Contacts of the strand formed by residues 131 - 135 (chain A) in PDB entry 1O2D
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.3 7.6 - - + +
102A ALA* 3.9 15.5 - - + +
103A LYS* 4.2 5.4 - - + -
106A ALA* 3.3 33.7 - - + -
129A LEU 3.6 2.0 + - - +
130A PRO* 1.3 74.7 - - - +
132A VAL* 1.3 69.0 + - - +
133A GLU* 3.5 35.2 - - + +
163A MSE 4.0 21.0 - - + +
165A PRO* 3.3 12.4 - - + +
166A VAL* 2.9 31.2 + - - +
167A TYR 3.8 1.4 + - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.0 15.9 - - + -
27A LEU* 3.5 32.1 - - + -
89A PHE* 4.1 10.3 - - + -
90A VAL 2.9 8.9 + - - +
91A VAL* 3.2 14.1 - - + -
92A GLY 2.9 25.8 + - - +
131A VAL* 1.3 75.7 - - - +
133A GLU* 1.3 65.1 + - - +
134A ILE* 4.4 10.1 - - + -
167A TYR* 3.4 13.0 - - + +
169A PHE* 3.6 33.4 - - + -
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Residues in contact with GLU 133 (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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92A GLY* 3.3 23.4 - - - -
99A MSE 2.7 43.8 - - - +
102A ALA* 4.5 0.2 - - - -
103A LYS* 3.3 16.2 - - - +
131A VAL* 3.5 17.3 - - + +
132A VAL* 1.3 73.2 - - - +
134A ILE* 1.3 64.7 - - - +
135A PRO* 3.6 2.6 - - - +
143A GLU* 3.7 25.4 - - + +
165A PRO* 3.5 25.6 - - + -
167A TYR 3.0 9.7 + - - +
168A ALA* 3.3 3.1 - - - -
169A PHE* 3.0 25.5 + - - +
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Residues in contact with ILE 134 (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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16A ILE* 6.4 0.2 - - + -
17A LEU* 4.1 22.2 - - + -
49A LEU* 3.9 24.7 - - + -
52A LEU* 5.8 0.4 - - + -
91A VAL* 3.7 25.6 - - + -
92A GLY 2.8 12.4 + - - +
93A LEU* 3.5 22.6 - - + +
94A GLY 3.1 23.3 + - - -
99A MSE 4.4 1.5 - - - -
132A VAL* 4.4 8.3 - - + -
133A GLU* 1.3 77.0 - - - +
135A PRO* 1.3 62.6 - - - +
169A PHE* 3.5 21.5 - - + +
174A TYR* 4.1 23.6 - - + -
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Residues in contact with PRO 135 (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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94A GLY 3.2 7.2 - - - +
99A MSE 3.6 22.0 - - + -
133A GLU 3.6 7.4 - - - +
134A ILE* 1.3 91.1 - - - +
136A THR* 1.3 64.2 + - - +
137A THR 4.4 4.7 - - - +
143A GLU* 3.6 26.0 - - + +
169A PHE 3.3 14.3 - - - +
170A LEU* 3.7 24.5 - - + -
171A ASP 5.1 0.2 + - - -
174A TYR* 4.3 9.2 - - - -
237A PHE* 3.4 27.8 - - + -
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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