Contacts of the strand formed by residues 176 - 181 (chain B) in PDB entry 5AN9
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 GLY 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.3 2.1 - - - +
93B VAL 3.0 29.9 + - - -
99B ILE* 4.8 3.2 - - - +
163B SER* 3.1 22.2 - - - -
174B LEU 3.3 0.2 + - - -
175B ASP* 1.3 80.5 + - - +
177B ILE* 1.3 64.7 - - - -
178B TYR* 3.4 16.4 - - - -
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.2 39.5 - - + +
91B ARG 3.6 4.9 - - - +
92B PHE* 3.6 17.9 - - + -
99B ILE* 3.8 10.3 - - + -
101B VAL* 3.8 33.4 - - + -
112B ILE* 4.0 13.2 - - + -
142B ILE* 4.2 17.5 - - + -
159B ILE* 4.1 11.0 - - + +
160B GLN* 3.2 19.8 + - - +
163B SER* 3.6 23.2 + - - +
176B GLY* 1.3 74.5 - - - -
178B TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.1 6.2 - - - -
91B ARG 2.8 39.5 + - - +
93B VAL* 4.2 10.5 - - + -
160B GLN* 3.7 20.2 - - + -
163B SER 5.2 0.9 - - - -
173B PHE* 4.8 1.2 - - - -
174B LEU* 3.5 16.5 + - - -
175B ASP 2.7 20.5 + - - -
176B GLY* 3.4 28.0 - - - -
177B ILE* 1.3 73.0 - - - +
179B VAL* 1.3 61.8 + - - +
180B SER* 3.4 1.4 + - - -
8H LEU* 4.6 11.9 - - + -
9H ALA* 4.2 23.8 - - - +
12H TYR* 3.3 43.7 - + + -
13H LYS* 3.8 26.5 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.7 21.1 - - + -
89B LYS 3.8 9.0 - - - +
90B MET* 3.9 11.2 - - + -
156B CYS* 3.6 30.5 - - + -
160B GLN* 3.5 15.0 + - - +
178B TYR* 1.3 70.6 - - - +
180B SER* 1.3 65.6 + - - +
181B GLU 4.3 3.4 - - - +
182B ARG* 3.7 38.3 + - + +
8H LEU* 3.6 9.0 - - - +
12H TYR* 2.7 31.3 + - - +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 2.8 15.5 + - - -
91B ARG* 3.1 32.8 + - - +
178B TYR 3.4 1.2 + - - -
179B VAL* 1.3 75.9 - - - +
181B GLU* 1.3 70.7 + - - +
182B ARG* 3.8 4.9 + - - +
8H LEU* 3.1 34.4 - - - +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU 3.7 2.1 - - - +
88B TYR* 3.4 2.8 - - - +
89B LYS* 2.8 52.7 + - + +
179B VAL* 4.4 0.7 - - - -
180B SER* 1.3 85.0 - - - +
182B ARG* 1.3 60.3 + - - +
183B ASN* 5.1 5.2 + - - +
184B VAL* 4.1 31.4 + - + +
139C ASP* 5.1 7.9 - - - +
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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
------------------------------------------------------------
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