Contacts of the helix formed by residues 313 - 334 (chain B) in PDB entry 3GV5
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 SER 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B SER* 1.3 81.1 - - - +
314B GLU* 1.3 62.3 + - - +
315B VAL* 3.9 6.8 + - - +
316B GLU* 3.1 37.8 + - - +
317B ALA* 3.1 22.7 + - - +
401B PHE* 3.6 9.2 - - - -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B SER* 1.3 70.7 - - - +
315B VAL* 1.3 61.2 + - + +
317B ALA* 4.3 4.5 - - - +
318B LYS* 2.9 35.6 + - + +
388B MSE 3.6 20.3 - - + +
391B PHE* 4.4 7.4 - - + -
392B ARG* 2.8 44.9 + - - +
397B VAL* 3.6 31.9 - - + +
401B PHE* 3.9 6.7 - - - -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B SER* 3.3 7.1 + - - +
314B GLU* 1.3 75.4 - - + +
316B GLU* 1.3 66.8 + - + +
317B ALA 3.1 0.7 + - - -
318B LYS* 3.6 6.8 - - - +
319B ASN* 3.2 33.0 + - - +
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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
----------------------------------------------------------
310B LYS* 4.0 17.0 + - - +
311B CYS* 3.5 15.5 - - - -
312B SER* 3.7 21.5 + - - -
313B SER* 3.1 32.7 + - - +
315B VAL* 1.3 77.1 - - + +
317B ALA* 1.4 59.5 + - - +
319B ASN* 3.2 8.9 + - - +
320B LYS* 3.1 46.6 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B CYS* 3.5 19.3 - - - -
313B SER 3.1 14.7 + - - +
314B GLU 3.0 4.8 + - - +
316B GLU* 1.4 76.1 - - - +
318B LYS* 1.4 61.3 + - - +
320B LYS* 3.4 3.1 + - - +
321B ILE* 3.1 37.4 + - - +
391B PHE* 3.9 32.5 - - + -
401B PHE* 5.2 0.2 - - + -
403B LEU* 4.9 0.7 - - + -
406B LEU* 4.0 10.1 - - + +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 2.9 20.2 + - + +
315B VAL* 3.6 7.6 - - - +
317B ALA* 1.4 71.1 - - - +
319B ASN* 1.3 65.9 + - - +
321B ILE* 3.4 2.2 + - - +
322B GLU* 3.0 47.5 + - + +
384B VAL* 4.6 16.4 - - + +
385B ASP* 5.6 4.0 + - - -
388B MSE 3.9 39.1 - - + +
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.2 31.2 + - - +
316B GLU* 3.2 11.3 + - - +
318B LYS* 1.3 74.4 - - - +
320B LYS* 1.3 65.1 + - + +
322B GLU* 3.7 15.7 + - - +
323B GLU* 3.2 22.7 + - - +
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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
----------------------------------------------------------
306B ASP* 5.1 7.0 + - + +
308B PHE* 4.2 33.0 - - + +
310B LYS 5.3 3.4 + - - -
311B CYS* 4.7 4.0 - - - -
316B GLU* 3.1 46.4 + - - +
317B ALA* 3.5 9.4 - - - +
319B ASN* 1.3 79.6 - - + +
321B ILE* 1.3 60.2 + - - +
323B GLU* 3.3 17.1 + - - +
324B LEU* 3.0 37.4 + - + +
406B LEU* 3.8 21.3 - - + -
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA 3.1 19.2 + - - +
318B LYS* 3.7 4.9 - - + +
319B ASN 3.4 0.2 - - - -
320B LYS* 1.3 77.0 - - - +
322B GLU* 1.3 57.2 + - - +
324B LEU* 3.1 7.8 + - - +
325B LEU* 2.7 38.0 + - + +
344B LEU* 3.9 34.8 - - + -
384B VAL* 5.1 7.0 - - + -
387B LEU* 3.7 36.1 - - + +
388B MSE 3.7 24.7 - - - -
391B PHE* 4.2 9.9 - - + -
406B LEU* 4.3 13.9 - - + -
408B VAL* 4.3 6.7 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 3.0 46.9 + - + +
319B ASN* 3.8 15.2 - - - +
320B LYS 3.4 0.2 - - - -
321B ILE* 1.3 75.5 - - + +
323B GLU* 1.3 57.0 + - - +
325B LEU* 3.8 2.9 - - - +
326B ALA* 3.0 30.1 + - - +
380B MSE 3.6 23.2 - - + +
384B VAL* 3.7 26.8 - - + +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASP* 5.0 8.8 - - - +
319B ASN 3.2 11.1 + - - +
320B LYS* 3.3 20.9 - - - +
321B ILE 3.2 0.4 - - - -
322B GLU* 1.3 79.0 - - - +
324B LEU* 1.3 71.6 + - + +
326B ALA* 3.4 7.5 + - - +
327B SER* 3.3 23.9 + - - +
422B GOL 5.2 7.3 - - - -
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.8 17.0 - - + +
305B GLU 3.9 17.3 - - - +
306B ASP* 4.3 10.8 - - + +
320B LYS* 3.0 25.8 + - + +
321B ILE* 3.1 4.7 + - + +
323B GLU* 1.3 84.7 - - + +
325B LEU* 1.3 63.5 + - - +
