Contacts of the helix formed by residues 235 - 244 (chain B) in PDB entry 3NAV
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B THR* 3.8 20.8 - - - +
64B ILE* 4.8 9.9 - - - -
213B GLY* 6.1 0.7 - - - -
214B ILE 5.4 0.2 + - - -
215B SER* 6.0 0.9 - - - -
234B GLY* 1.3 80.8 - - - +
236B ALA* 1.3 64.5 + - - +
237B VAL* 3.3 2.9 - - - -
238B VAL* 3.1 22.0 + - - +
239B LYS* 3.1 11.5 + - - +
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Residues in contact with ALA 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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214B ILE 3.9 1.0 + - - +
215B SER* 3.5 35.6 - - - +
233B SER* 3.1 21.1 + - - +
235B SER* 1.3 81.0 + - - +
237B VAL* 1.3 61.2 + - - +
239B LYS* 3.4 9.3 + - - +
240B ILE* 3.3 25.5 + - - +
258B PHE* 3.8 14.8 - - + -
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Residues in contact with VAL 237 (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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21B PRO* 3.9 23.6 - - + -
22B PHE 3.7 11.0 - - - +
23B VAL* 3.6 24.5 - - + -
40B LEU* 4.2 14.4 - - + -
233B SER* 4.1 8.0 + - - +
235B SER 3.3 1.0 - - - -
236B ALA* 1.3 73.0 - - - +
238B VAL* 1.3 65.6 + - - +
240B ILE* 3.1 14.1 + - - +
241B ILE* 3.2 13.9 + - + +
255B LEU* 3.6 23.3 - - + -
258B PHE* 3.7 26.5 - - + -
259B THR* 5.5 0.2 - - - +
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Residues in contact with VAL 238 (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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22B PHE* 3.8 38.8 - - + +
23B VAL* 4.3 7.9 - - + -
24B THR 4.7 3.6 - - - +
27B ASP* 3.9 3.4 - - - +
63B THR* 3.7 22.2 - - + +
64B ILE* 4.6 4.3 - - + +
67B ALA* 3.6 29.2 - - + -
70B ARG* 3.8 9.1 + - - +
235B SER* 3.1 13.8 + - - +
237B VAL* 1.3 77.2 - - - +
239B LYS* 1.3 57.2 + - - +
241B ILE* 3.1 10.8 + - + +
242B GLU* 2.9 26.6 + - + +
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Residues in contact with LYS 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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62B PRO* 6.3 0.8 - - - +
63B THR* 3.8 19.7 + - + +
235B SER 3.1 11.8 + - - +
236B ALA* 3.6 12.8 - - - +
237B VAL 3.2 0.4 - - - -
238B VAL* 1.3 77.6 - - - +
240B ILE* 1.3 58.9 + - + +
242B GLU* 3.3 33.0 + - - +
243B THR* 3.0 48.8 + - + +
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Residues in contact with ILE 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 ALA 3.3 12.9 + - - +
237B VAL 3.1 6.6 + - - +
239B LYS* 1.3 73.0 - - + +
241B ILE* 1.3 68.6 + - - +
243B THR* 3.1 17.2 + - - -
244B HIS* 3.2 33.3 - - + +
251B GLN* 4.5 2.0 - - - +
254B GLU* 3.7 19.3 - - + +
255B LEU* 3.6 24.7 - - + -
258B PHE* 3.5 48.5 - - + -
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Residues in contact with ILE 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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23B VAL* 4.2 25.1 - - + -
27B ASP* 3.7 37.9 - - - +
28B PRO* 4.3 11.4 - - + -
36B ILE* 3.7 29.6 - - + -
70B ARG* 3.9 3.8 - - - +
237B VAL* 3.2 14.1 + - + +
238B VAL* 3.1 11.3 + - + +
240B ILE* 1.3 77.4 - - - +
242B GLU* 1.3 62.5 + - - +
244B HIS 3.2 11.1 + - - -
245B LEU* 3.4 22.7 + - + +
251B GLN* 3.8 13.1 + - + +
255B LEU* 4.0 12.8 - - + -
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Residues in contact with GLU 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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62B PRO 4.6 3.0 - - - +
63B THR* 4.0 24.6 + - - +
66B GLY* 5.8 1.3 - - - -
70B ARG* 3.9 23.5 + - - +
238B VAL 2.9 15.0 + - - +
239B LYS* 3.5 37.0 + - - +
240B ILE 3.2 0.2 - - - -
241B ILE* 1.3 77.0 - - - +
243B THR* 1.3 62.0 + - + +
245B LEU* 3.3 26.4 + - + +
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Residues in contact with THR 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 LYS* 3.0 41.5 + - + +
240B ILE* 3.1 10.7 + - - -
242B GLU* 1.3 81.6 - - + +
244B HIS* 1.3 80.0 + - - +
245B LEU 3.7 0.9 - - - -
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Residues in contact with HIS 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 ILE* 3.2 38.2 + - + +
241B ILE 3.2 5.8 + - - -
243B THR* 1.3 96.9 + - - +
245B LEU* 1.3 63.0 + - - +
246B ASP 3.2 4.4 + - - +
247B ASN* 3.5 16.3 + - + +
250B LYS* 3.9 23.5 - - + +
251B GLN* 3.1 31.7 + - + +
254B GLU* 3.5 32.6 - - + +
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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