASN* 3.1 23.5 + - - -
501B ASP* 3.6 18.1 - - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 4.3 12.3 - - - +
98B ALA* 4.8 0.7 - - + -
99B VAL* 3.6 30.0 - - + +
314B MET 3.3 20.0 + - - +
315B ASP* 3.3 6.2 + - - +
316B GLY 3.2 0.6 - - - -
317B THR* 1.3 79.6 - - - +
319B LEU* 1.3 57.6 + - - +
321B GLN* 3.3 5.6 + - - +
322B GLY* 2.9 23.0 + - - -
348B ALA* 4.6 4.4 - - - +
352B SER* 3.8 18.1 - - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.4 29.3 + - + +
99B VAL* 4.7 1.6 - - - +
101B PHE* 4.3 4.0 - - + -
102B GLY* 3.6 13.9 - - - +
237B VAL* 4.2 15.5 - - + +
240B GLY* 3.4 43.7 - - - +
241B LEU* 4.2 9.4 - - + +
244B GLN* 4.1 14.8 - - + -
315B ASP 2.9 16.9 + - - +
316B GLY 3.8 3.4 - - - +
318B ALA* 1.3 73.7 - - - +
320B TYR* 1.3 68.2 + - - +
322B GLY* 3.7 0.8 - - - +
323B VAL* 2.9 45.1 + - + +
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Residues in contact with TYR 320 (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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237B VAL* 4.7 15.9 - - + +
316B GLY 2.9 17.2 + - - +
317B THR 3.3 6.9 + - - +
319B LEU* 1.3 79.2 - - - +
321B GLN* 1.3 64.0 + - + +
323B VAL* 3.4 2.7 + - - +
324B THR* 2.6 52.9 + - + -
362B GLY* 4.0 21.1 - - - -
363B ALA* 4.2 10.2 - - - +
366B LEU* 4.6 4.9 - - + +
390B ILE* 3.2 25.7 + - + +
394B ASP* 4.0 9.1 + - - -
397B LEU* 3.5 35.5 - - + +
401B ARG* 3.3 44.6 - - + -
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Residues in contact with GLN 321 (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 THR* 2.9 29.0 + - + +
318B ALA 3.7 4.3 - - - +
320B TYR* 1.3 85.7 - - + +
322B GLY* 1.3 59.1 + - - +
324B THR 4.4 0.2 - - - +
325B VAL* 2.9 37.0 + - - +
348B ALA* 3.7 20.2 - - + +
351B ALA* 3.4 28.7 + - - +
352B SER* 4.6 1.7 - - - -
362B GLY 3.7 5.3 + - - +
365B MET* 3.5 39.0 + - - +
366B LEU* 3.6 18.1 - - + +
369B VAL* 4.1 14.4 - - + +
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.6 20.2 - - - -
102B GLY 4.8 1.8 - - - -
103B LEU* 3.2 29.1 - - - +
318B ALA 2.9 16.0 + - - -
319B LEU* 3.2 4.4 + - - -
321B GLN* 1.3 77.5 - - - +
323B VAL* 1.3 60.8 + - - +
325B VAL* 4.4 4.0 - - - +
326B LEU* 3.7 8.5 + - - +
344B VAL* 5.2 5.6 - - - -
348B ALA* 5.0 1.7 - - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY* 3.3 33.0 - - - +
105B VAL* 4.1 5.8 - - + -
106B GLY* 4.6 7.2 - - - -
111B VAL* 4.2 25.6 - - + +
233B VAL* 5.4 5.4 - - + -
236B ALA* 4.7 7.2 - - + -
237B VAL* 4.5 21.3 - - + -
319B LEU* 2.9 27.8 + - + +
320B TYR 4.1 2.2 - - - +
322B GLY* 1.3 76.5 - - - +
324B THR* 1.3 59.1 + - - +
326B LEU* 3.4 5.1 + - - +
327B PHE* 2.9 25.3 + - - +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 5.4 4.9 - - - +
237B VAL* 5.4 0.9 - - - +
320B TYR* 2.6 41.5 + - - -
321B GLN 4.0 1.8 - - - -
323B VAL* 1.3 74.1 - - - +
325B VAL* 1.3 62.5 + - - +
327B PHE* 3.2 5.9 + - + +
328B VAL* 2.9 31.4 + - + +
366B LEU* 3.6 34.8 - - + -
390B ILE* 3.6 34.2 - - + +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN 2.9 21.4 + - - +
322B GLY 4.4 2.2 - - - +
324B THR* 1.3 76.2 - - - +
326B LEU* 1.3 57.3 + - - +
328B VAL* 3.2 10.2 - - + +
329B ALA* 2.9 28.4 + - + +
336B LEU* 4.1 17.5 - - + -
344B VAL* 4.1 12.3 - - + -
366B LEU* 4.2 2.0 - - + -
369B VAL* 3.6 37.2 - - + +
370B LEU* 3.9 13.0 - - + -
373B VAL* 3.6 27.8 - - + -
375B LEU* 6.1 0.9 - - + -
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Residues in contact with LEU 326 (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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103B LEU* 3.7 27.3 - - + +
