Contacts of the helix formed by residues 2279 - 2293 (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 THR2279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2278B LEU* 1.3 74.3 - - - +
2280B LEU* 1.3 53.9 + - - +
2281B MET* 4.0 8.2 + - - +
2282B GLN* 2.8 37.5 + - - +
2283B LYS* 2.8 32.8 + - - +
46D ASN* 3.5 26.9 - - + +
87D ASN* 3.9 22.4 - - + +
89D ALA* 5.1 11.4 - - + -
105D GLU* 4.4 9.0 - - + +
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Residues in contact with LEU2280 (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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2278B LEU 4.0 1.0 + - - -
2279B THR* 1.3 72.0 - - - +
2281B MET* 1.3 68.2 + - + +
2283B LYS* 3.1 9.6 + - - +
2284B VAL* 3.0 28.4 + - + +
2536B GLU* 3.5 57.0 - - + +
2539B CYS* 4.0 6.7 - - - -
2540B GLN* 3.5 26.7 - - + +
105D GLU* 5.2 6.7 + - - +
148D GLN* 3.4 38.6 - - - +
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Residues in contact with MET2281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2279B THR* 3.2 8.6 + - - +
2280B LEU* 1.3 83.7 - - + +
2282B GLN* 1.3 63.6 + - + +
2284B VAL* 3.5 19.7 + - + +
2285B GLU* 3.5 11.3 + - - +
2536B GLU* 5.8 4.3 - - - +
132D ASN* 5.7 8.5 - - - +
148D GLN* 6.1 0.9 - - - +
172D SER* 5.8 1.6 - - - +
174D THR* 3.7 31.9 - - + -
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Residues in contact with GLN2282 (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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2278B LEU* 3.3 23.3 - - + +
2279B THR* 2.8 42.1 + - - +
2281B MET* 1.3 81.5 - - + +
2283B LYS* 1.3 60.8 + - - +
2285B GLU* 3.6 8.3 + - - +
2286B VAL* 3.5 24.6 + - - +
20D TYR* 3.3 25.5 + - + +
44D GLN* 3.4 3.9 + - - +
45D VAL 4.2 4.9 + - - -
46D ASN* 3.2 36.6 + - - +
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Residues in contact with LYS2283 (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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2275B TYR* 3.4 42.3 - - + +
2276B ASP* 3.0 30.4 + - - +
2278B LEU* 3.4 30.1 - - + -
2279B THR 2.8 19.2 + - - +
2280B LEU* 3.1 9.6 + - - +
2282B GLN* 1.3 70.6 - - - +
2284B VAL* 1.3 60.8 + - - +
2286B VAL 3.2 1.7 + - - -
2287B PHE* 2.9 29.3 + - - +
2371B PHE* 5.1 7.5 - - - -
2539B CYS* 3.7 22.0 + - - +
2540B GLN* 4.7 20.4 + - + +
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Residues in contact with VAL2284 (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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2280B LEU* 3.0 21.7 + - + +
2281B MET* 3.8 14.1 - - + +
2282B GLN 3.4 0.2 - - - -
2283B LYS* 1.3 76.8 - - - +
2285B GLU* 1.3 52.8 + - - +
2287B PHE* 3.3 5.0 + - - +
2288B GLU* 2.7 62.5 + - + +
2535B HIS* 4.2 9.9 - - + +
2536B GLU* 4.0 27.8 - - + +
2539B CYS* 3.7 19.5 - - - -
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Residues in contact with GLU2285 (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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2271B MET* 3.5 25.8 - - + +
2281B MET 3.5 9.2 + - - +
2282B GLN* 3.7 8.9 - - - +
2283B LYS 3.3 0.2 - - - -
2284B VAL* 1.3 79.1 - - - +
2286B VAL* 1.3 52.3 + - - +
2288B GLU* 3.3 8.5 + - - +
2289B HIS* 2.7 36.2 + - + +
20D TYR* 4.1 12.8 + - - -
