Contacts of the helix formed by residues 314 - 332 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 4.7 6.4 + - - -
280A SER* 4.8 1.3 - - - +
309A GLY 5.2 0.4 - - - +
310A ALA 4.4 3.6 - - - +
311A THR* 3.6 19.3 - - - +
312A ILE 3.0 11.5 + - - +
313A ASN* 1.3 76.5 + - - +
315A ASP* 1.3 60.1 - - - +
316A GLY 3.6 0.2 - - - -
317A THR* 4.1 16.6 - - - -
318A ALA* 3.2 22.7 + - - +
352A SER* 3.2 32.8 + - - +
355A THR* 3.2 33.0 - - - +
356A ALA 3.7 8.5 - - - +
357A GLY* 4.2 1.8 - - - -
405A ASN* 3.2 25.1 - - - +
501A ASP* 3.3 26.0 - - - +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 5.0 0.7 + - - -
94A THR* 3.2 40.8 + - - +
95A SER* 3.3 7.4 + - - -
98A ALA* 3.7 14.3 - - + +
244A GLN* 4.1 7.4 - - - +
249A TYR* 2.5 33.0 + - - +
313A ASN* 3.4 18.9 + - - +
314A MET* 1.3 71.6 - - - +
316A GLY* 1.3 60.0 + - - +
318A ALA* 3.3 2.4 + - - +
319A LEU* 2.9 30.1 + - - +
404A VAL* 4.6 6.5 - - + +
405A ASN* 2.8 7.7 + - - +
408A GLY* 4.2 5.0 - - - -
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 3.7 18.3 - - - +
315A ASP* 1.3 74.0 - - - +
317A THR* 1.3 56.2 + - - -
319A LEU* 3.3 2.9 + - - +
320A TYR* 2.9 28.6 + - - +
401A ARG* 3.4 26.2 - - - +
404A VAL* 4.1 6.5 - - - +
405A ASN* 2.6 16.4 + - - -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A MET* 4.1 17.5 - - - -
315A ASP 3.4 0.2 - - - -
316A GLY* 1.3 75.2 - - - +
318A ALA* 1.3 57.8 + - - +
320A TYR* 3.6 2.2 - - + +
321A GLN* 2.9 37.8 + - - +
352A SER* 4.5 11.0 - - - -
355A THR* 4.8 7.9 - - + +
362A GLY* 3.9 28.5 - - - +
401A ARG* 3.7 16.9 - - - +
405A ASN* 3.4 18.2 + - - -
501A ASP* 3.7 17.3 - - - +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 4.3 9.9 - - - +
98A ALA* 4.7 0.7 - - + -
99A VAL* 3.7 29.6 - - + +
314A MET 3.2 21.1 + - - +
315A ASP* 3.3 7.1 + - - +
316A GLY 3.2 0.6 - - - -
317A THR* 1.3 79.2 - - - +
319A LEU* 1.3 57.3 + - - +
321A GLN* 3.4 5.6 + - - +
322A GLY* 2.9 25.1 + - - -
348A ALA* 4.6 4.7 - - - +
352A SER* 3.8 18.1 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.3 30.0 + - + +
99A VAL* 4.8 1.1 - - - +
101A PHE* 4.2 4.9 - - + -
102A GLY* 3.6 14.6 - - - +
237A VAL* 4.1 15.5 - - + +
240A GLY* 3.4 43.3 - - - +
241A LEU* 4.1 10.8 - - + +
244A GLN* 4.1 14.6 - - + -
315A ASP 2.9 17.5 + - - +
316A GLY 3.8 3.1 - - - +
318A ALA* 1.3 73.2 - - - +
320A TYR* 1.3 61.7 + - - +
322A GLY* 3.2 1.0 + - - +
323A VAL* 2.9 48.8 + - + +
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 6.3 0.2 - - + -
237A VAL* 4.7 20.8 - - + +
316A GLY 2.9 17.6 + - - +
317A THR* 3.6 6.3 - - + +
319A LEU* 1.3 77.6 - - - +
