Contacts of the helix formed by residues 311 - 332 (chain B) in PDB entry 2VLH
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 GLN 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 4.8 14.0 + - - +
307B ARG 4.2 1.2 + - - +
308B GLU* 3.1 17.1 + - - +
309B ALA 3.2 1.2 - - - +
310B MET* 1.3 77.6 - - - +
312B TYR* 1.3 69.7 + - - +
313B GLU* 3.7 25.2 + - - +
314B TYR* 3.2 29.7 + - + +
315B ILE* 3.2 12.4 + - - +
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.7 25.7 + + - -
226B LYS* 3.7 35.5 - - + +
236B SER* 6.5 0.2 - - - -
237B ILE* 4.0 23.1 - - + +
310B MET 3.2 4.8 + - - -
311B GLN* 1.3 72.7 - - - +
313B GLU* 1.3 79.3 + - + +
315B ILE* 3.2 3.6 + - - +
316B GLU* 2.8 64.2 + - + +
320B LYS* 5.2 0.5 + - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 5.6 0.2 - - - +
7B PRO* 3.4 29.4 - - + +
311B GLN* 3.3 24.3 + - - +
312B TYR* 1.3 96.1 + - + +
314B TYR* 1.3 63.5 + - - +
316B GLU* 3.9 11.0 - - - +
317B HIS* 3.1 19.1 + - - +
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.8 12.4 - - + +
8B PHE* 4.9 7.0 - + + -
258B ASP* 4.5 2.8 + - - -
260B LEU* 3.4 15.8 - - + +
308B GLU 3.9 4.3 - - - +
309B ALA* 3.6 38.1 - - + -
311B GLN* 3.2 27.8 + - + +
313B GLU* 1.3 78.9 - - - +
315B ILE* 1.3 90.2 + - + +
317B HIS* 3.4 3.4 + - - +
318B ARG* 2.9 38.5 + - + +
409B ARG* 3.3 31.7 + - + +
410B ARG* 3.8 39.3 - - + +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 3.7 28.9 - - + +
220B GLU* 3.8 27.8 - - + +
223B TYR* 3.8 13.2 - - + -
237B ILE* 3.8 35.7 - - + -
258B ASP* 4.4 2.0 - - - +
309B ALA 4.1 6.1 - - - +
311B GLN 3.2 5.1 + - - +
312B TYR 3.2 8.9 + - - +
314B TYR* 1.3 106.6 - - + +
316B GLU* 1.3 69.2 + - - +
318B ARG* 4.1 7.0 - - + -
319B VAL* 3.0 25.5 + - + +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.1 6.8 + - - +
4B PRO* 4.1 21.3 - - - +
223B TYR* 3.6 35.4 - - + +
312B TYR* 2.8 43.9 + - + +
313B GLU* 3.9 12.2 - - - +
315B ILE* 1.3 79.5 - - - +
317B HIS* 1.3 55.6 + - - +
319B VAL* 4.0 1.0 - - - +
320B LYS* 2.8 61.6 + - + +
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 3.6 38.8 - - + +
5B ALA 4.5 0.4 - - - +
6B GLU* 3.6 33.0 + - + +
7B PRO* 3.7 19.7 - - + +
8B PHE* 4.1 17.2 - + - -
313B GLU 3.1 19.3 + - - +
314B TYR* 3.8 2.9 + - - +
316B GLU* 1.3 74.1 - - - +
318B ARG* 1.3 72.3 + - - +
320B LYS 4.5 0.2 - - - +
321B GLN* 2.8 53.7 + - + +
410B ARG* 5.9 2.7 - - - -
412B TYR 5.0 0.7 - - - -
414B TYR* 3.7 10.1 + + - -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 3.6 2.0 + - - -
220B GLU* 2.7 36.9 + - - +
314B TYR* 2.9 33.5 + - + +
315B ILE* 3.3 13.0 + - + +
317B HIS* 1.3 84.9 + - - +
319B VAL* 1.3 64.7 + - - +
321B GLN* 3.6 6.8 + - - +
322B VAL* 3.4 23.4 + - - +
342B GLY 3.4 15.5 + - - -
343B HIS* 3.5 14.4 - - - +
407B ILE* 2.8 43.4 + - - +
408B PRO 4.0 4.6 + - - -
409B ARG* 3.3 45.4 - - + +
410B ARG 5.7 0.9 - - - +
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLU* 4.3 30.1 - - + +
223B TYR* 3.8 29.8 - - + -
