Contacts of the helix formed by residues 200 - 210 (chain F) in PDB entry 4O9U
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 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198F VAL 4.2 0.6 + - - -
199F ARG* 1.3 71.9 - - - +
201F ALA* 1.3 61.0 + - - +
203F LEU* 3.3 24.0 + - + +
204F GLU* 3.5 19.2 + - - +
216F LEU* 4.4 24.2 - - + -
217F PRO 5.9 0.4 - - - -
218F ILE 3.6 25.0 + - - +
219F SER* 5.5 7.9 + - - +
221F GLU* 4.1 8.3 + - - +
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Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ARG* 3.2 9.9 - - + +
200F LYS* 1.3 79.8 - - - +
202F ALA* 1.3 55.0 + - - +
203F LEU 3.3 1.1 - - - -
204F GLU* 4.1 7.0 - - - +
205F GLN* 3.5 32.6 + - - +
221F GLU* 4.9 6.2 + - - +
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F VAL* 3.3 32.3 - - - +
195F ALA 5.5 0.2 - - - +
197F ASP* 3.4 35.4 - - + +
199F ARG* 3.4 19.6 + - - +
200F LYS 3.3 0.6 - - - -
201F ALA* 1.3 77.2 - - - +
203F LEU* 1.3 63.4 + - - +
204F GLU 3.5 0.9 - - - -
205F GLN* 4.3 12.1 - - - +
206F ALA* 3.4 12.8 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ALA 4.6 6.7 - - - +
196F TYR* 5.0 1.8 - - + -
197F ASP* 3.3 38.4 - - + +
198F VAL 6.1 0.2 - - - -
199F ARG 3.2 21.1 - - - +
200F LYS* 3.3 19.9 + - + +
202F ALA* 1.3 80.4 - - - +
204F GLU* 1.3 64.9 - - - +
206F ALA* 4.0 4.6 - - - +
207F LEU* 3.2 24.6 + - - +
213F PRO* 3.7 28.1 - - + +
214F ILE 4.8 9.0 - - - +
216F LEU* 4.6 26.7 - - + -
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Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LYS* 3.5 16.6 + - + +
201F ALA* 4.4 6.1 - - - +
203F LEU* 1.3 83.7 - - - +
205F GLN* 1.3 60.9 + - - +
206F ALA 3.2 1.3 - - - -
207F LEU* 3.9 15.5 - - - +
208F SER* 3.0 27.0 + - - -
213F PRO* 5.7 1.6 - - - +
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Residues in contact with GLN 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D GLU* 6.2 2.2 - - - +
175F VAL 5.6 0.5 - - - +
180F LEU* 4.0 41.5 - - + +
199F ARG* 5.6 3.1 + - - -
201F ALA* 3.5 23.5 + - - +
202F ALA* 4.4 10.1 - - - +
203F LEU 3.6 0.2 - - - -
204F GLU* 1.3 78.6 - - - +
206F ALA* 1.3 59.3 + - - +
208F SER* 3.4 18.1 - - - -
209F LEU* 3.6 9.0 + - - +
500F NAD 3.8 26.3 + - - -
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F VAL* 4.6 2.2 - - + -
180F LEU* 4.8 2.9 - - + +
183F ILE* 4.2 13.3 - - + +
195F ALA* 3.7 30.7 - - + +
202F ALA 3.4 20.3 + - - +
203F LEU* 4.0 6.5 - - - +
204F GLU 3.2 0.2 - - - -
205F GLN* 1.3 76.2 - - - +
207F LEU* 1.3 63.3 + - - +
208F SER 3.2 1.6 - - - -
209F LEU* 3.4 13.7 + - - +
210F GLY 3.5 0.7 + - - -
211F ALA* 3.5 20.7 + - + +
213F PRO* 5.7 2.7 - - + -
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Residues in contact with LEU 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LEU 3.2 17.4 + - - +
204F GLU* 3.9 18.8 - - - +
206F ALA* 1.3 75.7 - - - +
208F SER* 1.3 65.7 + - - +
210F GLY* 3.2 15.7 + - - +
211F ALA 3.2 23.5 + - - +
212F LYS* 4.6 2.2 - - + -
213F PRO* 3.8 18.8 - - + +
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Residues in contact with SER 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLU 3.0 19.1 + - - -
205F GLN* 3.4 13.0 - - - -
207F LEU* 1.3 81.3 - - - +
209F LEU* 1.3 63.1 + - - +
210F GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F LEU* 3.5 49.4 - - + +
183F ILE* 4.6 17.3 - - + -
184F ALA* 4.4 19.7 - - + -
187F LYS* 4.2 17.0 - - + +
205F GLN 3.6 6.0 + - - +
206F ALA 3.4 8.5 + - - +
207F LEU 3.3 0.4 - - - -
208F SER* 1.3 80.9 - - - +
210F GLY* 1.3 56.5 + - - +
211F ALA 3.9 0.7 - - - -
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Residues in contact with GLY 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F LYS* 4.1 17.9 - - - -
206F ALA 3.5 0.2 + - - -
207F LEU* 3.2 14.5 + - - +
208F SER 3.2 0.9 - - - -
209F LEU* 1.3 80.6 - - - +
211F ALA* 1.3 65.5 + - - +
212F LYS 3.9 0.7 + - - -
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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