Contacts of the helix formed by residues 2222 - 2230 (chain B) in PDB entry 1WUF
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 PHE2222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1220A LYS 5.6 0.4 - - - -
1222A PHE* 4.2 19.7 - + - -
1250A GLN* 2.6 20.1 - - - +
2220B LYS 3.9 14.1 - - - -
2221B ASP* 1.3 78.3 - - - +
2223B VAL* 1.3 59.1 + - - +
2224B ASP 3.6 0.4 - - - -
2225B HIS* 3.4 1.3 + - - -
2226B ALA* 2.9 21.1 + - - +
2238B LEU* 4.3 4.3 - - + -
2241B ASN* 3.7 31.6 - - + -
2242B ILE* 5.0 0.4 - - + -
2247B ASP* 4.2 14.6 - - - -
2250B GLN* 4.0 21.1 - - + -
2251B ALA* 4.0 31.0 - - + -
2254B ILE* 3.8 22.0 - - + -
2256B SER* 2.6 35.0 + - - +
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Residues in contact with VAL2223 (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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1246A LYS* 6.1 0.4 - - - +
1250A GLN* 2.8 24.4 - - + +
1253A SER* 3.2 31.2 - - - +
1254A ILE* 3.5 26.2 - - + -
2196B ARG* 3.6 11.2 - - - +
2221B ASP* 3.9 1.3 - - - +
2222B PHE* 1.3 77.8 - - - +
2224B ASP* 1.3 70.9 + - - +
2226B ALA* 3.1 8.4 + - - +
2227B TRP* 2.9 26.5 + - - +
2254B ILE* 4.7 4.5 - - + -
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Residues in contact with ASP2224 (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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1246A LYS* 4.6 12.3 + - - -
2196B ARG* 2.7 48.5 + - + +
2217B PHE* 3.1 33.3 - - + +
2221B ASP* 2.9 25.7 + - - +
2223B VAL* 1.3 75.4 - - - +
2225B HIS* 1.3 64.3 + - - +
2227B TRP* 3.3 3.3 + - - +
2228B LEU 3.1 16.5 + - - -
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Residues in contact with HIS2225 (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 GLN* 3.7 12.3 + - - -
2216B PRO* 3.3 35.8 - - + +
2217B PHE* 3.3 25.3 - + + +
2218B GLY 3.4 18.8 + - - -
2221B ASP* 2.7 50.0 + - + -
2222B PHE 3.5 7.6 - - - +
2223B VAL 3.2 0.2 - - - -
2224B ASP* 1.3 74.7 - - - +
2226B ALA* 1.3 51.2 + - - +
2228B LEU* 3.0 5.3 + - - +
2229B GLN* 2.8 35.2 + - - +
2236B ILE* 3.7 12.3 - - - +
2238B LEU* 3.8 12.3 - - + +
2256B SER* 3.3 21.7 - - - +
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Residues in contact with ALA2226 (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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2222B PHE 2.9 13.4 + - - +
2223B VAL* 3.1 8.7 + - - +
2225B HIS* 1.3 75.5 - - - +
2227B TRP* 1.3 62.4 + - - +
2228B LEU 3.1 0.5 + - - -
2230B LYS* 3.1 39.6 + - - +
2254B ILE* 3.3 25.8 - - + +
2255B GLY 2.9 27.1 - - - +
2256B SER* 3.6 1.1 - - - +
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Residues in contact with TRP2227 (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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2196B ARG* 3.3 78.2 - - + +
2199B PHE* 3.6 46.2 - + + -
2217B PHE* 4.4 5.6 - + - -
2223B VAL 2.9 7.6 + - - +
2224B ASP 3.5 13.0 - - - +
2226B ALA* 1.3 76.7 - - - +
2228B LEU* 1.3 62.0 + - + +
2230B LYS* 4.4 9.1 + - - +
2231B GLN* 3.0 46.0 + - - +
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Residues in contact with LEU2228 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2199B PHE* 5.1 9.6 - - + -
2202B LEU* 4.4 17.3 - - + -
2203B LYS* 5.3 1.6 - - + -
2216B PRO* 4.1 14.8 - - + -
2217B PHE* 3.6 30.7 - - + -
2224B ASP 3.1 10.8 + - - +
2225B HIS* 3.0 8.8 + - - +
2227B TRP* 1.3 83.2 - - + +
2229B GLN* 1.3 65.3 + - - +
2230B LYS 3.2 1.8 - - - -
2231B GLN* 3.0 16.8 + - + +
2232B LEU* 3.2 35.6 - - + +
2236B ILE* 3.8 23.8 - - + -
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Residues in contact with GLN2229 (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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2225B HIS 2.8 19.2 + - - +
2226B ALA 3.3 0.4 + - - +
2228B LEU* 1.3 74.4 - - - +
2230B LYS* 1.3 59.9 + - + +
2231B GLN 3.0 0.2 - - - -
2232B LEU* 3.1 22.1 + - - +
2234B THR 3.1 19.6 - - - +
2235B ARG* 3.8 0.4 - - - +
2236B ILE* 2.9 38.7 - - + +
2255B GLY* 3.6 20.9 - - - +
2256B SER 4.1 5.2 - - - +
2257B CYS* 3.5 6.3 - - - +
2258B ARG* 3.2 52.0 + - + +
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Residues in contact with LYS2230 (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 ALA* 3.1 27.3 - - - +
2227B TRP* 4.5 8.1 - - - +
2228B LEU 3.2 0.4 - - - -
2229B GLN* 1.3 76.0 - - + +
2231B GLN* 1.3 60.3 + - + +
2232B LEU 3.5 0.9 - - - -
2254B ILE* 3.9 22.6 + - - +
2255B GLY* 4.4 7.6 - - - +
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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