Contacts of the helix formed by residues 82 - 88 (chain B) in PDB entry 2OZL
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 THR 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B TYR* 3.8 20.2 - - + +
80B PHE* 3.5 13.7 - - - +
81B MET* 1.3 83.7 - - + +
83B PHE* 1.3 65.4 + - - +
84B ASN* 3.1 28.0 + - - +
85B PHE* 3.2 44.7 + - + +
117B PRO* 3.4 16.8 - - + -
128B HIS* 5.2 7.4 - - + +
61C PHE* 6.4 1.1 - - + -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.9 19.1 - + + -
82B THR* 1.3 69.1 - - - +
84B ASN* 1.3 65.5 + - - +
85B PHE 3.0 2.5 - - - -
86B SER* 2.6 42.8 + - - +
114B PHE* 3.7 26.2 - - + -
115B ARG 3.7 5.4 - - - -
116B GLY* 3.3 40.2 - - - -
117B PRO 2.9 14.5 + - - +
118B ASN* 4.1 9.8 - - + +
130B GLN 5.4 0.2 - - - +
132B PHE* 3.5 25.7 - - + -
136B TYR* 3.8 17.9 - + - -
168B VAL* 3.8 22.2 - - + -
169B VAL 3.6 6.5 - - - -
170B LEU* 3.7 14.6 - - + -
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B THR* 3.1 26.0 + - - +
83B PHE* 1.3 78.4 - - - +
85B PHE* 1.3 67.3 + - + +
86B SER 3.4 0.2 + - - -
87B MET* 3.5 26.3 + - + +
118B ASN* 6.3 0.8 - - - +
119B GLY 5.0 2.6 + - - +
127B GLN 3.4 25.6 - - - +
128B HIS* 3.0 27.8 + - - +
130B GLN* 3.0 40.4 + - - +
132B PHE* 3.6 11.5 - - - -
137C ILE* 5.1 1.9 - - + +
91D ASP* 4.5 2.4 - - - +
95D ASN* 4.4 4.8 + - - +
99D LYS* 5.3 0.2 + - - -
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.4 32.9 - - + +
80B PHE* 4.8 2.2 - - + -
81B MET* 3.6 23.6 - - + +
82B THR* 3.2 40.2 - - + +
83B PHE 3.0 0.8 - - - -
84B ASN* 1.3 82.0 - - + +
86B SER* 1.3 58.9 + - - +
87B MET 3.1 6.8 + - - -
88B GLN* 3.4 14.4 + - - +
128B HIS* 3.7 27.6 - + - -
137C ILE* 4.1 16.8 - - + -
1330C TPP 3.4 66.9 - + + +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.7 39.4 - - - -
82B THR 3.8 1.6 + - - -
83B PHE* 2.6 33.4 + - - -
85B PHE* 1.3 76.1 - - - +
87B MET* 1.3 61.5 + - - +
88B GLN 3.1 0.2 - - - -
89B ALA 2.9 4.6 + - - +
90B ILE* 2.7 28.8 + - - +
132B PHE* 4.8 3.3 - - - -
136B TYR* 2.8 27.9 + - - -
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Residues in contact with MET 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 3.7 12.8 - - + +
85B PHE 3.1 1.2 - - - -
86B SER* 1.3 78.8 + - - +
88B GLN* 1.3 61.5 + - - +
89B ALA 3.2 0.5 + - - -
90B ILE* 3.5 23.9 + - + +
130B GLN* 3.9 16.2 - - - +
132B PHE* 3.5 32.3 - - + -
135B TRP* 4.0 24.5 - - + -
87D MET 3.6 9.2 - - - +
88D GLN 5.2 0.5 - - - +
90D ILE* 3.7 18.3 - - + +
91D ASP* 3.8 13.1 + - + +
94D ILE* 4.2 17.7 - - + -
95D ASN* 3.0 37.0 - - - +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 5.1 2.4 + - - -
59B GLU* 3.3 22.9 + - + +
60B MET* 3.2 33.3 - - + +
84B ASN 6.1 0.2 - - - +
85B PHE* 3.4 10.7 + - - +
86B SER 3.1 0.4 - - - -
87B MET* 1.3 78.4 - - - +
89B ALA* 1.3 56.4 + - - +
137C ILE* 3.7 8.3 - - + +
138C VAL 3.5 3.1 - - - +
172C GLN* 3.2 39.9 + - - +
174C GLN* 3.5 12.3 + - - -
1330C TPP 3.3 20.8 - - + +
60D MET* 5.0 8.3 - - - -
87D MET 5.3 0.4 - - - -
88D GLN* 4.7 8.3 - - - +
91D ASP* 4.4 20.8 - - + +
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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