321A GLN* 1.3 57.2 + - + +
323A VAL* 3.4 1.2 + - - +
324A THR* 2.3 61.3 + - + -
362A GLY* 3.2 29.2 - - - -
363A ALA* 3.8 17.7 - - - +
366A LEU* 4.3 3.9 - - + +
390A ILE* 3.3 24.0 - - + +
394A ASP* 4.2 4.6 + - - -
397A LEU* 3.5 31.9 - - + +
401A ARG* 3.3 43.7 - - + -
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Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A THR* 2.9 26.6 + - - +
318A ALA* 3.8 4.5 - - - +
320A TYR* 1.3 79.6 - - + +
322A GLY* 1.3 58.6 + - - +
324A THR* 4.2 2.5 - - - -
325A VAL* 2.9 37.0 + - - +
348A ALA* 3.8 19.9 - - + +
351A ALA* 3.6 25.0 + - - +
352A SER* 4.0 2.7 + - - -
362A GLY 3.7 14.0 + - - +
365A MET* 3.5 43.0 + - - +
366A LEU* 3.6 18.3 - - + +
369A VAL* 4.2 10.1 - - + +
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.4 16.4 - - - -
102A GLY 4.8 1.1 - - - -
103A LEU* 3.2 31.2 - - - +
318A ALA 2.9 15.5 + - - -
319A LEU* 3.2 3.8 + - - -
321A GLN* 1.3 78.2 - - - +
323A VAL* 1.3 61.4 + - - +
325A VAL* 4.3 3.6 - - - +
326A LEU* 3.6 10.9 + - - +
344A VAL* 5.3 3.4 - - - -
348A ALA* 5.1 2.9 - - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY* 3.4 32.5 - - - +
105A VAL* 4.2 6.1 - - + -
106A GLY* 4.6 7.0 - - - -
111A VAL* 4.1 25.7 - - + +
233A VAL* 5.5 4.7 - - + -
236A ALA* 4.6 7.6 - - + -
237A VAL* 4.5 21.1 - - + -
319A LEU* 2.9 28.8 + - + +
320A TYR 4.1 2.7 - - - +
322A GLY* 1.3 74.8 - - - +
324A THR* 1.3 59.5 + - - +
326A LEU* 3.4 5.5 + - - +
327A PHE* 2.9 26.3 + - + +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 5.7 4.1 - - - +
237A VAL* 5.4 1.4 - - - +
320A TYR* 2.3 43.8 + - - -
321A GLN 3.3 2.2 + - - -
323A VAL* 1.3 75.8 - - - +
325A VAL* 1.3 60.8 + - - +
327A PHE* 3.4 5.0 - - + +
328A VAL* 2.9 31.1 + - + +
366A LEU* 3.6 30.5 - - + -
370A LEU* 5.5 0.2 - - - -
390A ILE* 3.6 41.0 - - + +
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLN 2.9 22.0 + - - +
322A GLY 4.3 3.4 - - - +
324A THR* 1.3 75.5 - - - +
326A LEU* 1.3 58.4 + - - +
328A VAL* 3.1 10.4 - - + +
329A ALA* 2.9 28.8 + - + +
336A LEU* 4.2 11.7 - - + -
344A VAL* 4.1 16.4 - - + -
366A LEU* 4.1 2.2 - - + -
369A VAL* 3.6 37.2 - - + -
370A LEU* 3.9 13.5 - - + -
373A VAL* 3.7 27.4 - - + -
375A LEU* 6.4 0.7 - - + -
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 4.0 38.8 - - + +
106A GLY* 4.4 15.0 - - - +
107A ARG* 4.5 13.9 - - + +
111A VAL* 4.4 12.6 - - + -
322A GLY 3.6 10.2 + - - +
323A VAL* 3.4 9.3 + - - +
324A THR 3.3 0.4 - - - -
325A VAL* 1.3 80.2 - - - +
327A PHE* 1.3 58.1 + - - +
329A ALA* 3.4 5.5 + - + +
330A ASN* 2.9 48.7 + - - +
