Contacts of the strand formed by residues 172 - 176 (chain B) in PDB entry 6THQ
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 GLU 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B TYR* 4.2 2.4 - - - -
125B LEU* 4.0 8.9 - - + +
130B VAL* 4.8 2.9 - - + -
131B ARG 3.3 3.9 + - - +
132B ALA* 3.2 6.1 - - + -
133B ALA 3.1 23.9 + - - -
165B ALA* 3.6 9.7 - - - +
166B ARG* 3.0 29.8 + - - +
170B TYR* 3.5 1.9 - - - +
171B ASP* 1.3 83.3 - - + +
173B ALA* 1.3 80.5 + - - +
186B SER* 2.6 30.3 + - - -
188B GLU* 2.7 36.3 - - - +
245B PHE* 3.7 32.3 - - + -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA 3.5 5.2 - - - -
135B VAL* 3.6 13.7 - - + -
161B ALA* 3.3 41.3 - - + +
162B ALA* 4.3 0.4 - - - +
165B ALA* 3.6 5.2 - - + +
172B GLU* 1.3 90.2 + - - +
174B ILE* 1.3 64.0 + - - +
175B MET* 4.1 0.4 - - + -
185B GLY* 3.2 22.9 - - - -
186B SER* 3.5 4.2 + - - +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 3.9 13.7 - - + -
133B ALA 2.7 14.2 + - - +
134B VAL* 3.3 15.3 - - + +
135B VAL* 3.0 26.1 + - - +
173B ALA* 1.3 77.6 - - - +
175B MET* 1.3 66.4 + - - +
176B LEU* 5.1 0.7 - - + -
182B VAL* 3.9 29.2 - - + -
184B GLU 3.6 7.2 - - - +
190B ILE* 3.9 16.4 - - + -
237B LEU* 3.9 16.8 - - + -
245B PHE* 3.8 19.7 - - + -
255B ILE* 4.5 4.7 - - + -
258B ILE* 3.5 27.1 - - + -
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Residues in contact with MET 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B VAL* 3.9 7.2 - - + -
137B TRP* 3.7 10.3 - - + +
138B ARG 3.6 13.5 - - - +
139B ARG* 3.7 26.2 - - + +
157B ASN* 3.5 38.1 - - - +
158B SER* 4.8 3.4 - - - -
161B ALA* 3.6 33.2 - - + -
174B ILE* 1.3 77.7 - - - +
176B LEU* 1.3 66.0 + - - +
182B VAL* 3.9 1.2 - - - -
183B VAL* 2.9 29.0 + - + +
184B GLU 2.8 18.7 + - - +
185B GLY 4.7 13.0 - - - +
186B SER* 4.7 4.7 - - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 3.8 30.9 - - + +
135B VAL 5.4 0.8 + - - +
137B TRP 4.6 3.8 + - - -
138B ARG* 3.4 40.0 - - - +
139B ARG 2.9 23.0 + - - -
174B ILE* 4.2 1.1 + - + -
175B MET* 1.3 75.4 - - - +
177B ASN* 1.3 68.6 + - - +
180B GLY* 3.9 17.7 - - - +
181B LYS 3.1 5.4 - - - +
182B VAL* 3.6 38.1 - - + +
183B VAL* 4.2 2.0 - - - -
234B ARG* 4.2 20.9 - - + +
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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