Contacts of the helix formed by residues 235 - 244 (chain B) in PDB entry 1NBF
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B THR* 2.9 22.2 + - - +
232B LEU* 2.9 18.5 + - - +
233B PHE 4.1 0.9 - - - -
234B PHE* 1.3 75.0 - - - +
236B ASN* 1.3 53.1 + - - +
237B GLN 3.2 0.9 - - - -
238B LEU* 2.7 46.0 + - + +
239B ARG 3.1 8.0 + - - -
323B LEU* 4.5 4.0 - - + -
324B PHE* 4.3 12.3 - - + -
401B VAL* 4.1 31.8 - - + +
403B HIS* 5.6 1.0 + - - -
451B HIS* 4.9 6.6 + - - -
517B VAL* 5.7 1.7 - - - +
519B ILE* 6.3 0.4 - - + -
527B VAL* 4.0 12.8 - - + -
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Residues in contact with ASN 236 (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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234B PHE* 3.0 18.3 + - - +
235B THR* 1.3 72.9 - - - +
237B GLN* 1.3 64.7 + - - +
239B ARG* 3.1 35.3 + - - +
240B LYS* 3.0 26.8 + - - +
471B PRO 5.2 2.0 + - - +
527B VAL 3.2 11.6 + - - +
528B LEU* 3.6 12.6 + - - +
529B GLN 2.6 34.8 + - - +
530B ALA* 4.1 5.3 - - - +
531B VAL* 3.9 11.8 - - + +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR 3.0 0.8 + - - -
236B ASN* 1.3 73.2 - - - +
238B LEU* 1.3 59.6 + - - +
240B LYS* 3.7 13.8 + - + +
241B ALA* 3.4 19.4 + - - +
319B THR* 4.7 3.7 - - + +
322B LYS* 4.3 17.3 - - - +
323B LEU* 3.3 32.3 - - + +
526B GLU* 3.4 35.0 + - - +
527B VAL* 2.8 48.9 + - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.7 43.7 - - + +
235B THR* 2.7 20.3 + - + +
237B GLN* 1.3 70.9 - - - +
239B ARG* 1.3 65.6 + - - +
240B LYS 3.1 1.8 - - - -
241B ALA* 3.1 3.5 + - - +
242B VAL* 2.9 41.5 + - + +
264B PHE* 5.3 2.5 - - + -
304B LEU* 4.7 5.6 - - + -
307B VAL* 5.5 1.3 - - + -
311B MET* 4.7 4.7 - - + -
319B THR* 4.4 10.5 - - + -
320B ILE* 4.2 25.8 - - + -
323B LEU* 3.8 17.3 - - + +
324B PHE* 3.9 15.5 - - + -
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Residues in contact with ARG 239 (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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232B LEU 4.6 0.4 + - - -
233B PHE* 2.8 64.7 + - + +
234B PHE* 4.1 7.3 - - - -
235B THR 3.1 4.2 + - - -
236B ASN* 3.1 36.1 + - - +
238B LEU* 1.3 76.7 - - - +
240B LYS* 1.3 62.5 + - - +
242B VAL* 3.3 3.8 + - - +
243B TYR* 3.1 34.8 + - + -
264B PHE* 3.6 32.5 - - + -
268B GLN* 3.0 39.6 - - - +
531B VAL* 4.0 20.0 + - + +
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Residues in contact with LYS 240 (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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236B ASN 3.0 15.9 + - - +
237B GLN* 3.7 13.6 - - + +
239B ARG* 1.3 74.2 - - - +
241B ALA* 1.3 66.7 + - - +
243B TYR* 3.0 20.7 + - - +
244B MET* 3.1 19.3 + - + +
526B GLU 5.1 0.8 + - - -
529B GLN* 2.8 51.2 + - - +
530B ALA 3.7 9.2 + - - -
531B VAL* 3.5 33.9 - - + -
535B ASP* 4.2 23.0 + - + +
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Residues in contact with ALA 241 (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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237B GLN 3.4 6.2 + - - +
238B LEU* 3.1 9.0 + - - +
240B LYS* 1.3 78.9 - - - +
242B VAL* 1.3 63.8 + - - +
244B MET* 3.0 15.8 + - - +
245B MET* 3.4 11.3 + - - +
311B MET* 4.1 7.6 - - + -
316B VAL* 3.3 32.9 - - + +
319B THR* 3.5 27.8 - - + +
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Residues in contact with VAL 242 (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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238B LEU* 2.9 27.8 + - + +
239B ARG 3.5 7.9 - - - +
240B LYS 3.2 0.2 - - - -
241B ALA* 1.3 76.1 - - - +
243B TYR* 1.3 59.6 + - + +
245B MET* 3.1 21.0 + - - +
257B PRO 4.4 1.3 - - - +
260B LEU* 4.0 26.2 - - + -
261B GLN* 2.8 40.9 + - + +
264B PHE* 3.8 31.4 - - + -
307B VAL* 5.0 2.7 - - + -
311B MET* 4.2 13.0 - - + -
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Residues in contact with TYR 243 (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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239B ARG* 3.1 32.7 + - - -
240B LYS* 3.0 12.9 + - - +
242B VAL* 1.3 77.4 - - + +
244B MET* 1.3 59.4 + - - +
245B MET 3.3 1.6 - - - +
261B GLN* 3.5 35.5 + - - +
264B PHE* 3.0 29.5 + - + +
265B TYR* 3.4 9.7 + - + -
268B GLN* 2.6 34.4 + - - -
531B VAL* 4.1 8.3 - - + -
535B ASP* 4.1 15.3 - - + +
536B ILE* 3.7 30.5 - - + +
537B PRO* 3.3 24.3 - - + +
540B LEU* 3.9 17.9 - - + +
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Residues in contact with MET 244 (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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240B LYS* 3.4 15.5 - - + +
241B ALA* 3.0 11.4 + - - +
243B TYR* 1.3 76.7 - - - +
245B MET* 1.3 63.9 + - - +
246B PRO* 3.4 8.5 - - - +
315B CYS* 4.0 25.5 - - - -
316B VAL* 4.5 11.9 - - + -
535B ASP 4.1 13.7 - - - +
537B PRO* 3.8 23.1 - - + -
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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