Contacts of the strand formed by residues 200 - 206 (chain C) in PDB entry 2F4N
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 THR 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C TYR 4.7 2.1 + - - -
199C ASP* 1.3 75.2 + - - +
201C ILE* 1.3 67.1 + - - +
202C MSE 3.9 1.6 + - - +
216C LYS* 4.3 17.7 - - + -
217C CYS 3.3 10.8 - - - +
218C LYS* 5.2 5.5 - - - +
264C GLU 5.5 0.3 - - - +
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PHE* 3.6 42.4 - - + -
199C ASP* 3.7 15.9 - - + +
200C THR* 1.3 77.5 - - - +
202C MSE 1.3 62.8 + - - +
203C ILE* 3.6 21.3 + - + -
215C ILE 3.9 0.2 - - - +
216C LYS* 3.5 2.6 - - - -
217C CYS* 2.8 39.1 + - + +
219C PHE* 3.5 32.1 - - + +
232C CYS* 4.8 8.3 - - - -
263C ILE* 3.5 28.7 - - + -
264C GLU 4.4 2.9 - - - +
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Residues in contact with MSE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C THR 3.9 2.1 + - - +
201C ILE* 1.3 75.0 - - - +
203C ILE* 1.3 60.1 + - - +
214C ILE* 4.9 8.1 - - + -
215C ILE 3.6 5.8 - - - +
216C LYS* 4.7 3.6 - - + +
263C ILE* 3.6 3.1 - - - -
264C GLU* 3.0 55.3 + - + +
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Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ILE* 3.6 18.2 - - + +
202C MSE 1.3 77.5 - - - +
204C LYS* 1.3 64.2 + - - +
205C ILE* 3.9 21.6 - - + +
213C LYS 3.4 2.1 - - - +
214C ILE* 3.3 6.3 - - - +
215C ILE* 2.9 45.1 + - + +
217C CYS* 3.9 29.8 - - + -
232C CYS* 4.6 8.7 - - + -
240C LEU* 5.2 6.3 - - + -
242C ILE* 4.1 24.0 - - + -
261C ILE* 4.2 15.3 - - + -
262C GLU 3.5 5.6 - - - +
263C ILE* 4.3 10.5 - - + -
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C MSE 4.2 0.6 + - - -
203C ILE* 1.3 74.2 - - - +
205C ILE* 1.3 62.5 + - - +
206C ARG 4.2 0.4 + - - -
212C GLU* 5.5 8.7 - - + +
213C LYS 3.2 6.7 - - - +
214C ILE* 4.4 15.3 - - + +
260C GLU 3.8 0.2 - - - +
261C ILE* 3.6 2.9 - - - -
262C GLU* 2.8 50.5 + - + +
264C GLU* 4.6 16.5 - - - +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ILE* 5.0 0.2 - - + -
203C ILE* 3.9 9.6 - - + +
204C LYS* 1.3 76.1 - - - +
206C ARG* 1.3 61.4 + - - +
207C HIS* 3.8 16.1 + - + -
211C ILE 3.8 1.2 - - - +
212C GLU* 3.3 5.5 - - - +
213C LYS* 2.8 45.1 + - + +
215C ILE* 5.3 3.8 - - + -
242C ILE* 4.3 18.8 - - + -
253C LEU* 4.4 13.9 - - + -
255C VAL* 3.9 23.6 - - + -
259C ASP* 3.8 19.7 - - + -
260C GLU 3.2 9.9 - - - +
261C ILE* 3.3 26.0 - - + -
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Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LYS 4.2 0.4 - - - -
205C ILE* 1.3 71.7 - - - +
207C HIS* 1.3 66.5 + - - +
210C GLY 5.1 2.7 - - - +
211C ILE 3.8 5.6 - - - +
212C GLU* 3.9 22.7 - - + +
259C ASP* 3.5 3.5 - - - -
260C GLU* 2.9 65.1 + - + +
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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