Contacts of the strand formed by residues 211 - 216 (chain F) in PDB entry 4OA5
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 MET 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F LEU* 3.8 34.3 - - + -
44F GLU* 4.6 8.3 - - + -
47F MET* 3.8 33.9 - - + -
48F LEU* 4.5 6.3 - - + -
51F LEU* 5.7 0.2 - - + -
134F PHE* 3.9 15.5 - - + -
160F VAL* 3.9 11.4 - - + -
161F ALA 3.4 22.9 - - - +
162F ASP* 3.7 13.9 - - + +
204F ILE* 3.9 0.9 - - - -
205F ILE* 2.8 43.5 + - + +
207F THR* 3.5 7.9 + - - +
210F GLY* 1.3 70.5 - - - +
212F MET* 1.3 69.0 + - - +
213F VAL* 3.5 6.5 + - + -
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Residues in contact with MET 212 (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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17A PHE* 3.7 18.2 - - + -
159F ILE 4.5 5.8 - - - +
160F VAL* 3.2 12.3 - - - +
161F ALA* 2.8 40.3 + - + +
164F THR* 3.5 19.4 + - + +
190F PHE* 4.2 4.0 - - + -
191F ASN* 3.5 24.0 - - - +
194F LEU* 3.7 34.1 - - + -
202F SER* 4.0 19.3 - - - -
203F THR 3.6 12.1 - - - +
204F ILE* 3.6 20.2 - - + +
211F MET* 1.3 70.9 - - - +
213F VAL* 1.3 69.1 + - - +
214F SER* 4.5 0.4 - - - -
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Residues in contact with VAL 213 (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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50A LEU* 3.6 26.5 - - + +
54A MET* 4.1 19.3 - - + -
47F MET* 5.9 0.2 - - + -
51F LEU* 3.7 32.8 - - + -
158F LEU* 5.0 4.5 - - + -
159F ILE 3.6 2.7 - - - -
160F VAL* 4.4 10.8 - - + -
202F SER* 3.4 1.4 - - - -
203F THR 2.9 35.2 + - - +
205F ILE* 4.0 17.0 - - + -
211F MET* 3.9 12.6 - - + +
212F MET* 1.3 81.0 - - - +
214F SER* 1.3 62.6 + - - +
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Residues in contact with SER 214 (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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50A LEU* 4.6 0.9 - - - -
158F LEU* 3.3 8.2 - - - +
159F ILE* 2.8 48.4 + - - +
194F LEU* 3.7 18.1 - - - +
200F TYR* 3.3 17.5 - - - +
201F LEU 3.4 3.8 - - - -
202F SER* 2.7 26.8 + - - -
212F MET* 4.5 4.9 - - - -
213F VAL* 1.3 76.3 - - - +
215F ILE* 1.3 65.3 + - - +
216F LYS 3.9 0.3 + - - -
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Residues in contact with ILE 215 (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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50A LEU* 3.6 18.8 - - + +
53A ARG* 3.3 36.3 - - + +
54A MET* 3.4 30.5 - - + +
156F GLY* 3.9 20.9 - - - +
157F GLY 3.5 2.9 - - - -
158F LEU* 3.8 7.9 - - + -
200F TYR* 3.2 7.3 - - - +
201F LEU* 2.9 37.2 + - + +
214F SER* 1.3 74.7 - - - +
216F LYS* 1.3 72.9 + - - +
217F LEU* 3.4 12.0 + - + +
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Residues in contact with LYS 216 (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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149F ALA 3.4 12.6 - - - +
150F LYS* 3.3 32.1 + - - +
151F MET 5.5 0.2 - - - -
153F ILE* 2.8 37.4 + - + +
154F ARG 3.7 11.4 - - - +
155F LYS 4.0 0.6 - - - +
156F GLY* 2.7 34.0 + - - -
157F GLY 2.9 17.1 + - - +
159F ILE* 4.3 20.0 - - + -
199F LYS 4.0 4.3 - - - +
200F TYR* 4.0 12.1 - - + -
214F SER 3.9 0.8 + - - -
215F ILE* 1.3 72.2 - - - +
217F LEU* 1.3 57.1 + - - +
218F THR* 2.7 36.0 + - - +
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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