Contacts of the strand formed by residues 2262 - 2269 (chain B) in PDB entry 4D0N
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 ILE2262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2220B MET* 4.0 20.0 - - + -
2226B PHE* 4.2 15.0 - - + -
2234B LYS* 3.7 24.9 - - - +
2258B LEU* 4.1 0.2 - - - -
2259B LEU* 2.8 36.7 + - + +
2261B ASP* 1.3 94.9 + - + +
2263B LEU* 1.3 66.7 + - - +
2264B VAL* 3.6 24.7 - - + -
2284B VAL* 3.8 11.0 - - + -
2285B ILE 3.3 11.2 - - - +
2286B SER* 4.3 8.5 - - - -
2287B LEU* 3.7 7.4 - - - +
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Residues in contact with LEU2263 (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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2256B ALA* 4.9 5.2 - - + -
2257B VAL 3.5 31.9 - - - +
2258B LEU* 3.7 15.7 - - + +
2262B ILE* 1.3 72.7 - - - +
2264B VAL* 1.3 63.8 + - - +
2265B PHE* 4.1 20.4 - - + -
2283B THR 3.7 1.7 - - - +
2284B VAL* 3.5 2.4 - - - -
2285B ILE* 2.7 49.3 + - + +
2287B LEU* 4.0 14.0 - - + +
2290B LEU* 5.0 5.2 - - + -
2304B LEU* 3.6 32.8 - - + -
2328B TRP* 5.3 2.7 - - + -
2332B ILE* 4.3 20.2 - - + -
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Residues in contact with VAL2264 (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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2226B PHE* 4.6 8.1 - - + -
2231B LEU* 4.7 7.2 - - + -
2256B ALA* 3.7 0.5 - - - -
2257B VAL* 2.8 49.0 + - + +
2259B LEU* 4.0 17.0 - - + -
2262B ILE* 3.6 19.5 - - + -
2263B LEU* 1.3 80.0 - - - +
2265B PHE* 1.3 66.8 + - - +
2266B LEU* 3.5 31.2 - - + -
2275B PHE* 3.9 17.5 - - + -
2283B THR 3.4 5.4 - - - +
2284B VAL* 4.4 11.2 - - + -
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Residues in contact with PHE2265 (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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2242B VAL* 4.0 17.0 - - + -
2244B LEU* 3.8 29.2 - - + -
2254B VAL* 3.7 28.9 - - + -
2255B GLN 3.5 1.1 - - - -
2256B ALA* 4.0 18.2 - - + -
2263B LEU* 4.1 30.7 - - + -
2264B VAL* 1.3 76.8 - - - +
2266B LEU* 1.3 63.9 + - - +
2275B PHE* 3.6 1.6 - - - +
2276B ALA* 2.8 34.7 + - + -
2283B THR* 3.1 31.5 + - + -
2285B ILE* 4.3 14.1 - - + -
2304B LEU* 4.2 11.9 - - + -
2315B VAL* 4.4 3.8 - - + -
2317B VAL* 4.3 9.0 - - + -
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Residues in contact with LEU2266 (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 ILE* 3.5 32.8 - - + -
2212B THR* 4.0 7.4 - - + +
2231B LEU* 4.7 5.8 - - + -
2254B VAL* 3.1 8.1 - - - +
2255B GLN* 2.8 39.0 + - + +
2257B VAL* 4.3 14.4 - - + -
2264B VAL* 3.5 22.4 - - + -
2265B PHE* 1.3 81.4 - - - +
2267B GLN* 1.3 60.8 + - - +
2268B GLU 4.0 0.7 + - - -
2273B TYR* 3.7 31.0 - - + -
2274B ILE 3.1 11.7 - - - +
2275B PHE* 3.6 23.1 - - + +
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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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2252B LYS* 3.5 27.3 - - + +
2253B GLU 4.2 17.9 - - - +
2254B VAL* 4.5 1.8 - - + -
2266B LEU* 1.3 72.8 - - - +
2268B GLU* 1.3 63.9 + - - +
2269B LYS* 3.5 3.6 + - + +
2273B TYR* 3.3 3.5 - - - -
2274B ILE* 2.8 64.3 + - + +
2276B ALA* 3.4 16.3 - - + +
2277B SER* 3.1 31.7 + - - -
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Residues in contact with GLU2268 (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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2211B LYS* 3.0 36.9 + - - -
2253B GLU 5.0 2.4 + - - -
2254B VAL* 5.8 0.4 - - - +
2266B LEU 4.0 1.0 + - - -
2267B GLN* 1.3 70.5 - - - +
2269B LYS* 1.3 58.1 + - - +
2270B ASP 4.5 0.2 + - - -
2271B GLN* 4.4 11.6 - - - +
2272B LYS 3.4 12.3 - - - +
2273B TYR* 3.9 14.8 - - + -
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Residues in contact with LYS2269 (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 LYS* 4.2 6.0 + - - +
2267B GLN* 3.5 5.5 + - + +
2268B GLU* 1.3 73.6 - - - +
2270B ASP* 1.3 87.4 + - - +
2271B GLN 3.2 1.1 - - - -
2272B LYS* 2.9 23.1 + - - +
2274B ILE* 4.1 28.5 - - + -
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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