224B PHE* 3.9 17.5 - - + -
315B ILE* 3.0 20.3 + - + +
318B ARG* 1.3 78.1 - - - +
320B LYS* 1.3 58.6 + - - +
322B VAL* 3.4 5.5 + - - +
323B ARG* 2.9 44.9 + - + +
341B GLY 5.0 2.5 - - - +
342B GLY* 4.2 19.3 - - - +
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Residues in contact with LYS 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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1B MET 2.6 35.5 + - - +
2B ASN* 3.3 23.8 - - - +
3B TYR* 3.7 4.7 - - - -
4B PRO* 3.6 19.3 - - + -
223B TYR* 3.2 24.5 + - + +
227B GLU* 3.7 10.5 + - - -
312B TYR* 5.2 0.8 + - - -
316B GLU* 2.8 38.9 + - + +
317B HIS 4.2 1.1 - - - +
319B VAL* 1.3 74.9 - - - +
321B GLN* 1.3 60.3 + - - +
323B ARG* 3.4 25.3 - - - +
324B TYR* 2.8 27.7 + - - +
414B TYR* 4.6 2.5 - - - +
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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
----------------------------------------------------------
317B HIS* 2.8 43.7 + - + +
318B ARG* 3.6 8.6 + - - +
319B VAL 3.3 0.2 - - - -
320B LYS* 1.3 75.1 - - - +
322B VAL* 1.3 64.8 + - - +
324B TYR* 3.3 4.0 + - - +
325B LEU* 3.3 19.8 + - - +
407B ILE* 3.4 24.7 - - - +
408B PRO 4.6 2.8 - - - +
410B ARG 5.5 2.9 + - - -
412B TYR* 2.8 36.1 + - - +
413B THR* 3.7 11.5 - - - +
414B TYR* 3.8 17.7 + - + +
417B MET* 3.8 22.6 - - + +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG* 3.4 15.9 + - - +
319B VAL 3.4 6.4 + - - +
321B GLN* 1.3 76.6 - - - +
323B ARG* 1.3 62.8 + - - +
325B LEU* 3.2 9.6 + - - +
326B GLY* 3.0 17.8 + - - -
340B VAL* 3.8 4.6 - - + +
341B GLY 3.6 15.3 - - - +
342B GLY 3.5 20.2 - - - +
343B HIS 4.0 4.3 - - - -
344B ALA* 3.4 35.9 - - - +
345B VAL* 3.7 4.9 - - + +
407B ILE* 3.9 31.2 - - + -
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Residues in contact with ARG 323 (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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2B ASN 5.4 1.3 + - - -
3B TYR* 4.8 4.5 - - + -
223B TYR* 4.2 0.4 - - - -
224B PHE* 4.0 13.3 - - - -
227B GLU* 2.7 44.8 + - - -
228B GLN* 4.1 3.9 - - - +
319B VAL* 2.9 34.7 + - + +
320B LYS* 3.4 33.6 - - - +
321B GLN 3.2 0.2 - - - -
322B VAL* 1.3 76.5 - - - +
324B TYR* 1.3 54.2 + - - +
326B GLY* 3.2 1.1 + - - +
327B ASP* 2.7 60.7 + - - +
340B VAL* 4.6 16.1 + - + +
341B GLY 5.4 0.2 + - - -
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Residues in contact with TYR 324 (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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3B TYR* 3.5 46.4 - + + -
320B LYS 2.8 17.2 + - - +
321B GLN 3.4 8.7 - - - +
323B ARG* 1.3 72.8 - - - +
325B LEU* 1.3 65.0 + - - +
327B ASP* 3.8 1.2 - - - +
328B LYS* 3.0 42.3 + - + +
414B TYR* 3.5 42.1 - + + +
417B MET* 3.8 14.8 - - + -
418B ASP* 2.6 36.0 + - - -
421B ALA* 6.0 0.2 - - + -
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Residues in contact with LEU 325 (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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47B LEU* 5.1 0.2 - - + -