327B SER* 3.4 8.7 + - - -
328B LEU* 3.1 20.7 + - - +
406B LEU* 3.6 38.6 - - + +
408B VAL* 3.9 19.5 - - + +
422B GOL 3.6 24.7 - - - +
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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
----------------------------------------------------------
321B ILE 2.7 21.1 + - - +
322B GLU 3.8 3.4 - - - +
324B LEU* 1.3 71.7 - - - +
326B ALA* 1.3 63.9 - - - +
328B LEU* 3.1 5.9 + - + +
329B LEU* 2.9 39.9 + - + +
380B MSE 3.8 15.5 - - - +
383B MSE 3.6 29.8 - - + -
384B VAL* 3.5 31.0 - - + -
387B LEU* 3.9 17.3 - - + -
408B VAL* 4.4 7.3 - - + +
410B PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLU 3.0 19.0 + - - +
323B GLU* 3.5 8.1 - - - +
325B LEU* 1.3 77.3 - - - +
327B SER* 1.3 61.5 + - - +
329B LEU* 3.5 5.5 + - - +
330B ASN* 3.3 29.9 + - - +
380B MSE 4.3 15.0 - - + -
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Residues in contact with SER 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.7 26.1 + - - +
323B GLU* 3.3 12.0 + - - +
324B LEU* 3.5 9.8 - - - -
326B ALA* 1.3 78.2 - - - +
328B LEU* 1.3 62.7 + - - +
330B ASN* 3.4 24.0 + - - +
331B ARG* 3.4 9.4 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.6 37.2 - - + +
303B SER 3.9 1.8 - - - +
304B GLU* 3.6 24.9 - - + +
324B LEU 3.1 9.0 + - - +
325B LEU* 3.1 9.8 + - - +
327B SER* 1.3 76.9 - - - +
329B LEU* 1.3 57.7 + - - +
331B ARG* 2.9 26.8 + - - +
332B VAL* 3.1 13.7 + - - +
408B VAL* 3.4 43.7 - - + +
409B CYS 4.0 2.0 - - - +
410B PHE* 3.7 32.5 - - + +
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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
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325B LEU* 2.9 27.8 + - + +
326B ALA* 3.8 5.4 - - - +
328B LEU* 1.3 76.0 - - - +
330B ASN* 1.3 64.6 + - - +
332B VAL* 3.5 5.1 + - - +
333B CYS* 3.2 24.1 + - - +
371B LYS* 3.5 28.4 + - - +
379B VAL* 4.0 29.2 - - + -
380B MSE 3.7 33.4 - - + +
383B MSE 5.1 2.5 - - + -
410B PHE* 4.1 16.8 - - + -
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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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326B ALA* 3.3 17.7 + - - +
327B SER* 3.4 12.5 - - - +
328B LEU 3.2 0.4 - - - -
329B LEU* 1.3 78.1 - - - +
331B ARG* 1.3 56.8 + - + +
333B CYS* 3.4 15.0 - - - +
334B GLN* 3.1 26.6 - - - +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 6.3 3.1 - - + -
103B ARG* 3.3 39.0 - - - +
299B PRO* 5.6 1.2 - - - +
302B PHE* 3.8 37.8 - - + +
303B SER 2.6 32.3 + - - +
304B GLU* 2.8 24.0 + - - +
327B SER 3.4 7.1 + - - +
328B LEU* 2.9 14.9 + - - +
330B ASN* 1.3 79.1 - - + +
332B VAL* 1.3 61.3 + - - -
333B CYS 3.4 0.2 - - - -
334B GLN* 3.4 19.9 + - + +
335B ASP* 3.3 18.7 - - - +
843T C 3.0 23.8 + - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.7 18.6 - - + -
328B LEU 3.1 9.5 + - - +
329B LEU* 3.5 6.5 + - - +
331B ARG* 1.3 71.5 - - - +
333B CYS* 1.3 69.2 + - - +
335B ASP* 2.9 18.7 + - - +
336B GLY 3.8 4.7 + - - -
337B ARG 3.8 18.5 - - - +
338B LYS* 4.7 1.6 - - - -
339B PRO* 3.9 16.6 - - + -
371B LYS* 3.9 20.6 - - - +
372B LEU* 4.8 13.8 - - + +
410B PHE* 3.5 38.1 - - + -
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Residues in contact with CYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU 3.2 11.4 + - - +
330B ASN* 3.4 16.8 - - - +
332B VAL* 1.3 78.8 - - - +
334B GLN* 1.3 64.6 + - - +
335B ASP 3.1 1.4 + - - -
336B GLY* 4.7 1.4 + - - -
372B LEU* 4.5 25.7 - - + +
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 5.5 2.4 - - - +
104B GLU* 4.1 18.6 + - - +
330B ASN* 3.1 22.0 + - - +
331B ARG* 3.7 19.0 - - + +
332B VAL 3.1 1.6 + - - -
333B CYS* 1.3 77.9 - - + +
335B ASP* 1.3 60.4 + - + +
336B GLY 3.8 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