Contacts of the helix formed by residues 2261 - 2273 (chain B) in PDB entry 2H7C
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 VAL2261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2179B SER* 3.7 18.1 - - - +
2181B GLY* 3.4 38.8 - - - +
2257B LYS* 4.1 18.2 - - + +
2258B LYS 5.4 0.7 - - - +
2259B GLY 3.4 13.0 + - - +
2260B ASP* 1.3 73.9 + - - +
2262B LYS* 1.3 64.2 + - - +
2263B PRO* 3.4 2.7 - - - -
2264B LEU* 3.4 12.5 + - + +
2265B ALA* 3.3 18.5 + - - +
2322B VAL* 4.0 26.7 - - + -
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Residues in contact with LYS2262 (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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2180B THR* 4.1 19.3 + - - +
2260B ASP* 3.1 25.4 + - - +
2261B VAL* 1.3 79.3 - - - +
2263B PRO* 1.3 64.5 - - + +
2265B ALA* 3.2 5.5 + - + +
2266B GLU* 3.0 47.4 + - - +
2276B THR 5.4 2.8 + - - -
2278B THR* 4.6 2.8 - - - +
2279B SER* 3.0 30.7 + - - +
2282B MET* 3.4 23.3 - - + +
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Residues in contact with PRO2263 (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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2260B ASP* 3.0 29.8 - - + +
2261B VAL 3.5 3.8 - - - -
2262B LYS* 1.3 91.6 - - + +
2264B LEU* 1.3 56.3 + - - +
2266B GLU* 3.3 9.6 + - + +
2267B GLN* 3.0 27.0 + - - +
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Residues in contact with LEU2264 (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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2261B VAL* 3.4 12.8 + - + +
2262B LYS 3.3 0.6 - - - -
2263B PRO* 1.3 75.7 - - - +
2265B ALA* 1.3 67.1 + - - +
2267B GLN* 3.2 22.1 + - - +
2268B ILE* 3.0 30.7 + - + +
2301B MET* 4.0 16.6 - - + -
2303B PHE* 4.8 0.2 - - + -
2316B GLN* 3.4 49.6 - - + +
2318B LEU 4.6 2.9 - - - +
2319B LEU* 3.2 32.8 - - + -
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Residues in contact with ALA2265 (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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2178B PHE* 3.8 26.0 - - + -
2179B SER 3.2 27.5 + - - +
2180B THR* 4.1 12.1 - - + -
2261B VAL 3.3 4.4 + - - +
2262B LYS* 3.2 10.2 + - - +
2264B LEU* 1.3 78.6 - - - +
2266B GLU* 1.3 57.1 + - - +
2268B ILE* 3.4 4.9 + - - +
2269B ALA* 3.0 28.2 + - - +
2282B MET* 4.4 7.9 - - + -
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Residues in contact with GLU2266 (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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2262B LYS* 3.0 49.3 + - - +
2263B PRO* 3.7 7.9 - - + +
2265B ALA* 1.3 74.8 - - - +
2267B GLN* 1.3 61.2 + - - +
2269B ALA* 3.3 1.4 + - - +
2270B ILE* 2.9 41.4 + - + +
2276B THR* 3.8 26.4 + - + +
2282B MET* 3.9 23.3 - - - -
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Residues in contact with GLN2267 (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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2263B PRO 3.0 13.0 + - - +
2264B LEU* 3.2 25.8 + - - +
2266B GLU* 1.3 76.6 - - - +
2268B ILE* 1.3 55.6 + - - +
2270B ILE* 3.8 7.6 - - - +
2271B THR* 2.7 40.9 + - - +
2301B MET* 4.0 21.4 - - + +
2314B GLU 5.0 6.3 + - - +
2316B GLN* 5.0 6.2 - - - +
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Residues in contact with ILE2268 (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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2174B ILE* 4.1 23.1 - - + -
2178B PHE* 4.1 27.1 - - + -
2264B LEU* 3.0 25.3 + - + +
2265B ALA* 3.6 4.5 - - - +
2267B GLN* 1.3 73.9 - - - +
2269B ALA* 1.3 65.2 + - - +
2271B THR* 3.4 2.9 + - - -
2272B ALA* 3.0 22.7 + - - +
2286B LEU* 4.6 8.7 - - + -
2294B LEU* 6.3 0.2 - - + -
2297B THR* 3.8 5.4 - - + +
2301B MET* 3.6 27.6 - - + -
2303B PHE* 4.5 2.2 - - + -
2319B LEU* 3.7 42.4 - - + -
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Residues in contact with ALA2269 (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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2265B ALA 3.0 17.6 + - - +
2266B GLU* 3.7 4.5 - - - +
2268B ILE* 1.3 77.2 - - - +
2270B ILE* 1.3 57.8 + - - +
2272B ALA 3.1 2.6 + - - -
2273B GLY 3.0 5.2 + - - -
2274B CYS* 2.7 50.6 + - + +
2276B THR* 4.4 2.5 - - + -
2282B MET* 4.0 27.4 - - + -
2286B LEU* 4.4 13.5 - - + -
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Residues in contact with ILE2270 (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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2266B GLU* 2.9 27.8 + - + +
2267B GLN* 3.8 6.7 - - - +
2269B ALA* 1.3 74.1 - - - +
2271B THR* 1.3 61.3 + - - +
2273B GLY* 2.9 20.0 + - - -
2274B CYS 3.8 9.0 - - - +
2276B THR* 3.7 21.8 - - + +
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Residues in contact with THR2271 (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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2267B GLN* 2.7 27.2 + - - +
2268B ILE 3.7 4.9 - - - -
2270B ILE* 1.3 78.6 - - - +
2272B ALA* 1.3 59.7 + - - +
2273B GLY 3.2 0.8 + - - -
2297B THR* 3.7 21.8 + - + +
2300B LYS* 3.9 46.4 + - + -
2301B MET* 3.7 16.7 - - - +
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Residues in contact with ALA2272 (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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2268B ILE 3.0 17.3 + - - +
2269B ALA 3.1 4.9 + - - +
2271B THR* 1.3 76.7 - - - +
2273B GLY* 1.3 58.3 + - - +
2274B CYS* 3.5 0.4 - - - -
2286B LEU* 3.7 23.3 - - + -
2289B LYS* 3.0 33.7 + - + +
2293B GLU* 6.1 0.6 - - + +
2294B LEU* 4.9 2.0 - - + -
2297B THR* 3.5 22.4 + - + +
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Residues in contact with GLY2273 (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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2270B ILE 2.9 13.7 + - - -
2271B THR 3.2 1.4 + - - -
2272B ALA* 1.3 81.1 - - - +
2274B CYS* 1.3 62.4 + - - +
2275B LYS* 5.8 0.5 - - - +
2285B CYS* 4.6 1.4 - - - -
2289B LYS* 4.3 6.9 + - - -
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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