Contacts of the helix formed by residues 199 - 210 (chain F) in PDB entry 5OOM
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 ASP 199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195F LEU* 5.3 0.2 - - - +
197F THR* 3.4 19.7 + - + +
198F GLY* 1.3 82.1 - - - +
200F PRO* 1.3 72.7 - - + +
201F GLN* 3.5 9.8 + - + +
202F TYR* 3.7 17.1 + - + +
203F LEU* 4.0 2.4 + - - +
233F ALA* 3.8 8.5 - - - +
236F ARG* 4.6 6.1 + - - -
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Residues in contact with PRO 200 (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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198F GLY 4.0 1.8 - - - +
199F ASP* 1.3 86.9 - - + +
201F GLN* 1.3 57.5 + - - +
203F LEU* 2.9 19.2 + - - +
204F THR* 3.0 17.9 + - - +
233F ALA* 4.1 16.2 - - + +
236F ARG* 3.4 44.9 - - + +
237F LEU* 3.8 25.7 - - + +
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Residues in contact with GLN 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 ASP* 3.3 6.1 - - + +
200F PRO* 1.3 77.5 - - + +
202F TYR* 1.3 64.8 + - - +
204F THR* 3.0 11.4 + - - +
205F GLU* 3.0 53.7 + - + +
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Residues in contact with TYR 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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69F LEU 3.0 17.4 + - - -
70F ARG 3.3 13.0 + - - -
72F PHE* 3.5 37.2 + + + -
195F LEU* 3.8 16.8 - - + -
196F PRO* 3.5 28.7 - - + -
197F THR* 3.8 31.6 - - + -
199F ASP* 3.7 11.4 + - + +
200F PRO 3.2 0.4 - - - -
201F GLN* 1.3 78.9 - - - +
203F LEU* 1.3 59.4 + - + +
205F GLU* 3.4 8.7 + - - +
206F LEU* 2.9 52.0 + - + +
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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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69F LEU* 5.2 7.4 - - + -
195F LEU* 3.8 15.9 - - + -
199F ASP 4.0 3.8 + - - +
200F PRO 2.9 11.5 + - - +
202F TYR* 1.3 82.3 - - + +
204F THR* 1.3 62.1 + - - +
206F LEU* 3.7 6.1 - - + +
207F ALA* 3.0 26.0 + - - +
212F TRP* 4.9 15.5 - - + -
216F VAL* 6.1 0.2 - - + -
218F LEU* 4.8 9.0 - - + -
230F ILE* 3.7 27.8 - - + -
233F ALA* 3.7 20.4 - - + -
234F THR* 3.8 12.3 - - + -
237F LEU* 4.6 3.6 - - + -
240F PHE* 3.6 24.5 - - + -
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Residues in contact with THR 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 PRO* 3.0 12.2 + - + +
201F GLN* 3.0 23.8 + - - +
203F LEU* 1.3 77.9 - - - +
205F GLU* 1.3 56.9 + - - +
207F ALA* 3.8 1.6 - - - +
208F HIS* 2.9 30.0 + - - +
237F LEU* 3.8 23.3 - - + -
240F PHE* 3.7 21.5 - - + -
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Residues in contact with GLU 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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72F PHE* 3.6 25.8 - - + -
201F GLN* 3.0 48.4 + - + +
202F TYR* 3.8 8.2 - - - +
204F THR* 1.3 77.6 + - - +
206F LEU* 1.3 58.5 + - - +
208F HIS* 3.3 6.8 + - - +
209F TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 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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69F LEU* 3.6 37.0 - - + +
71F GLY 4.0 8.3 - - - +
72F PHE* 3.7 17.6 - - + +
195F LEU* 5.1 1.3 - - + -
202F TYR* 2.9 47.9 + - + +
203F LEU* 3.7 8.3 - - + +
204F THR 3.3 0.2 - - - -
205F GLU* 1.3 75.5 - - - +
207F ALA* 1.3 60.7 + - - +
209F TYR* 3.3 3.2 + - - +
210F ARG* 3.2 56.5 + - - +
212F TRP* 3.8 13.5 - - + -
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Residues in contact with ALA 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 3.0 16.8 + - - +
204F THR 4.0 1.6 - - - +
205F GLU 3.3 0.2 - - - -
206F LEU* 1.3 77.1 - - - +
208F HIS* 1.3 58.8 + - - +
210F ARG 4.2 0.4 - - - -
211F ARG* 3.6 1.6 + - - -
212F TRP* 3.2 59.2 + - + +
213F GLY 4.2 8.3 + - - +
216F VAL* 4.4 2.9 - - + -
240F PHE* 3.5 27.6 - - + -
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Residues in contact with HIS 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 THR 2.9 17.8 + - - +
205F GLU* 3.7 7.2 + - - +
207F ALA* 1.3 78.1 - - - +
209F TYR* 1.3 64.4 + - - +
210F ARG 3.4 0.2 - - - -
211F ARG* 3.5 15.9 + - - +
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Residues in contact with TYR 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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72F PHE* 3.4 31.6 - + + -
73F GLU* 3.5 49.1 + - + +
75F GLU* 6.0 3.4 - - + -
205F GLU 2.9 16.6 + - - +
206F LEU* 3.3 3.5 + - - +
208F HIS* 1.3 82.4 - - - +
210F ARG* 1.3 72.8 + - + +
211F ARG* 3.2 5.6 + - - +
56h ARG* 2.6 77.3 + - + +
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Residues in contact with ARG 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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67F GLU* 3.2 20.1 + - - +
68F SER 2.9 25.5 + - - -
69F LEU* 4.3 1.2 - - - +
71F GLY 2.9 28.1 + - - -
72F PHE 4.4 5.7 + - - -
74F GLN 3.1 22.0 + - - +
75F GLU* 3.3 38.8 - - - +
188F HIS* 5.5 1.9 - - - -
206F LEU* 3.2 38.6 + - - +
209F TYR* 1.3 85.4 - - + +
211F ARG* 1.3 69.0 + - - +
212F TRP* 3.3 32.2 + - + +
58h ARG* 4.6 3.1 + - - -
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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