336A LEU* 5.1 21.3 - - + +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.6 17.9 - - + +
112A GLY* 3.5 32.9 - - - +
115A VAL* 4.7 7.9 - - + -
229A PRO* 5.4 3.1 - - + -
230A LEU* 4.7 3.6 - - + -
233A VAL* 3.7 25.8 - - + -
323A VAL 2.9 18.3 + - - +
324A THR* 3.4 8.7 - - - +
326A LEU* 1.3 76.6 - - - +
328A VAL* 1.3 75.7 + - + +
330A ASN* 3.1 3.8 + - - +
331A ALA* 2.9 33.4 + - + +
386A ALA* 4.3 7.9 - - + -
389A MET* 3.5 33.2 - - + -
390A ILE* 3.5 36.6 - - + -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A THR* 2.9 17.3 + - + +
325A VAL* 3.1 15.7 - - + +
327A PHE* 1.3 85.3 - - + +
329A ALA* 1.3 61.4 + - + +
331A ALA* 3.7 8.1 + - - +
332A ILE* 3.6 19.5 + - + +
370A LEU* 3.5 38.4 - - + -
375A LEU* 5.2 10.0 - - + +
383A VAL* 4.7 19.1 - - + +
386A ALA* 3.6 28.3 - - + -
387A TYR* 5.2 0.7 - - - +
390A ILE* 6.0 0.7 - - + -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A VAL* 2.9 20.8 + - + +
326A LEU* 3.7 4.3 - - + +
328A VAL* 1.3 79.5 - - + +
330A ASN* 1.3 59.8 + - - +
332A ILE* 3.9 4.6 + - - +
333A GLY 3.4 3.6 + - - -
334A HIS* 2.8 50.1 + - + +
335A PRO* 4.9 0.4 - - + -
336A LEU* 3.7 24.5 - - + +
375A LEU* 5.3 11.7 - - + -
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Residues in contact with ASN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 3.1 28.9 - - - +
111A VAL 3.5 9.6 + - - +
112A GLY 3.2 19.3 - - - +
113A ALA* 4.9 4.6 - - - +
326A LEU* 2.9 35.2 + - - +
327A PHE 3.7 0.7 - - - +
329A ALA* 1.3 74.6 - - - +
331A ALA* 1.3 64.4 + - - +
332A ILE 3.5 0.2 - - - -
333A GLY* 3.6 8.8 + - - +
334A HIS 4.7 1.3 - - - +
335A PRO* 3.2 37.8 - - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLY 3.8 8.3 - - - +
113A ALA 6.1 0.7 - - - -
115A VAL* 4.7 18.6 + - + +
116A ASN* 4.6 6.2 + - - -
117A LEU* 4.2 25.3 + - + -
118A GLY 4.5 1.9 + - - -
327A PHE* 2.9 28.8 + - + +
328A VAL* 4.0 9.0 - - - +
329A ALA 3.3 0.6 - - - -
330A ASN* 1.3 79.8 - - - +
332A ILE* 1.3 65.7 + - + +
333A GLY* 3.3 0.9 + - - -
386A ALA* 5.0 3.6 - - + -
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.3 20.4 - - + -
118A GLY* 4.8 3.3 - - - +
119A SER* 3.6 41.0 + - - +
328A VAL* 3.6 18.8 - - + +
329A ALA* 4.2 2.0 - - - +
331A ALA* 1.3 80.2 - - + +
333A GLY* 1.3 57.1 + - - +
334A HIS* 3.0 41.1 + - + +
375A LEU* 3.6 31.0 - - + -
382A PRO* 4.4 10.1 - - + -
383A VAL* 3.8 17.5 - - + +
386A ALA* 5.6 0.2 - - + -
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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
------------------------------------------------------------
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