Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 1POP
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 ASP 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU 3.0 2.0 + - - -
135A GLN* 4.0 0.5 - - - +
136A ALA* 2.9 31.8 + - - +
137A ALA* 3.2 30.9 + - - +
156A LYS 3.4 12.2 - - - +
157A VAL* 1.3 75.5 - - - +
159A HIS* 1.3 63.3 + - - +
434A MOH 4.0 3.8 + - - -
301B LEU 4.2 6.5 - - - +
302B LEU* 3.7 12.2 - - - +
303B AR7 3.0 42.5 + - - +
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Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.8 3.6 - - - -
25A CYS* 3.7 26.4 - - + +
132A VAL 4.2 0.2 - - - +
133A VAL* 3.2 5.4 - - - +
134A LEU* 3.0 45.1 + - + +
136A ALA* 3.7 15.0 - - + -
141A PHE* 4.5 4.0 - + - -
158A ASP* 1.3 90.8 - - - +
160A ALA* 1.3 61.0 + - - +
161A VAL* 3.4 20.4 + - + +
175A ASN* 2.7 31.0 + - - -
176A SER* 4.5 0.4 - - - -
177A TRP* 3.4 27.0 - + - -
434A MOH 3.5 16.3 - - - +
302B LEU* 3.8 5.4 - - - +
303B AR7 3.8 0.4 - - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A CYS* 3.4 29.1 - - - +
26A TRP* 4.0 11.9 - - - -
29A SER* 3.8 14.5 + - - +
68A PRO* 3.6 30.7 - - + -
131A SER* 5.0 0.2 - - - +
132A VAL 3.4 7.6 - - - +
133A VAL* 4.4 2.7 - - + +
159A HIS* 1.3 72.7 - - - +
161A VAL* 1.3 64.3 + - - +
176A SER* 4.8 2.6 + - - -
302B LEU* 4.0 10.1 - - + +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 2.7 20.6 + - - +
132A VAL* 2.8 44.0 + - + +
134A LEU* 4.2 21.3 - - + -
141A PHE* 5.5 1.6 - - + -
159A HIS* 3.4 22.0 - - + +
160A ALA* 1.3 71.7 - - - +
162A ALA* 1.3 61.2 + - - +
173A ILE* 3.6 24.2 - - + -
174A LYS 3.7 7.2 - - - +
175A ASN* 3.3 31.4 - - - +
176A SER* 5.3 0.7 - - - +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER 4.3 5.6 - - - +
32A VAL* 3.4 43.5 - - + -
33A THR* 4.8 2.0 - - + -
130A VAL 3.2 12.3 - - - +
132A VAL* 4.2 2.9 - - - -
161A VAL* 1.3 78.2 - - - +
163A ALA* 1.3 61.3 + - - +
164A VAL* 3.6 3.7 + - + -
173A ILE* 3.5 3.1 - - - -
174A LYS* 2.9 34.2 + - + +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 3.6 34.5 - - + +
129A PRO* 3.3 6.1 - - - +
130A VAL* 2.8 32.9 + - + +
132A VAL* 3.9 15.4 - - + +
162A ALA* 1.3 71.8 - - - +
164A VAL* 1.3 59.1 + - - +
165A GLY 3.7 1.1 - - - +
171A ILE* 4.2 2.9 - - + -
172A LEU 3.4 8.5 - - - +
173A ILE* 3.8 17.0 - - + -
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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