321B GLN 3.3 7.4 + - - +
322B VAL* 3.2 9.2 + - - +
324B TYR* 1.3 83.9 - - - +
326B GLY* 1.3 64.1 + - - +
328B LYS* 3.8 3.0 - - - +
329B LEU* 3.1 44.3 + - + +
345B VAL* 3.8 18.8 - - + -
405B LEU* 4.2 17.0 - - + -
407B ILE* 4.0 26.7 - - + -
417B MET* 3.8 35.7 - - + +
420B VAL* 3.8 19.7 - - + -
421B ALA* 3.9 9.6 - - + -
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Residues in contact with GLY 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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322B VAL 3.0 10.9 + - - -
323B ARG 3.6 2.2 - - - -
325B LEU* 1.3 77.2 - - - +
327B ASP* 1.3 56.5 + - - +
329B LEU* 3.3 3.3 + - - +
330B LYS* 2.9 31.4 + - - +
336B ILE* 3.9 10.7 - - - +
340B VAL* 3.9 16.6 - - - -
345B VAL* 3.6 19.8 - - - +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 5.4 0.7 + - - -
3B TYR* 2.4 38.9 + - - +
323B ARG* 2.7 38.6 + - - +
324B TYR 3.8 1.8 - - - +
326B GLY* 1.3 72.4 - - - +
328B LYS* 1.3 53.3 + - - +
330B LYS* 3.4 6.4 + - - +
331B ALA* 2.8 37.0 + - - +
340B VAL* 5.3 3.8 - - - +
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Residues in contact with LYS 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 TYR* 3.0 32.2 + - + +
325B LEU* 3.8 4.0 - - - +
327B ASP* 1.3 76.1 - - - +
329B LEU* 1.3 62.9 + - - +
331B ALA* 3.5 6.6 + - - +
332B ALA* 3.3 15.1 + - - +
418B ASP* 2.7 34.3 + - - +
421B ALA* 3.8 20.6 - - + -
422B ASP* 3.0 28.7 + - - -
425B ILE* 3.8 17.3 - - + +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.1 39.2 + - + +
326B GLY 3.7 3.1 - - - +
328B LYS* 1.3 72.4 - - - +
330B LYS* 1.3 65.2 + - - +
332B ALA* 3.1 10.2 + - - +
334B VAL* 3.1 36.5 + - + +
336B ILE* 4.3 5.8 - - + -
345B VAL* 4.0 23.1 - - + -
347B LEU* 4.0 15.5 - - + -
405B LEU* 4.0 6.7 - - + -
421B ALA* 4.0 20.2 - - + +
424B ILE* 3.8 33.0 - - + -
425B ILE* 4.1 8.5 - - + -
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 4.1 9.3 + - - +
326B GLY 2.9 21.0 + - - +
327B ASP* 3.8 6.5 - - - +
329B LEU* 1.3 72.8 - - - +
331B ALA* 1.3 60.6 + - - +
333B GLY* 2.8 20.4 + - - -
334B VAL 4.1 10.3 + - - +
336B ILE* 4.3 14.1 - - + +
338B GLU* 3.0 41.5 + - + +
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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
----------------------------------------------------------
327B ASP 2.8 21.4 + - - +
328B LYS* 3.8 7.6 - - - +
329B LEU 3.3 0.2 - - - -
330B LYS* 1.3 71.5 - - - +
332B ALA* 1.3 60.2 + - - +
333B GLY 3.4 1.0 + - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS 3.3 2.3 + - - +
329B LEU 3.1 8.0 + - - +
331B ALA* 1.3 76.5 - - - +
333B GLY* 1.3 60.0 + - - +
334B VAL* 3.3 3.0 + - + -
425B ILE* 3.6 47.8 - - + -
428B TYR* 4.0 13.9 - - + -
429B GLN* 6.0 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
------------------------------------------------------------
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