Contacts of the strand formed by residues 133 - 137 (chain A) in PDB entry 1OJ7
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 MET 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.8 6.7 - - - -
89A LEU* 3.1 22.9 - - + +
91A ALA* 3.9 15.3 - - + -
98A LEU* 3.8 20.6 - - + +
101A THR* 3.8 20.9 - - + +
102A LYS* 3.5 37.9 - - + -
105A ALA* 4.9 3.1 - - + -
131A ILE 4.3 4.5 - - - +
132A PRO* 1.3 76.9 - - - +
134A GLY* 1.3 61.3 + - - +
135A CYS* 4.9 0.2 - - + -
168A VAL* 4.0 9.6 - - - +
169A GLN 5.0 2.1 + - - +
170A PRO* 4.1 22.9 - - + -
171A VAL* 2.7 36.5 + - - +
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Residues in contact with GLY 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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88A PHE* 3.7 4.0 - - - -
89A LEU 3.0 7.6 + - - +
90A LEU* 3.6 7.3 - - - -
91A ALA* 3.0 22.9 + - - +
133A MET* 1.3 79.6 - - - +
135A CYS* 1.3 63.1 + - - +
170A PRO* 4.5 1.3 - - - -
172A PHE* 3.3 33.2 - - - -
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Residues in contact with CYS 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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90A LEU* 3.8 4.5 - - - +
91A ALA* 3.1 15.0 - - + +
98A LEU* 3.7 38.4 - - + -
133A MET* 4.9 1.8 - - + -
134A GLY* 1.3 75.7 - - - +
136A VAL* 1.3 63.8 + - - +
137A LEU 5.1 2.5 - - - -
145A GLU* 3.8 13.2 - - - -
170A PRO* 4.5 5.2 - - - -
172A PHE* 3.1 12.9 + - - -
173A ALA* 3.5 27.2 - - - -
174A VAL* 2.8 31.5 + - - +
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Residues in contact with VAL 136 (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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19A ILE* 4.1 22.2 - - + -
22A LEU* 4.5 4.0 - - + -
46A VAL* 4.6 1.8 - - + -
50A VAL* 4.2 13.2 - - + -
90A LEU* 4.3 15.3 - - + -
91A ALA 2.8 8.5 + - - +
92A VAL* 3.4 20.4 - - + -
93A GLY 3.1 24.8 + - - +
98A LEU* 4.7 0.4 - - - +
135A CYS* 1.3 80.1 - - - +
137A LEU* 1.3 60.4 + - - +
138A THR* 3.7 2.1 + - + +
174A VAL* 3.7 18.8 - - + +
179A TYR* 3.7 34.1 - - + -
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Residues in contact with LEU 137 (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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93A GLY 3.5 13.5 - - - +
94A GLY* 4.4 6.3 - - - -
95A GLY* 4.6 1.8 - - - +
98A LEU* 4.0 19.7 - - + -
135A CYS* 4.0 1.7 - - - -
136A VAL* 1.3 71.5 - - - +
138A THR* 1.3 60.2 + - - +
139A LEU 3.3 28.3 - - - +
140A PRO* 4.2 12.6 - - + -
142A THR* 5.6 1.6 - - - +
145A GLU* 3.4 43.7 - - + +
174A VAL 3.1 16.9 + - - +
175A LEU* 4.2 11.9 - - + -
176A ASP 4.7 0.5 + - - +
179A TYR* 4.4 11.6 - - - +
245A MET* 3.7 28.7 - - + +
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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