Contacts of the strand formed by residues 194 - 200 (chain C) in PDB entry 1T9G
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 PHE 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C VAL 4.6 0.2 - - - -
145C ALA* 3.5 32.5 - - + -
147C ILE* 3.6 33.4 - - + -
179C LEU* 3.7 19.7 - - + -
180C ALA 3.1 26.2 - - - +
181C ARG* 3.5 26.0 - - + -
182C SER* 3.5 4.0 - - - -
190C ALA* 3.5 40.2 + - + -
192C LYS 3.5 0.8 - - - -
193C ALA* 1.3 87.5 - - + +
195C THR* 1.3 59.2 + - - +
242C GLY* 3.0 16.3 - - - -
244C GLY 2.8 17.6 + - - -
245C PHE* 4.0 15.9 - + + +
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Residues in contact with THR 195 (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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151C ALA* 5.3 0.2 - - - -
158C TYR* 5.2 0.7 - - + -
178C LEU 3.6 0.2 - - - +
179C LEU* 3.5 1.8 - - - +
180C ALA 3.2 27.8 + - - -
182C SER* 2.3 25.4 + - - -
194C PHE* 1.3 71.9 - - - +
196C GLY* 1.3 65.2 + - - +
197C PHE* 3.1 47.0 - - + -
237C VAL* 4.1 13.0 - - + -
240C GLY 4.3 7.0 - - - +
241C ASP* 3.2 14.0 - - - +
242C GLY 3.2 15.6 + - - +
244C GLY* 3.7 6.5 - - - +
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Residues in contact with GLY 196 (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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177C PHE* 4.0 15.9 - - - -
178C LEU 3.5 5.2 - - - -
179C LEU* 4.4 0.9 - - - -
195C THR* 1.3 75.1 - - - +
197C PHE* 1.3 61.4 + - - -
237C VAL* 3.4 6.4 - - - +
238C LEU* 3.0 37.6 + - - +
240C GLY 5.0 1.0 + - - -
244C GLY* 3.4 16.1 - - - +
247C VAL* 5.4 0.4 - - - -
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Residues in contact with PHE 197 (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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151C ALA* 3.7 30.3 - - + -
158C TYR* 3.5 36.8 - + + -
160C ILE* 4.3 3.6 - - + -
177C PHE* 3.2 8.4 - - - -
178C LEU* 2.7 58.2 + - + +
180C ALA* 4.2 4.0 - - + -
195C THR* 3.1 48.2 - - + -
196C GLY* 1.3 74.0 - - - -
198C ILE* 1.3 63.6 + - - +
199C VAL* 3.9 18.6 - - + -
232C VAL* 3.9 17.9 - - + -
236C ASN 3.4 11.4 - - - +
237C VAL* 3.6 9.2 - - + -
238C LEU* 3.9 3.6 - - - -
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Residues in contact with ILE 198 (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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108C ILE* 4.2 25.6 - - + -
116C GLN* 4.1 31.2 - - + +
120C TYR* 3.8 47.3 - - + -
175C TRP* 3.9 23.8 - - + -
176C TYR 3.3 3.6 - - - +
197C PHE* 1.3 74.2 - - - +
199C VAL* 1.3 67.3 + - - +
232C VAL* 3.7 5.2 - - - +
236C ASN* 3.1 35.1 + - - +
238C LEU* 4.0 13.0 - - + -
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Residues in contact with VAL 199 (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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160C ILE* 5.3 0.7 - - + -
175C TRP* 3.4 2.5 - - - -
176C TYR* 2.8 43.5 + - + +
178C LEU* 4.2 20.0 - - + -
197C PHE* 3.9 15.7 - - + -
198C ILE* 1.3 80.1 - - - +
200C GLU* 1.3 75.7 + - - +
203C THR* 4.7 2.0 - - - +
206C ILE* 3.9 17.5 - - + -
227C PHE* 4.1 14.1 - - + -
230C VAL* 4.3 13.0 - - + -
232C VAL* 3.7 22.9 - - + -
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Residues in contact with GLU 200 (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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119C LYS* 3.4 14.2 + - - -
120C TYR* 2.9 39.9 + - + +
123C ARG* 4.5 11.9 + - - +
174C ASN* 4.0 7.0 - - - +
175C TRP* 4.0 4.5 - - + -
198C ILE 4.2 0.8 + - - -
199C VAL* 1.3 74.8 - - - +
201C ALA* 1.3 66.3 + - - +
202C ASP* 3.1 17.6 - - - +
203C THR* 3.0 27.0 + - - +
206C ILE* 3.3 7.6 - - - +
236C ASN* 5.4 1.6 - - - +
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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