Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 3TPP
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 ILE 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 5.1 0.4 - - + -
202A ILE* 1.3 72.0 - - - +
204A VAL* 1.3 64.7 + - - +
205A ARG 3.7 15.7 - - - +
206A VAL* 3.9 12.3 - - + -
217A CYS* 3.9 6.1 - - - +
220A TYR* 3.9 19.8 - - + +
221A ASN* 2.9 31.7 + - - +
225A SER* 3.6 24.5 - - - +
236A LEU* 6.0 0.9 - - + -
285A LEU* 4.4 15.9 - - + -
286A TYR 3.3 13.0 - - - +
287A LEU* 3.8 18.2 - - + -
331A THR* 3.7 25.6 - - + +
333A MET* 4.3 12.1 - - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 3.7 20.2 - - + -
203A ILE* 1.3 77.9 - - - +
205A ARG* 1.3 64.9 + - + +
217A CYS* 3.7 20.0 - - - +
220A TYR* 4.4 2.1 - - - -
286A TYR* 2.8 30.9 + - + +
287A LEU 4.2 1.6 - - - -
288A MET* 4.1 8.1 - - + +
295A SER* 4.0 19.5 - - - -
376A THR* 4.0 24.8 - - + +
379A MET* 3.7 25.8 - - + -
382A CYS* 4.0 8.0 - - - -
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Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 3.7 3.5 - - - +
204A VAL* 1.3 85.5 - - + +
206A VAL* 1.4 73.7 + - - +
207A GLU* 2.8 27.5 + - - +
212A ASP* 3.1 40.7 + - - +
220A TYR* 3.9 7.4 - - - -
285A LEU* 3.7 1.0 - - - -
286A TYR* 2.8 62.4 + - + -
376A THR* 5.5 7.2 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 3.9 7.2 - - + -
205A ARG* 1.4 80.8 - - - +
207A GLU* 1.3 71.5 + - - +
208A ILE* 4.7 8.3 - - + -
212A ASP* 3.4 7.3 - - - +
213A LEU* 2.9 43.8 + - + +
220A TYR* 3.6 40.4 + - + +
236A LEU* 6.3 1.6 - - + -
240A VAL* 5.4 4.3 - - + -
244A ALA* 5.8 1.6 - - + -
283A ILE* 5.0 4.3 - - + -
284A SER 3.5 8.5 - - - +
285A LEU* 3.9 22.2 - - + -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG* 2.8 28.9 + - - +
206A VAL* 1.3 78.4 - - - +
208A ILE* 1.3 68.9 + - - +
209A ASN 4.2 0.4 - - - -
210A GLY* 4.0 26.6 - - - +
211A GLN 3.3 7.6 - - - +
212A ASP* 3.7 15.9 - - - +
213A LEU 4.5 0.2 - - - +
283A ILE* 3.6 2.3 - - - +
284A SER* 2.9 45.2 + - - +
286A TYR* 3.0 33.5 + - + -
297A ARG* 4.2 6.8 + - - -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 4.7 5.4 - - + -
207A GLU* 1.3 75.3 - - - +
209A ASN* 1.3 75.1 + - - +
210A GLY 3.1 0.2 - - - -
211A GLN* 2.9 17.0 + - - +
213A LEU* 4.2 13.0 - - + -
244A ALA* 3.7 37.9 - - + +
247A SER* 3.4 21.1 - - - +
248A ILE* 3.8 17.9 - - + +
281A PRO* 3.8 25.6 - - + -
282A VAL 3.6 4.5 - - - +
283A ILE* 4.4 15.7 - - + -
410A URE 2.9 26.7 + - - +
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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