106B GLY* 4.4 17.3 - - - +
107B ARG* 4.2 25.8 - - + +
110B ASN* 5.8 0.2 - - - -
111B VAL* 4.4 12.6 - - + +
322B GLY 3.7 10.9 + - - +
323B VAL* 3.4 8.6 + - - +
324B THR 3.3 0.6 - - - -
325B VAL* 1.3 79.7 - - - +
327B PHE* 1.3 57.6 + - - +
329B ALA* 3.7 5.7 - - + +
330B ASN* 2.9 50.1 + - - +
336B LEU* 4.9 21.1 - - + +
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Residues in contact with PHE 327 (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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111B VAL* 3.6 18.3 - - + +
112B GLY* 3.5 34.2 - - - +
115B VAL* 4.8 6.1 - - + -
229B PRO* 5.4 3.1 - - + -
230B LEU* 4.6 2.5 - - + -
233B VAL* 3.7 24.0 - - + -
323B VAL 2.9 15.1 + - - +
324B THR* 3.4 11.2 - - - +
325B VAL 3.2 0.2 - - - -
326B LEU* 1.3 75.9 - - - +
328B VAL* 1.3 76.4 + - + +
330B ASN* 3.2 4.2 + - - +
331B ALA* 2.9 34.6 + - + +
386B ALA* 4.4 10.3 - - + -
389B MET* 3.6 33.0 - - + -
390B ILE* 3.4 36.1 - - + -
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Residues in contact with VAL 328 (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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324B THR* 2.9 18.3 + - + +
325B VAL* 3.2 14.6 - - + +
327B PHE* 1.3 84.1 - - + +
329B ALA* 1.3 61.8 + - + +
331B ALA* 3.6 7.9 + - - +
332B ILE* 3.6 21.2 + - + +
370B LEU* 3.5 35.9 - - + -
375B LEU* 4.8 9.7 - - + +
383B VAL* 4.8 17.0 - - + -
386B ALA* 3.7 26.9 - - + -
387B TYR* 4.7 6.5 - - - +
390B ILE* 6.0 0.9 - - + -
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Residues in contact with ALA 329 (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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325B VAL* 2.9 19.0 + - + +
326B LEU* 3.7 5.2 - - + +
328B VAL* 1.3 78.5 - - + +
330B ASN* 1.3 64.0 + - - +
331B ALA 3.3 0.5 + - - -
332B ILE* 3.8 1.0 + - - -
333B GLY 3.4 4.2 + - - -
334B HIS* 2.8 53.3 + - + +
335B PRO* 4.6 1.6 - - + -
336B LEU* 3.9 20.6 - - + -
375B LEU* 5.1 10.8 - - + -
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Residues in contact with ASN 330 (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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110B ASN* 3.5 25.6 - - - +
111B VAL 3.6 6.4 + - - +
112B GLY 3.2 19.9 - - - +
113B ALA* 4.9 4.4 - - - +
326B LEU* 2.9 37.9 + - - +
327B PHE 3.8 0.7 - - - +
329B ALA* 1.3 74.8 - - - +
331B ALA* 1.3 62.7 + - - +
333B GLY* 4.0 5.4 + - - -
334B HIS 4.9 1.3 - - - +
335B PRO* 3.3 34.7 - - - +
336B LEU 4.9 0.2 + - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY 3.8 7.9 - - - +
113B ALA 6.2 0.2 - - - -
115B VAL* 4.9 16.0 + - + +
116B ASN* 4.6 5.5 + - - -
117B LEU* 4.2 18.2 + - + -
118B GLY* 4.4 1.7 + - - -
327B PHE* 2.9 27.2 + - + +
328B VAL* 3.8 11.2 - - - +
329B ALA 3.2 0.6 - - - -
330B ASN* 1.3 80.4 - - - +
332B ILE* 1.3 65.7 + - + +
333B GLY 3.3 2.4 + - - -
386B ALA* 4.8 10.5 - - + -
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Residues in contact with ILE 332 (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 30.3 - - + -
118B GLY* 4.4 3.6 - - - +
119B SER* 3.5 48.2 + - - +
328B VAL* 3.6 14.3 + - + +
329B ALA* 4.6 2.9 - - - +
331B ALA* 1.3 80.8 - - + +
333B GLY* 1.3 62.2 + - - +
334B HIS* 5.3 3.6 - - + +
375B LEU* 3.6 30.5 - - + -
382B PRO* 3.9 17.3 - - + -
383B VAL* 3.8 15.9 - - + +
386B ALA* 4.9 4.0 - - + -
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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