Contacts of the strand formed by residues 201 - 208 (chain A) in PDB entry 1CTM
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 ARG 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A THR 4.8 2.6 + - - -
175A ALA* 3.9 19.6 - - - +
195A VAL* 3.7 4.6 - - - +
196A ASP* 2.8 56.7 + - + +
199A ASN* 3.8 28.5 + - + +
200A GLU* 1.3 78.1 - - - +
202A GLN* 1.3 70.0 + - - +
203A VAL* 3.9 14.5 - - + +
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Residues in contact with GLN 202 (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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180A SER* 4.9 0.6 + - - -
193A THR* 3.7 26.5 - - + +
194A ILE 3.4 10.3 - - - +
195A VAL* 4.5 14.3 - - + +
201A ARG* 1.3 79.5 - - - +
203A VAL* 1.3 66.6 + - - +
204A ILE* 4.5 12.2 - - + +
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Residues in contact with VAL 203 (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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174A THR* 3.7 23.8 - - - +
175A ALA* 3.7 28.5 - - + -
192A ILE 3.7 0.2 - - - +
193A THR* 3.5 3.6 - - - +
194A ILE* 2.9 49.4 + - + +
196A ASP* 5.4 0.4 - - + -
201A ARG* 3.9 24.2 - - + +
202A GLN* 1.3 77.8 - - - +
204A ILE* 1.3 63.1 + - - +
205A ASP* 4.2 6.1 - - - +
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Residues in contact with ILE 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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191A GLU* 3.8 33.9 - - + +
192A ILE 3.2 13.0 - - - +
193A THR* 3.5 24.7 - - + +
202A GLN* 4.5 13.5 - - - +
203A VAL* 1.3 75.7 - - - +
205A ASP* 1.3 64.5 + - - +
206A ILE* 3.9 14.0 + - + +
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Residues in contact with ASP 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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172A ASN 4.6 2.7 - - - +
173A ALA* 3.2 13.0 - - - -
174A THR* 2.7 55.1 + - - +
190A TYR 4.1 0.2 - - - +
191A GLU* 3.7 0.7 - - - -
192A ILE* 2.8 43.7 + - + +
194A ILE* 3.4 15.2 - - + +
203A VAL* 4.1 2.4 - - - +
204A ILE* 1.3 75.1 - - - +
206A ILE* 1.3 63.7 + - - +
207A ILE* 3.9 3.5 + - + +
227A LEU* 3.9 16.3 - - + +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A TYR* 4.1 11.8 - - - -
185A LYS* 4.2 17.5 - - - +
190A TYR 3.4 8.3 - - - +
191A GLU* 3.9 23.8 - - + +
204A ILE* 3.9 12.5 + - + +
205A ASP* 1.3 76.8 - - - +
207A ILE* 1.3 73.5 + - - +
208A PRO* 4.0 6.0 - - + +
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Residues in contact with ILE 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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171A TYR* 4.3 12.8 - - + -
185A LYS* 4.8 1.6 + - - -
189A GLY* 3.1 4.9 - - - -
190A TYR* 2.9 59.1 + - + +
192A ILE* 3.5 30.7 - - + -
205A ASP* 4.5 4.9 - - + +
206A ILE* 1.3 85.9 - - - +
208A PRO* 1.3 74.8 - - + +
211A LEU* 4.4 5.8 - - + -
213A LEU* 3.8 2.9 - - + -
227A LEU* 3.8 20.2 - - + -
228A THR* 3.6 35.2 - - + -
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Residues in contact with PRO 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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167A ASN* 3.7 18.2 - - + -
171A TYR* 3.7 35.2 - - + +
189A GLY* 4.0 3.9 - - - -
190A TYR* 5.1 0.2 - - - -
206A ILE* 4.0 3.1 - - + +
207A ILE* 1.3 90.8 - - + +
209A ARG* 1.3 65.5 + - + +
211A LEU* 3.6 38.6 + - + +
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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