Contacts of the helix formed by residues 2230 - 2235 (chain B) in PDB entry 1CVU
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 LEU2230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2208B GLN* 2.9 24.9 + - - +
2228B VAL* 3.6 20.0 - - + -
2229B ASP* 1.3 82.3 - - - +
2231B ASN* 1.3 56.7 + - - +
2232B HIS* 3.0 19.3 - - + -
2233B ILE* 3.0 40.3 + - + -
2234B TYR* 3.1 28.0 + - + -
2305B TRP* 5.0 0.9 - - + -
2336B LEU* 3.8 24.9 - - + -
2337B ILE* 3.8 14.8 - - + -
2340B THR* 3.7 25.4 - - + +
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Residues in contact with ASN2231 (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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2208B GLN* 2.7 31.8 + - - +
2211B LYS* 2.9 30.0 + - - +
2229B ASP* 2.7 37.5 + - - +
2230B LEU* 1.3 72.1 - - - +
2232B HIS* 1.3 62.7 + - - +
2233B ILE 3.0 5.6 - - - -
2234B TYR* 4.7 1.1 - - - -
2235B GLY* 2.7 49.0 + - - +
2236B GLU* 3.7 13.4 + - - +
2288B GLY 3.7 5.2 - - - +
2289B GLN* 4.6 2.3 - - - +
2333B LYS* 5.3 1.8 - - - +
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Residues in contact with HIS2232 (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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2204B HIS* 3.2 59.0 + + - -
2205B PHE* 4.4 2.4 - - - -
2208B GLN* 3.4 49.3 + - + +
2230B LEU* 3.4 22.7 - - + -
2231B ASN* 1.3 80.0 + - - +
2233B ILE* 1.3 68.3 + - + +
2287B VAL* 4.8 1.7 - - - +
2288B GLY* 3.3 3.5 + - - -
2289B GLN* 3.0 38.7 + - + +
2292B PHE* 3.5 24.4 - + + -
2302B ALA* 5.8 0.9 - - - +
2305B TRP* 5.5 1.2 + + - -
2340B THR* 5.9 0.6 - - + +
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Residues in contact with ILE2233 (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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2204B HIS* 4.9 4.0 - - + +
2230B LEU* 3.0 34.5 + - + +
2231B ASN 3.0 0.2 - - - -
2232B HIS* 1.3 99.2 - - + +
2234B TYR* 1.3 80.9 + - + +
2235B GLY 3.6 0.7 - - - -
2244B LEU* 3.8 7.6 - - - +
2252B LEU* 4.1 19.0 - - + +
2287B VAL* 5.0 1.0 - - - -
2288B GLY* 3.3 16.7 + - - +
2302B ALA* 5.7 4.3 - - - +
2305B TRP* 3.4 42.8 - - + +
2306B LEU* 5.1 5.8 - - + +
2336B LEU* 4.6 4.5 - - + -
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Residues in contact with TYR2234 (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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2230B LEU* 3.1 41.0 + - + +
2233B ILE* 1.3 94.4 - - + +
2235B GLY* 1.3 58.8 + - - +
2241B GLN* 3.1 34.8 - - + +
2244B LEU* 4.0 7.8 - - - +
2252B LEU* 4.1 12.8 - - + -
2309B HIS* 2.8 40.2 + + - -
2329B PHE* 3.6 25.6 - + + -
2333B LYS* 3.4 58.8 - - + +
2336B LEU* 3.3 17.9 - - + +
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Residues in contact with GLY2235 (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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2231B ASN* 2.7 31.8 + - - +
2233B ILE 3.6 1.6 - - - -
2234B TYR* 1.3 80.3 - - - +
2236B GLU* 1.3 63.1 + - - -
2237B THR 3.3 5.3 + - - +
2240B ARG* 3.9 20.6 - - - -
2241B GLN* 5.2 1.4 + - - +
2288B GLY* 3.7 10.2 - - - -
2333B LYS* 5.0 3.8 + - - -
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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