Contacts of the strand formed by residues 157 - 163 (chain B) in PDB entry 5INQ
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 VAL 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE* 6.5 0.7 - - + -
125B SER 3.3 3.3 + - - +
126B PHE* 3.1 34.6 - - + +
127B ILE 3.1 3.8 + - - -
155B PRO* 3.3 1.8 - - - +
156B ASP* 1.3 90.7 - - + +
158B VAL* 1.3 71.4 + - - +
159B PHE* 3.7 30.1 - - + -
192B ILE* 4.0 16.4 - - + -
193B LEU 3.2 10.8 - - - +
194B LEU* 4.1 8.3 - - + -
199B VAL* 4.3 8.7 - - + -
225B LEU* 5.8 3.1 - - + -
232B LEU* 3.9 21.5 - - + -
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Residues in contact with VAL 158 (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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127B ILE* 3.3 11.4 - - + +
150B LEU* 4.1 32.5 - - + -
155B PRO* 3.7 22.0 - - + -
157B VAL* 1.3 80.2 - - - +
159B PHE* 1.3 63.2 + - - +
160B LEU* 3.5 32.1 - - + -
178B TYR* 4.4 16.4 - - + -
192B ILE* 3.3 5.7 - - - +
193B LEU* 2.8 46.7 + - + +
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Residues in contact with PHE 159 (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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126B PHE* 3.6 31.2 - + + -
127B ILE 2.8 17.6 + - - +
128B THR* 3.2 14.7 - - - +
129B TRP 2.9 26.0 + - - -
157B VAL* 3.7 20.4 - - + -
158B VAL* 1.3 73.1 - - - +
160B LEU* 1.3 64.3 + - - +
161B GLN* 3.6 1.8 + - - -
191B ALA 3.6 3.6 - - - -
192B ILE* 3.9 15.0 - - + -
232B LEU* 3.8 32.8 - - + -
233B MET 3.8 15.9 - - - -
234B THR* 3.8 23.8 - - - +
268B ILE* 4.8 6.3 - - + -
270B ALA* 3.6 27.6 - - + +
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Residues in contact with LEU 160 (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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129B TRP* 3.3 16.8 - - + +
131B ILE* 3.9 23.1 - - + -
146B VAL* 5.1 7.4 - - + -
150B LEU* 5.3 3.4 - - + -
158B VAL* 3.5 26.7 - - + -
159B PHE* 1.3 76.0 - - - +
161B GLN* 1.3 67.5 + - - +
163B VAL* 3.7 17.0 - - + -
167B TYR* 5.3 1.3 - - + -
171B LEU* 3.5 36.6 - - + -
190B THR* 3.2 8.4 - - - -
191B ALA* 2.9 35.2 + - + +
193B LEU* 3.8 17.9 - - + -
234B THR* 4.6 0.3 - - - +
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Residues in contact with GLN 161 (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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128B THR* 3.3 19.8 + - - -
129B TRP 3.0 9.3 + - - -
130B ASN* 3.1 35.2 + - + +
131B ILE* 2.9 29.5 + - - +
159B PHE 3.6 6.5 + - - -
160B LEU* 1.3 84.4 - - - +
162B GLU* 1.3 67.4 + - - +
163B VAL* 3.3 3.1 - - - -
189B PHE 4.2 3.4 - - - -
190B THR* 3.9 11.2 - - + -
234B THR* 3.0 21.8 + - - -
235B SER 3.7 17.7 - - - +
236B HIS* 4.0 18.2 - - + -
271B GLY* 3.6 2.0 - - - -
272B ASP* 3.8 17.0 + - + +
326B ASP* 4.2 1.2 - - - +
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Residues in contact with GLU 162 (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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130B ASN* 2.8 28.4 + - - +
131B ILE* 3.2 2.0 - - - +
132B ASP* 3.5 13.2 - - - +
133B GLY* 2.8 32.4 + - - +
134B LEU* 3.6 22.2 + - + +
161B GLN* 1.3 76.5 - - - +
163B VAL* 1.3 62.2 + - - +
188B TYR* 4.1 20.4 - - + -
189B PHE 3.4 7.7 + - - -
190B THR* 5.2 0.4 - - - +
236B HIS* 3.1 28.2 + - + +
401B CA 2.2 31.3 - - - -
1C C 2.8 8.1 + - - -
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Residues in contact with VAL 163 (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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131B ILE* 4.0 12.3 - - + -
160B LEU* 3.7 35.4 - - + -
161B GLN 4.3 2.0 - - - -
162B GLU* 1.3 78.9 - - - +
164B ILE* 1.3 73.5 + - - +
167B TYR* 4.2 8.7 - - + -
168B CYS* 3.7 20.0 - - + +
171B LEU* 4.6 4.5 - - + -
188B TYR* 3.1 5.2 - - - -
189B PHE* 2.8 57.1 + - + +
191B ALA* 4.3 12.8 - - + -
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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