Contacts of the helix formed by residues 2262 - 2272 (chain B) in PDB entry 5WBY
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 ASN2262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2247B HIS* 5.6 2.5 - - - -
2260B LEU* 3.3 8.3 - - + +
2261B LEU* 1.3 95.2 - - - +
2263B ILE* 1.3 60.8 + - - +
2264B GLU* 3.5 4.5 - - - -
2265B HIS* 3.7 23.3 - - + +
2266B ARG* 3.3 32.0 + - - +
2546B CYS* 5.3 4.9 - - - -
2548B PHE* 5.9 3.2 - - - -
2549B TRP* 4.2 14.6 - - - -
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Residues in contact with ILE2263 (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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2254B ARG* 3.8 13.5 - - - +
2259B ILE* 4.3 12.3 - - + -
2260B LEU* 3.2 40.8 + - + +
2261B LEU 3.4 1.4 + - - -
2262B ASN* 1.3 74.3 - - - +
2264B GLU* 1.3 78.0 + - - +
2266B ARG* 3.2 6.4 + - + +
2267B ILE* 2.9 48.5 + - + +
2294B THR* 3.9 13.2 - - + -
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Residues in contact with GLU2264 (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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2254B ARG* 2.8 37.0 + - - -
2261B LEU 4.3 0.5 - - - +
2262B ASN* 4.5 1.0 - - - -
2263B ILE* 1.3 81.3 + - - +
2265B HIS* 1.3 58.0 + - - +
2267B ILE* 3.3 6.0 + - - +
2268B MET* 2.9 36.4 + - - +
2290B ALA* 4.0 13.4 - - + +
2294B THR* 4.0 18.4 + - + +
2381B ARG* 3.4 16.8 + - - -
2382B MET* 4.5 0.2 - - - +
2548B PHE* 3.4 47.3 - - + -
2549B TRP* 3.4 12.5 + - - -
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Residues in contact with HIS2265 (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 ASN* 3.7 26.6 - - + +
2264B GLU* 1.3 78.5 - - - +
2266B ARG* 1.3 61.5 + - - +
2268B MET* 3.4 6.6 + - - +
2269B LEU* 3.2 51.9 + - + +
2543B ILE* 3.6 45.5 - - + +
2548B PHE* 4.0 13.0 - - + -
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Residues in contact with ARG2266 (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 LEU* 3.5 41.3 - - - +
2262B ASN* 3.3 26.5 + - - +
2263B ILE* 3.2 12.5 + - + +
2265B HIS* 1.3 75.3 - - - +
2267B ILE* 1.3 64.7 + - - +
2269B LEU* 3.6 6.5 + - - +
2270B ARG* 3.0 48.6 + - - +
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Residues in contact with ILE2267 (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 ILE* 2.9 35.8 + - + +
2264B GLU* 3.6 5.2 - - - +
2266B ARG* 1.3 76.8 - - + +
2268B MET* 1.3 63.7 + - - +
2270B ARG* 3.4 9.3 + - - +
2271B MET* 3.0 21.3 + - - +
2289B HIS* 3.5 32.4 + - + +
2290B ALA* 3.9 16.8 - - + +
2293B ASN* 4.2 14.6 - - + +
2294B THR* 3.7 28.7 - - + -
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Residues in contact with MET2268 (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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2264B GLU 2.9 19.4 + - - +
2265B HIS* 3.7 4.9 - - - +
2267B ILE* 1.3 76.6 - - - +
2269B LEU* 1.3 53.9 + - + +
2271B MET* 3.2 4.4 + - - +
2272B ALA 2.8 34.7 + - - +
2275B TYR* 3.3 50.7 - - + +
2286B VAL* 3.6 23.8 - - + +
2287B PHE* 4.4 14.4 - - + -
2290B ALA* 3.7 17.7 - - + -
2543B ILE* 3.9 16.6 - - + -
2547B PRO* 6.4 0.9 - - + -
2548B PHE* 3.6 33.4 - - + -
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Residues in contact with LEU2269 (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 HIS* 3.2 44.9 + - + +
2266B ARG* 4.1 4.7 - - - +
2268B MET* 1.3 75.7 - - + +
2270B ARG* 1.3 66.0 + - - +
2272B ALA 3.6 7.0 - - - +
2273B PRO* 3.1 47.0 - - + +
2275B TYR* 4.7 11.4 - - + +
2276B ASP* 5.5 5.6 - - - +
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Residues in contact with ARG2270 (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 ARG* 3.0 52.7 + - - +
2267B ILE* 3.5 9.1 - - - +
2268B MET 3.3 0.2 - - - -
2269B LEU* 1.3 79.2 - - - +
2271B MET* 1.3 60.7 + - - +
2273B PRO* 4.8 2.9 - - - +
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Residues in contact with MET2271 (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 ILE 3.0 13.6 + - - +
2268B MET 3.2 7.2 + - - +
2270B ARG* 1.3 80.6 - - - +
2272B ALA* 1.3 58.7 + - + +
2273B PRO* 3.9 4.6 - - - +
2285B GLU* 3.5 41.5 - - + +
2286B VAL* 3.8 26.7 - - + -
2289B HIS* 3.7 40.2 - - + +
20D TYR* 3.6 21.6 - - + +
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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 MET 2.8 16.1 + - - +
2269B LEU* 3.2 6.5 - - - +
2271B MET* 1.3 75.1 - - - +
2273B PRO* 1.3 68.6 - - - +
2274B ASP 3.2 2.0 - - - +
2275B TYR* 3.2 16.3 + - - +
2278B LEU* 3.8 17.3 - - + -
2286B VAL* 3.8 23.8 - - + -
20D TYR* 3.6 21.1 - - + -
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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