Contacts of the helix formed by residues 2224 - 2235 (chain B) in PDB entry 2NVU
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 LEU2224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A ASP* 3.9 30.3 - - + +
339A TYR* 4.3 20.0 - - + +
343A GLN* 5.0 6.1 - - - +
2213B PHE* 5.9 1.8 - - + -
2223B ARG* 1.3 85.6 - - - +
2225B PRO* 1.3 71.8 - - + +
2226B GLU* 3.2 19.5 - - + +
2227B HIS* 2.9 43.2 + - + +
2228B CYS* 3.5 6.9 + - - -
2273B ILE* 3.7 2.9 - - - -
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Residues in contact with PRO2225 (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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2223B ARG 4.6 0.2 - - - +
2224B LEU* 1.3 89.1 - - + +
2226B GLU* 1.3 80.1 + - - +
2228B CYS* 3.1 14.3 + - - +
2229B ILE* 3.2 18.4 + - - +
2273B ILE* 3.6 10.5 - - + -
2274B ARG 3.7 20.0 - - - +
2275B GLY* 3.7 17.7 - - - +
2276B VAL* 3.6 24.0 - - + +
2280B LEU* 3.8 12.6 - - + -
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Residues in contact with GLU2226 (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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2213B PHE* 3.9 21.8 - - + -
2224B LEU* 3.2 17.5 - - + +
2225B PRO* 1.3 96.0 - - - +
2227B HIS* 1.3 62.4 + - - +
2229B ILE* 3.0 6.1 + - - +
2230B GLU* 2.9 25.8 + - - +
2280B LEU* 3.9 22.0 - - + +
2284B VAL* 3.8 29.8 - - + +
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Residues in contact with HIS2227 (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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331A ASP* 4.0 5.7 + - - -
2213B PHE* 3.5 35.3 - + - -
2214B PRO* 5.9 1.3 - - + -
2217B THR* 3.6 24.2 - - + +
2218B ILE* 3.3 24.5 - - + +
2222B PRO* 4.0 16.6 - - + -
2223B ARG* 3.2 26.3 + - + -
2224B LEU* 2.9 51.5 + - + +
2226B GLU* 1.3 78.1 - - - +
2228B CYS* 1.3 60.0 + - - +
2231B TYR* 3.3 19.9 + - - +
2267B ARG* 4.4 1.4 + - - -
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Residues in contact with CYS2228 (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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2222B PRO* 4.5 5.2 - - - -
2224B LEU 3.9 5.2 - - - -
2225B PRO 3.1 8.0 + - - +
2227B HIS* 1.3 74.3 - - - +
2229B ILE* 1.3 66.3 + - - +
2231B TYR* 3.2 12.0 + - - +
2232B VAL* 3.2 17.8 + - - +
2264B SER* 4.1 12.8 - - - +
2267B ARG* 4.0 28.8 - - + +
2268B ALA* 3.7 29.6 - - + -
2273B ILE* 3.7 28.7 - - - -
2276B VAL* 4.8 1.8 - - + -
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Residues in contact with ILE2229 (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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2225B PRO 3.2 13.7 + - - +
2226B GLU 3.0 6.8 + - - +
2228B CYS* 1.3 77.8 - - - +
2230B GLU* 1.3 56.3 + - - +
2232B VAL* 3.3 4.2 + - - +
2233B ARG* 2.9 26.2 + - + +
2260B ILE* 4.5 1.6 - - + +
2264B SER* 3.4 24.9 - - - +
2276B VAL* 4.3 9.6 - - + -
2280B LEU* 3.8 22.9 - - + +
2281B THR* 3.5 52.7 - - + +
2284B VAL* 3.7 25.8 - - + -
2285B VAL* 4.3 7.0 - - + -
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Residues in contact with GLU2230 (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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2213B PHE* 3.2 36.4 - - + +
2218B ILE* 3.8 13.7 - - + -
2226B GLU 2.9 8.8 + - - +
2227B HIS 3.8 7.9 - - - +
2228B CYS 3.2 0.2 - - - -
2229B ILE* 1.3 73.6 - - - +
2231B TYR* 1.3 67.8 + - - +
2233B ARG* 2.6 46.6 + - - -
2234B MET* 2.8 48.8 + - + +
2284B VAL* 4.0 4.3 - - + +
2287B ARG* 2.8 30.0 + - - +
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Residues in contact with TYR2231 (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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2218B ILE* 3.5 19.7 - - + +
2219B ALA* 4.5 5.4 - - + -
2227B HIS 3.3 3.7 + - - +
2228B CYS 3.2 6.4 + - - +
2230B GLU* 1.3 78.4 - - - +
2232B VAL* 1.3 63.8 + - + +
2234B MET* 4.8 0.2 - - - -
2235B LEU* 2.8 65.5 + - + +
2236B GLN* 3.1 37.0 + - + +
2267B ARG* 3.1 61.7 - - - +
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Residues in contact with VAL2232 (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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2228B CYS 3.2 12.7 + - - +
2229B ILE 3.6 7.0 - - - +
2230B GLU 3.2 0.6 - - - -
2231B TYR* 1.3 80.4 - - + +
2233B ARG* 1.3 60.8 + - - +
2236B GLN* 3.7 24.0 - - + +
2237B TRP* 3.0 29.8 + - - +
2259B TRP* 4.0 15.9 - - + -
2260B ILE* 3.9 21.1 - - + +
2263B LYS* 3.9 20.9 - - + +
2264B SER* 3.5 27.6 - - - +
2267B ARG* 4.7 2.5 - - + -
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Residues in contact with ARG2233 (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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2229B ILE* 2.9 18.3 + - + +
2230B GLU* 2.6 52.0 + - - +
2232B VAL* 1.3 80.5 - - - +
2234B MET* 1.3 75.7 + - - +
2237B TRP* 3.9 5.2 - - - +
2238B PRO* 3.7 12.0 - - - +
2249B LEU* 3.7 31.5 - - + +
2260B ILE* 4.7 4.5 - - + +
2284B VAL* 5.3 0.2 - - - -
2285B VAL* 4.5 30.3 + - + +
2287B ARG* 3.8 16.4 - - - +
117C GLU* 2.5 41.2 + - - -
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Residues in contact with MET2234 (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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2213B PHE 5.3 8.3 - - - +
2215B MET* 4.5 23.3 - - + +
2218B ILE* 5.0 10.8 - - + -
2230B GLU* 2.8 48.0 + - - +
2231B TYR* 4.8 0.9 - - - -
2233B ARG* 1.3 95.6 - - - +
2235B LEU* 1.3 75.3 + - + +
2238B PRO* 3.5 16.2 - - - +
117C GLU* 4.0 15.0 - - - +
142C GLU 5.3 1.0 - - - +
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Residues in contact with LEU2235 (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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2215B MET* 4.7 22.4 - - + -
2218B ILE* 4.7 5.4 - - + -
2219B ALA* 4.4 17.9 - - + -
2231B TYR* 2.8 52.0 + - + +
2233B ARG 3.6 0.6 - - - -
2234B MET* 1.3 91.9 - - + +
2236B GLN* 1.3 66.6 + - - +
2237B TRP 3.3 1.1 - - - -
2238B PRO* 3.1 10.9 - - - +
2239B LYS* 3.2 18.8 + - - +
142C GLU* 4.9 24.4 - - + +
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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