Contacts of the helix formed by residues 281 - 290 (chain B) in PDB entry 2NVT
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 PRO 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ILE 4.1 1.3 - - - +
270B LYS* 4.0 22.2 - - + -
279B ASP 3.7 7.9 - - - +
280B ILE* 1.4 86.9 - - + +
282B ILE* 1.3 66.1 + - - +
283B VAL* 3.3 4.0 - - + +
284B ILE* 3.1 35.2 + - + +
285B ILE 3.6 2.4 + - - -
317B CYS* 5.4 2.5 - - + +
320B ASP* 3.5 44.0 - - + +
333B PHE* 4.7 14.1 - - + -
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Residues in contact with ILE 282 (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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256B VAL* 5.4 0.2 - - + -
269B ILE* 3.1 35.3 + - + +
270B LYS 4.1 13.2 - - - +
271B ALA* 4.2 10.1 - - + -
280B ILE 3.9 1.8 - - - -
281B PRO* 1.3 72.6 - - - +
283B VAL* 1.3 69.3 + - + +
285B ILE* 2.9 26.0 + - + +
286B PHE* 3.2 24.4 + - + -
301B ILE* 4.1 18.4 - - + -
314B LEU* 4.9 8.1 - - + -
317B CYS* 4.8 8.1 - - + +
378B LEU* 5.3 5.8 - - + -
382B ILE* 3.8 40.4 - - + -
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Residues in contact with VAL 283 (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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281B PRO* 4.7 3.1 - - + +
282B ILE* 1.3 85.6 - - + +
284B ILE* 1.3 68.4 + - + +
285B ILE 3.2 0.2 + - - -
286B PHE* 3.3 5.2 + - - +
287B ARG* 3.1 34.5 + - - +
294B ASP* 6.1 0.7 - - - +
297B ILE* 4.0 32.7 - - + +
298B LEU* 6.2 0.2 - - + -
317B CYS* 3.2 36.8 - - + +
318B VAL* 4.4 11.7 - - + +
320B ASP 4.7 0.4 - - - -
321B GLY* 3.3 28.7 - - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.7 11.7 - - + -
281B PRO* 3.1 34.1 + - + +
283B VAL* 1.3 76.9 - - + +
285B ILE* 1.3 63.0 + - - +
287B ARG* 3.4 8.8 - - - +
288B ALA* 3.1 20.3 + - - +
320B ASP 4.6 3.8 - - - +
321B GLY* 3.9 18.2 - - - -
323B VAL* 5.9 0.4 - - + -
324B ILE* 3.8 33.7 - - + -
330B ALA* 3.5 25.6 - - + +
333B PHE* 3.8 27.8 - - + -
334B ILE* 5.4 1.6 - - + -
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Residues in contact with ILE 285 (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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271B ALA* 4.6 9.4 - - + -
273B LEU* 3.7 29.8 - - + -
280B ILE* 3.6 37.7 - - + +
281B PRO 3.9 4.3 - - - +
282B ILE* 2.9 16.7 + - + +
284B ILE* 1.3 73.6 - - - +
286B PHE* 1.3 64.1 + - - +
288B ALA* 3.0 11.5 + - - +
289B LEU* 3.0 25.8 + - + +
334B ILE* 5.1 4.5 - - + -
356B LEU* 5.3 8.7 - - + -
360B PHE* 4.6 14.8 - - + -
378B LEU* 3.8 25.8 - - + -
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Residues in contact with PHE 286 (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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282B ILE* 3.2 37.0 + - + -
283B VAL* 3.7 8.3 - - - +
285B ILE* 1.3 78.3 - - - +
287B ARG* 1.3 62.7 + - - +
289B LEU* 3.1 9.7 + - - +
290B GLY 2.9 19.9 + - - -
291B ILE* 3.0 20.7 + - + +
297B ILE* 3.7 32.1 - - + -
300B HIS* 3.7 27.6 - + + -
301B ILE* 4.1 20.2 - - + -
375B ALA* 3.8 23.6 - - + -
378B LEU* 3.7 21.3 - - + -
379B GLY* 3.8 27.1 - - - -
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Residues in contact with ARG 287 (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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283B VAL* 3.1 26.5 + - - +
284B ILE 3.4 2.5 - - - +
286B PHE* 1.3 74.0 - - - +
288B ALA* 1.3 55.2 + - - +
289B LEU 2.6 15.6 + - - -
290B GLY* 3.0 9.2 + - - -
291B ILE 3.1 16.6 - - - -
292B ILE* 3.0 38.4 + - + +
294B ASP* 3.2 25.3 + - - -
297B ILE* 4.2 12.1 - - - +
318B VAL 5.7 1.4 + - - -
321B GLY 3.7 13.3 + - - -
324B ILE* 2.4 43.4 + - + +
325B GLN* 3.0 27.6 + - - +
326B ASP 4.6 1.6 - - - +
327B ARG* 3.3 17.8 - - - +
330B ALA* 3.3 18.4 - - + -
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Residues in contact with ALA 288 (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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284B ILE 3.1 9.3 + - - +
285B ILE* 3.0 12.7 + - - +
287B ARG* 1.3 78.0 - - - +
289B LEU* 1.3 55.3 + - - +
327B ARG* 3.2 21.5 + - - -
330B ALA* 3.3 14.3 - - + +
331B LEU* 3.6 35.3 - - + +
334B ILE* 4.8 7.9 - - + -
356B LEU* 3.4 21.3 - - + +
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Residues in contact with LEU 289 (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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285B ILE* 3.0 13.7 + - + +
286B PHE* 3.3 11.7 - - - +
287B ARG 2.6 7.2 + - - -
288B ALA* 1.3 75.6 - - - +
290B GLY* 1.3 57.2 + - - +
291B ILE* 4.6 6.1 - - + -
327B ARG* 3.2 20.9 + - - +
356B LEU* 4.0 22.0 - - + -
357B GLN* 4.7 9.2 - - - +
360B PHE* 4.4 12.6 - - + -
371B GLU* 3.4 46.2 - - + +
374B LYS* 4.2 11.4 - - + -
375B ALA* 3.7 35.2 - - + +
378B LEU* 4.6 11.2 - - + -
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Residues in contact with GLY 290 (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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286B PHE 2.9 1.6 + - - -
287B ARG 3.0 5.9 + - - -
289B LEU* 1.3 81.0 - - - +
291B ILE* 1.3 73.3 + - - +
292B ILE* 3.5 14.0 + - - +
327B ARG* 4.0 12.6 - - - +
371B GLU* 4.9 4.7 - - - -
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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