Contacts of the strand formed by residues 174 - 179 (chain C) in PDB entry 1T4P
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 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C VAL* 3.3 29.6 - - + +
122C TRP* 4.4 9.0 - - + -
145C VAL* 4.2 22.0 - - + -
149C LEU* 4.8 7.0 - - + -
169C ILE* 5.2 7.2 - - + -
170C SER 4.3 7.6 - - - +
171C ALA* 3.8 21.8 - - - +
172C LYS 3.5 0.8 + - - -
173C ASP* 1.3 79.9 - - - +
175C VAL* 1.3 81.5 - - - +
176C TYR* 4.1 24.5 - - + -
195C ILE* 3.8 20.2 - - + -
196C LYS 3.7 11.1 + - - +
218C TYR* 4.1 3.5 - - - -
219C LEU* 4.6 0.2 - - - -
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Residues in contact with VAL 175 (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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120C VAL 3.0 7.4 + - - +
121C ILE* 3.5 7.9 - - + +
122C TRP 2.9 25.5 + - - -
174C ILE* 1.3 82.6 - - - +
176C TYR* 1.3 65.5 + - - +
177C ILE* 4.1 2.6 + - + -
196C LYS* 3.3 11.0 - - + +
198C PHE* 3.9 15.5 - - + -
215C THR* 3.0 36.1 - - + -
218C TYR* 3.4 31.2 - - + -
219C LEU* 3.5 20.6 - - + -
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Residues in contact with TYR 176 (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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122C TRP* 3.4 41.3 - + + -
127C THR* 2.4 47.1 + - + -
129C ILE* 3.8 4.5 - - - +
145C VAL* 3.4 20.8 - - - +
174C ILE* 4.1 12.6 - - + -
175C VAL* 1.3 70.9 - - - +
177C ILE* 1.3 64.5 + - - +
179C LEU* 3.5 35.9 - - + -
190C ILE* 4.5 9.9 - - + -
195C ILE* 4.0 30.7 - - + -
196C LYS 3.1 7.4 + - - -
197C TYR* 3.4 6.9 - - + -
198C PHE* 2.7 32.7 + - - +
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Residues in contact with ILE 177 (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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121C ILE* 4.1 18.8 - - + -
122C TRP 3.0 8.7 + - - +
123C VAL* 3.2 14.2 - - + +
124C ASP 3.0 23.1 + - - -
175C VAL* 4.4 6.3 - - + +
176C TYR* 1.3 80.6 - - - +
178C GLY* 1.3 62.3 + - - +
179C LEU* 3.6 1.8 - - - -
198C PHE* 3.4 18.2 - - + +
203C VAL* 4.6 7.9 - - + -
208C ILE* 4.8 2.7 - - + -
211C VAL* 4.3 15.7 - - + -
212C MET* 4.0 26.7 - - - -
215C THR* 4.0 17.3 - - + +
252C LEU* 4.5 4.5 - - + -
260C ILE* 4.1 23.1 - - + -
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Residues in contact with GLY 178 (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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124C ASP 3.0 10.7 - - - +
125C ALA* 3.7 0.3 - - - -
177C ILE* 1.3 75.5 - - - +
179C LEU* 1.3 66.5 + - - +
180C ARG* 3.2 27.8 + - - -
198C PHE 3.0 9.3 + - - -
200C MET* 3.3 21.1 - - - +
203C VAL* 4.8 0.6 - - - +
252C LEU* 4.1 14.8 - - - -
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Residues in contact with LEU 179 (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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308B ARG* 3.8 3.1 - - - +
309B GLU* 5.3 1.8 - - - +
124C ASP* 3.3 10.4 + - + +
125C ALA 3.7 4.0 - - - +
126C HIS 3.7 32.1 - - - +
127C THR* 3.5 25.8 - - + -
176C TYR* 3.5 33.9 - - + -
177C ILE 5.1 0.7 - - - +
178C GLY* 1.3 78.1 - - - +
180C ARG* 1.3 61.0 + - - +
182C VAL* 4.5 9.9 - - + -
190C ILE* 5.0 3.6 - - + -
197C TYR* 3.9 23.6 - - + -
198C PHE 3.9 2.5 + - - +
199C SER* 3.4 18.1 - - - -
200C MET* 2.8 27.4 + - - +
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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