Contacts of the helix formed by residues 312 - 323 (chain B) in PDB entry 2VM8
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 THR 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B LYS* 2.8 29.3 + - - +
310B ASP* 2.6 26.8 + - - +
311B PRO* 1.3 77.6 - - + +
313B THR* 1.3 63.3 + - - +
314B PRO* 3.3 2.0 - - - -
315B ASP* 3.2 19.2 + - - +
316B PHE* 3.3 11.8 + - - +
310C ASP* 5.9 1.1 - - - +
312C THR* 5.0 16.8 - - + -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLU* 5.0 0.5 + - - -
256B MET 3.6 24.0 - - - +
257B SER* 4.1 0.7 - - - -
258B LYS* 3.9 28.1 + - + +
282B SER* 4.5 3.4 - - - +
285B THR 5.6 0.9 - - - -
308B SER* 3.2 20.4 + - - -
310B ASP* 2.9 25.7 + - - +
312B THR* 1.3 77.8 - - - +
314B PRO* 1.3 71.2 - - - +
316B PHE* 3.1 3.8 + - - +
317B LEU* 3.0 35.7 + - + +
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Residues in contact with PRO 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER 3.5 14.4 - - - +
283B LEU* 3.7 9.6 - - - +
285B THR* 3.2 34.1 - - - +
286B ASP* 4.8 2.5 - - + +
310B ASP 4.3 1.8 - - - +
311B PRO* 3.6 15.0 - - + +
312B THR 3.5 2.9 - - - -
313B THR* 1.3 95.8 - - - +
315B ASP* 1.3 58.8 + - - +
317B LEU* 3.9 1.8 - - + +
318B ASN* 2.6 34.4 + - - -
368B LYS* 3.2 27.1 - - - +
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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
----------------------------------------------------------
311B PRO 5.3 0.6 + - - +
312B THR* 3.2 14.0 + - - +
313B THR 3.2 1.0 - - - -
314B PRO* 1.3 77.4 - - - +
316B PHE* 1.3 59.6 + - - +
318B ASN* 4.0 1.5 - - - +
319B SER* 2.6 33.2 + - - -
368B LYS* 4.8 3.8 - - - +
374B LYS* 2.4 43.1 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS* 3.9 21.8 - - - -
258B LYS* 3.8 61.2 - - + -
261B ALA* 4.2 0.7 - - + -
262B GLU* 4.0 7.6 - - + -
312B THR 3.3 6.4 + - - +
313B THR 3.1 7.8 + - - +
315B ASP* 1.3 80.2 - - - +
317B LEU* 1.3 63.6 + - + +
319B SER* 3.2 7.7 + - - -
320B LEU* 2.9 67.5 + - + +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 3.7 12.6 - - + +
256B MET 4.1 8.5 - - - -
257B SER 3.7 13.7 - - - +
261B ALA* 3.5 32.5 - - + -
278B PRO* 4.5 4.9 - - + -
282B SER* 3.3 43.1 - - - +
283B LEU* 4.0 15.9 - - + +
313B THR* 3.0 22.3 + - + +
314B PRO 4.5 1.8 - - - +
316B PHE* 1.3 82.9 - - + +
318B ASN* 1.3 57.3 + - - +
320B LEU* 4.6 0.7 - - - +
321B LEU* 3.0 27.4 + - - +
326B LEU* 3.9 17.7 - - + +
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Residues in contact with ASN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.0 39.3 + - - +
314B PRO 2.6 26.8 + - - +
315B ASP* 4.1 3.4 - - - +
316B PHE 3.2 0.4 - - - -
317B LEU* 1.3 76.0 - - - +
319B SER* 1.3 64.8 + - - +
321B LEU* 3.2 13.3 - - - +
322B SER* 2.9 26.5 + - - -
365B ILE* 4.4 6.4 - - - -
368B LYS* 3.5 34.1 - - - +
369B ALA* 3.6 19.4 - - + +
374B LYS* 4.3 6.1 - - + -
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Residues in contact with SER 319 (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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269A LYS 3.8 20.4 - - - +
270A LYS 5.7 2.2 - - - -
271A GLY* 6.2 0.7 - - - -
315B ASP* 2.6 11.5 + - - -
316B PHE* 3.3 12.7 - - - -
318B ASN* 1.3 77.2 - - - +
320B LEU* 1.3 62.8 + - - +
322B SER* 2.8 22.7 + - - -
323B CYS* 3.1 13.3 + - - +
374B LYS* 2.6 33.7 + - - +
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Residues in contact with LEU 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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269A LYS* 3.7 26.0 - - + +
261B ALA* 3.9 30.3 - - + +
262B GLU* 4.4 2.0 - - - +
265B ALA* 4.5 6.3 - - + -
316B PHE* 2.9 62.1 + - + +
317B LEU* 4.8 0.2 - - - -
319B SER* 1.3 77.6 - - - +
321B LEU* 1.3 60.3 + - - +
323B CYS* 3.6 4.9 - - - -
324B GLY 3.4 2.4 + - - -
325B ASP* 3.0 50.8 + - + +
326B LEU* 3.2 16.3 + - + -
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Residues in contact with LEU 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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278B PRO* 4.5 7.2 - - + -
283B LEU* 4.0 14.1 - - + -
317B LEU 3.0 17.8 + - - +
318B ASN* 3.2 26.9 - - - +
320B LEU* 1.3 76.7 - - - +
322B SER* 1.3 58.8 + - - +
324B GLY* 3.6 5.4 + - - -
326B LEU* 3.2 37.7 - - + +
327B GLN 4.8 0.4 - - - +
328B VAL 4.6 1.3 - - - +
329B THR* 3.8 26.5 - - + -
365B ILE* 4.1 14.6 - - + -
375B MET* 3.7 21.0 - - + +
379B GLN* 3.3 10.9 - - - +
383B VAL* 3.8 21.5 - - + +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ASN 2.9 12.8 + - - -
319B SER* 2.8 10.3 + - - -
321B LEU* 1.3 77.2 - - - +
323B CYS* 1.3 57.7 + - - +
324B GLY 3.3 0.4 - - - -
369B ALA* 4.1 0.5 - - - +
374B LYS* 3.2 43.4 - - - +
375B MET* 3.4 20.4 - - - +
379B GLN* 2.9 19.5 - - - +
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Residues in contact with CYS 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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268A ARG* 3.0 59.3 + - - +
269A LYS* 3.7 20.9 - - - -
268B ARG* 5.7 0.7 + - - -
319B SER 3.1 7.6 + - - +
320B LEU* 3.6 21.5 - - - -
322B SER* 1.3 75.8 - - - +
324B GLY* 1.3 57.2 + - - +
325B ASP* 3.5 25.4 + - - -
379B GLN* 4.8 0.4 - - - -
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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