Contacts of the helix formed by residues 202 - 209 (chain B) in PDB entry 4F4W
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 LYS 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B ASN 4.1 0.4 - - - +
178B GLU* 3.1 40.8 - - - +
179B LEU 3.4 7.0 - - - +
180B ASP* 3.5 21.2 + - - +
181B ILE* 4.0 10.1 - - - +
201B GLN* 1.3 79.5 - - + +
203B LEU* 1.3 68.4 + - - +
204B ARG* 3.4 42.9 - - + +
205B ASP* 2.8 29.3 + - - +
206B ILE 4.0 0.7 + - - -
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Residues in contact with LEU 203 (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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176B LEU* 3.7 40.6 - - + +
179B LEU* 2.8 28.1 + - + +
181B ILE* 4.2 10.0 - - - +
184B ILE* 3.6 24.2 - - + -
202B LYS* 1.3 71.8 - - - +
204B ARG* 1.3 58.7 + - - +
206B ILE* 2.9 39.7 + - + +
226B LEU* 3.9 12.1 - - + +
229B LEU* 3.8 20.9 - - + -
230B ALA* 3.8 29.3 - - + +
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Residues in contact with ARG 204 (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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176B LEU 4.3 3.9 + - - +
177B ASN* 2.7 63.6 + - - +
178B GLU* 3.2 24.7 + - - -
202B LYS* 3.4 27.6 - - + +
203B LEU* 1.3 79.8 - - - +
205B ASP* 1.3 73.5 + - - +
206B ILE 3.0 1.3 + - - -
207B LEU* 3.1 34.3 + - + +
208B SER* 4.4 0.9 + - - -
230B ALA* 5.2 1.8 - - - -
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Residues in contact with ASP 205 (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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199B GLY 3.8 9.8 - - - +
200B ILE* 3.9 24.5 - - + +
201B GLN* 3.1 12.9 + - - +
202B LYS* 2.8 37.6 + - - +
204B ARG* 1.3 89.1 + - - +
206B ILE* 1.3 57.7 + - - +
207B LEU 3.2 0.2 - - - -
208B SER* 2.7 32.2 + - - +
209B LYS 4.3 0.2 + - - -
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Residues in contact with ILE 206 (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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181B ILE* 4.2 11.4 - - + -
195B LEU* 4.8 1.8 - - + -
200B ILE* 3.6 26.2 - - + -
203B LEU* 2.9 33.1 + - + +
205B ASP* 1.3 78.9 - - - +
207B LEU* 1.3 60.4 + - - +
208B SER 3.0 0.4 - - - -
209B LYS* 3.1 25.7 + - - +
214B LEU* 4.1 20.9 - - + -
226B LEU* 3.9 35.9 - - + +
227B LEU* 3.5 28.0 - - + +
230B ALA* 4.2 5.8 - - + -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ARG* 3.1 22.5 + - + +
206B ILE* 1.3 78.5 - - - +
208B SER* 1.3 60.4 + - - +
209B LYS 3.2 7.0 + - - +
227B LEU* 4.7 9.0 - - + +
230B ALA* 3.9 30.7 - - + +
231B GLN* 3.7 32.3 - - + +
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Residues in contact with SER 208 (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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200B ILE* 5.1 2.8 - - - +
204B ARG 4.4 0.6 + - - -
205B ASP* 2.7 24.2 + - - +
207B LEU* 1.3 78.9 - - - +
209B LYS* 1.3 67.7 + - - +
213B GLU* 4.4 2.6 - - - +
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Residues in contact with LYS 209 (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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198B LEU* 5.8 8.8 - - - +
200B ILE* 4.2 23.8 - - + -
206B ILE 3.1 18.8 + - - +
207B LEU* 3.7 6.6 - - - +
208B SER* 1.3 92.9 + - - +
210B ASN* 1.3 65.1 + - - +
213B GLU* 3.2 41.1 - - + +
214B LEU* 4.7 15.7 - - + +
217B ILE* 4.5 15.0 - - - +
227B LEU* 4.0 8.8 - - - +
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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