Contacts of the strand formed by residues 243 - 249 (chain B) in PDB entry 3NMV
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 HIS 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B TRP* 4.1 24.8 - + + -
202B GLN* 2.9 33.8 + - - -
238B VAL 3.8 1.3 - - - +
240B PHE* 2.8 41.3 + - + +
242B THR* 1.3 97.2 - - + +
244B ILE* 1.3 62.4 + - - +
245B PHE* 4.0 22.0 - - + -
322B SER* 4.7 3.6 + - - -
323B VAL 3.4 8.8 + - - +
324B ARG* 3.8 33.3 + - + +
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Residues in contact with ILE 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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237B ALA* 4.6 0.7 - - + -
238B VAL 3.4 7.2 - - - +
239B VAL* 4.3 13.5 - - + -
243B HIS* 1.3 79.4 - - - +
245B PHE* 1.3 69.9 + - - +
246B VAL* 4.2 4.7 + - + +
256B LEU* 4.4 11.2 - - + -
265B LEU* 4.0 19.7 - - + +
321B THR 4.0 0.2 - - - +
322B SER* 3.1 4.9 - - - -
323B VAL* 2.9 44.8 + - + +
325B ARG* 3.7 31.0 - - + -
332B LEU* 4.2 21.8 - - + -
411B LEU* 4.0 24.9 - - + -
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Residues in contact with PHE 245 (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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201B TRP* 3.8 21.5 - + - -
202B GLN* 3.8 22.4 - - + -
205B TRP* 3.6 29.4 - + + -
206B LYS* 4.2 13.2 - - + -
209B LEU* 3.7 23.5 - - + +
236B VAL 3.7 0.3 - - - +
237B ALA* 3.1 5.9 - - - +
238B VAL* 2.8 40.3 + - + +
240B PHE* 3.7 38.1 - + - -
243B HIS* 4.0 12.3 - - + -
244B ILE* 1.3 75.0 - - - +
246B VAL* 1.3 62.4 + - - +
247B ALA 4.3 0.4 - - - -
320B VAL* 5.3 0.2 - - + -
321B THR 3.2 7.0 - - - +
322B SER* 3.6 22.9 - - - -
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Residues in contact with VAL 246 (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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235B VAL* 3.9 13.5 - - + -
236B VAL 3.1 8.5 - - - +
237B ALA* 4.1 13.2 - - + -
244B ILE* 4.2 3.6 - - + -
245B PHE* 1.3 77.8 - - - +
247B ALA* 1.3 64.9 + - - +
248B ASN* 4.6 0.2 - - + -
254B ALA* 3.7 26.0 - - + -
265B LEU* 3.7 50.4 - - + +
266B SER* 4.1 6.5 - - - -
319B GLU 3.6 1.4 - - - +
320B VAL* 3.2 4.4 - - - -
321B THR* 2.7 39.9 + - - +
332B LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 247 (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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209B LEU* 4.0 22.3 - - + +
213B PHE* 3.6 30.1 - - + -
235B VAL* 3.6 0.2 - - - -
236B VAL 2.9 32.8 + - - +
245B PHE 4.3 0.2 - - - -
246B VAL* 1.3 73.7 - - - +
248B ASN* 1.3 62.8 + - - +
318B PRO* 4.3 2.9 - - + -
319B GLU 3.4 4.7 - - - -
320B VAL* 3.9 20.6 - - + +
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Residues in contact with ASN 248 (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 SER 3.5 3.1 - - - +
235B VAL* 3.7 18.5 - - + +
246B VAL* 4.6 0.2 - - + -
247B ALA* 1.3 77.3 - - - +
249B CYS* 1.3 64.4 + - - +
250B GLY 3.4 21.2 + - - +
252B SER 3.3 19.9 + - - +
266B SER* 3.5 29.3 - - - -
267B VAL 3.6 13.1 + - - +
269B HIS* 3.1 22.1 + - + -
318B PRO* 3.0 6.6 - - - +
319B GLU* 2.9 36.9 + - + +
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Residues in contact with CYS 249 (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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213B PHE* 4.0 6.7 - - + -
233B THR* 3.4 3.6 - - - -
234B SER* 2.9 41.8 + - - +
248B ASN* 1.3 76.0 - - - +
250B GLY* 1.3 59.9 + - - +
269B HIS* 3.5 4.0 - - - -
303B ARG* 4.0 11.2 - - + -
304B SER* 3.7 28.5 - - - -
305B ILE* 3.8 18.6 - - - -
316B PRO 3.5 26.9 - - - +
317B ASP 4.4 0.4 - - - +
318B PRO* 4.0 5.8 - - + -
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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