Contacts of the strand formed by residues 88 - 93 (chain C) 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 PHE 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLN 4.7 3.4 - - - -
26C ILE* 3.9 27.6 - - + -
27C PRO* 4.0 25.6 - - + -
30C ALA* 4.0 17.9 - - + -
31C ARG 3.3 2.8 + - - -
32C VAL* 3.2 12.6 - - + -
33C LEU 2.9 24.4 + - - -
86C VAL* 3.5 3.7 - - - +
87C THR* 1.3 80.7 - - - +
89C LEU* 1.3 92.1 + - - +
90C LEU* 4.4 2.7 - - + -
131C ILE* 3.7 1.0 - - - +
132C PRO* 3.5 32.1 - - + -
133C MET 3.7 4.0 - - - -
134C GLY 3.5 14.4 - - - -
171C VAL* 4.7 7.6 - - + -
172C PHE* 3.6 28.5 - + - -
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.5 37.2 - - + +
35C THR* 4.7 2.5 - - + -
81C VAL* 4.1 12.8 - - + -
86C VAL* 4.2 3.1 - - + -
88C PHE* 1.3 80.8 - - - +
90C LEU* 1.3 60.2 + - - +
91C ALA 4.1 0.9 - - - -
101C THR* 3.7 24.9 - - + +
104C ILE* 4.1 8.5 - - + -
105C ALA* 3.5 44.6 - - + +
131C ILE* 3.8 16.4 - - + +
132C PRO 3.0 6.9 + - - -
133C MET* 3.1 9.6 - - + +
134C GLY 2.9 24.9 + - - -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.8 19.5 - - + -
26C ILE* 4.6 3.6 - - + -
32C VAL* 4.1 13.7 - - + -
33C LEU 2.9 10.6 + - - +
34C ILE* 3.3 8.7 - - + +
35C THR* 2.9 25.0 + - - +
50C VAL* 3.6 30.7 - - + -
54C LEU* 3.9 14.4 - - + -
88C PHE* 4.3 3.8 + - + -
89C LEU* 1.3 73.6 - - - +
91C ALA* 1.3 59.5 + - - +
92C VAL* 3.5 9.0 + - + -
134C GLY* 3.5 21.3 - - - -
135C CYS* 3.9 2.2 - - - +
136C VAL* 4.1 8.7 - - + -
172C PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 3.2 9.2 + - - +
89C LEU 4.1 0.8 - - - -
90C LEU* 1.3 69.6 - - - +
92C VAL* 1.3 56.0 + - - +
93C GLY 3.9 0.6 + - - -
97C VAL* 4.0 9.6 - - + -
98C LEU* 4.1 13.2 - - + -
101C THR* 3.6 28.6 - - + +
133C MET* 4.3 2.0 - - + -
134C GLY 3.0 14.1 + - - +
135C CYS* 3.1 10.8 - - + +
136C VAL 2.8 32.6 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.6 26.7 - - + -
35C THR 2.8 12.7 + - - +
36C TYR* 3.4 27.5 - - + +
37C GLY 4.4 0.5 + - - -
41C VAL* 4.2 18.9 - - + +
46C VAL* 4.0 26.7 - - + -
47C LEU* 4.7 6.3 - - + -
50C VAL* 4.2 22.4 - - + -
90C LEU* 3.9 4.5 - - + +
91C ALA* 1.3 74.8 - - - +
93C GLY* 1.3 58.6 + - - +
97C VAL* 4.0 3.0 - - - +
136C VAL* 3.5 19.5 - - + +
138C THR* 4.3 1.1 - - + -
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Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY 5.7 0.2 - - - -
41C VAL* 4.7 2.9 - - - -
91C ALA* 3.9 2.6 - - - +
92C VAL* 1.3 74.6 - - - +
94C GLY* 1.3 61.6 + - - -
97C VAL* 4.3 9.6 - - - -
98C LEU* 5.2 0.6 - - - +
136C VAL 3.1 7.8 + - - +
137C LEU* 3.3 14.7 - - - +
138C THR* 3.0 38.9 + - - -
139C LEU* 5.4 0.2 - - - -
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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