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Residues in contact with VAL2286 (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* 3.6 35.5 - - + +
2271B MET* 3.8 28.7 - - + -
2272B ALA* 3.8 22.2 - - + -
2275B TYR* 3.6 21.5 - - + -
2278B LEU* 4.0 5.6 - - + -
2282B GLN 3.5 14.1 + - - +
2283B LYS 3.2 6.8 + - - +
2285B GLU* 1.3 72.3 - - - +
2287B PHE* 1.3 65.1 + - - +
2289B HIS* 3.4 3.7 + - + +
2290B ALA* 3.1 22.7 + - - +
20D TYR* 4.3 3.8 - - + -
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Residues in contact with PHE2287 (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* 4.4 12.6 - - + -
2275B TYR* 4.4 3.1 - - - +
2283B LYS 2.9 16.4 + - - +
2284B VAL* 3.5 3.1 - - - +
2286B VAL* 1.3 76.4 - - - +
2288B GLU* 1.3 58.7 + - + +
2290B ALA* 3.1 7.1 + - - +
2291B VAL* 3.0 46.4 + - + +
2535B HIS* 4.1 40.4 - + + -
2538B LEU* 4.1 16.6 - - + -
2539B CYS* 3.8 25.6 - - + -
2547B PRO* 3.5 45.3 - - + -
2548B PHE* 4.0 17.9 - + + -
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Residues in contact with GLU2288 (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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2284B VAL* 2.7 42.3 + - + +
2285B GLU* 3.7 6.9 - - - +
2287B PHE* 1.3 73.6 - - + +
2289B HIS* 1.3 60.3 + - - +
2291B VAL* 3.9 4.9 - - - +
2292B ASN* 2.9 49.0 + - - +
2535B HIS* 2.8 40.0 + - + +
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Residues in contact with HIS2289 (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* 3.5 31.7 + - + +
2268B MET* 6.0 0.2 - - - -
2271B MET* 3.7 34.1 - - + +
2285B GLU* 2.7 21.7 + - + +
2286B VAL 3.5 5.8 - - - +
2288B GLU* 1.3 74.0 - - - +
2290B ALA* 1.3 59.7 + - - +
2292B ASN* 4.7 2.5 - - - +
2293B ASN* 2.6 54.5 + - - +
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Residues in contact with ALA2290 (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* 4.0 22.0 - - + +
2267B ILE* 3.9 15.0 - - + -
2268B MET* 3.7 23.6 - - + -
2286B VAL 3.1 14.0 + - - +
2287B PHE* 3.1 8.3 + - - +
2289B HIS* 1.3 73.9 - - - +
2291B VAL* 1.3 58.8 + - + +
2293B ASN* 3.3 8.3 + - - +
2294B THR* 2.7 31.1 + - - +
2548B PHE* 5.3 2.0 - - + -
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Residues in contact with VAL2291 (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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2287B PHE* 3.0 51.3 + - + +
2288B GLU* 3.9 6.5 - - - +
2290B ALA* 1.3 76.8 - - - +
2292B ASN* 1.3 66.8 + - - +
2293B ASN 3.3 0.2 + - - -
2294B THR* 3.0 30.1 + - - +
2381B ARG* 3.1 33.5 + - + +
2535B HIS* 5.4 9.6 - - + +
2548B PHE* 4.4 13.5 - - + -
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Residues in contact with ASN2292 (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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2288B GLU* 2.9 37.9 + - - +
2289B HIS* 4.1 5.6 - - - +
2291B VAL* 1.3 85.5 - - - +
2293B ASN* 1.3 64.6 + - - +
2294B THR 3.5 1.7 + - - +
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Residues in contact with ASN2293 (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* 4.2 13.4 - - + +
2289B HIS* 2.6 58.3 + - + +
2290B ALA 3.3 1.1 + - - +
2291B VAL 3.2 0.6 - - - -
2292B ASN* 1.3 83.9 - - - +
2294B THR* 1.3 68.3 + - - +
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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