Contacts of the helix formed by residues 2237 - 2245 (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 THR2237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2235B GLY 3.3 2.3 - - - -
2236B GLU* 1.3 90.6 - - + +
2238B LEU* 1.3 64.7 + - - +
2239B ASP* 3.7 8.8 + - - +
2240B ARG* 3.2 22.7 + - - +
2241B GLN* 3.0 22.5 + - - +
1D NAG 5.3 3.4 - - - -
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Residues in contact with LEU2238 (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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140A GLU* 4.4 20.6 - - - +
2237B THR* 1.3 70.1 - - - +
2239B ASP* 1.3 61.3 + - - +
2241B GLN* 3.2 19.5 + - - +
2242B HIS* 2.8 72.2 + - + +
1D NAG 4.0 39.5 + - - +
2D NAG 3.6 36.6 - - - +
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Residues in contact with ASP2239 (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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2237B THR* 3.3 8.9 + - - +
2238B LEU* 1.3 78.5 - - - +
2240B ARG* 1.3 64.1 + - - +
2242B HIS* 3.8 6.9 - - - +
2243B LYS* 3.3 34.5 + - + +
2D NAG 2.5 33.8 + - - -
3D MAN 4.0 19.0 + - - +
4D MAN 5.3 7.8 - - - +
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Residues in contact with ARG2240 (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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2235B GLY* 3.9 16.4 - - - -
2236B GLU 5.1 1.8 - - - +
2237B THR* 3.2 20.9 + - - +
2238B LEU 3.1 0.6 - - - -
2239B ASP* 1.3 76.9 - - - +
2241B GLN* 1.3 67.3 - - - +
2243B LYS* 2.8 24.7 + - - +
2244B LEU* 3.1 19.2 + - + +
2271B VAL* 4.7 8.9 - - + +
2272B GLU* 3.0 29.1 + - - +
2273B MET* 2.7 33.5 - - - +
2287B VAL 3.1 12.7 + - - -
2288B GLY 3.3 14.5 + - - -
2290B GLU* 3.3 35.0 - - - +
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Residues in contact with GLN2241 (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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140A GLU* 4.8 8.7 + - - +
2234B TYR* 3.1 25.2 + - + +
2235B GLY 5.2 1.3 - - - +
2237B THR 3.0 9.3 + - - +
2238B LEU* 3.5 19.4 - - - +
2240B ARG* 1.3 78.3 - - - +
2242B HIS* 1.3 72.2 + - - +
2244B LEU* 3.0 15.5 + - - +
2245B ARG* 2.9 50.6 + - + +
2329B PHE* 3.7 27.5 - - + -
2330B GLN* 4.6 5.6 + - - +
2333B LYS* 4.7 11.9 - - - +
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Residues in contact with HIS2242 (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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2238B LEU* 2.8 53.6 + - + +
2239B ASP* 3.8 6.5 - - - +
2241B GLN* 1.3 90.8 + - - +
2243B LYS* 1.3 60.7 + - + +
2244B LEU 3.3 0.5 + - - -
2245B ARG* 3.4 19.6 + - - +
2247B PHE* 3.3 46.7 - + + -
2253B LYS* 5.5 0.5 - - - -
2326B GLU* 4.8 2.9 - - - -
2D NAG 4.9 8.5 - - - -
3D MAN 5.7 2.5 - - - -
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Residues in contact with LYS2243 (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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2239B ASP* 3.3 26.5 + - + +
2240B ARG* 2.8 14.2 + - - +
2242B HIS* 1.3 73.7 - - + +
2244B LEU* 1.3 59.4 + - - +
2245B ARG 3.4 0.2 - - - -
2253B LYS* 3.6 10.7 + - - +
2269B THR* 3.3 35.8 - - - +
2270B GLN* 3.1 32.3 + - - +
2271B VAL* 3.3 21.3 - - + -
2272B GLU* 3.8 15.2 - - - +
4D MAN 5.0 18.2 - - - -
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Residues in contact with LEU2244 (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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2233B ILE 3.8 12.3 - - - +
2234B TYR* 4.0 14.6 - - - +
2240B ARG* 3.7 17.9 - - + +
2241B GLN* 3.0 7.2 + - - +
2243B LYS* 1.3 78.4 - - - +
2245B ARG* 1.3 61.3 + - - +
2252B LEU* 3.5 16.1 - - + +
2253B LYS* 2.8 28.1 + - - +
2264B PRO* 4.8 4.3 - - + +
2269B THR* 4.7 5.2 - - + -
2271B VAL* 3.8 20.2 - - + -
2286B ALA* 3.7 33.7 - - + +
2287B VAL* 3.9 2.7 - - - +
2288B GLY* 3.8 28.3 - - - +
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Residues in contact with ARG2245 (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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2241B GLN* 2.9 47.9 + - + +
2242B HIS* 3.4 26.3 + - - +
2244B LEU* 1.3 79.9 - - - +
2246B LEU* 1.3 63.1 + - - +
2247B PHE* 3.4 27.5 - - + +
2251B LYS 3.7 5.9 + - - +
2252B LEU* 4.1 7.4 - - + +
2253B LYS* 3.4 18.8 - - - +
2325B ASP* 2.8 31.5 + - - -
2326B GLU* 2.6 40.0 + - - +
2329B PHE* 3.8 41.4 - - + +
2330B GLN* 4.5 0.6 - - - +
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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