Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2O7R
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 LEU 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.7 31.4 - - + -
75A HIS* 4.3 9.2 - - + +
76A ALA* 4.1 18.2 - - + -
79A ASN* 6.0 1.8 - - - +
81A ALA* 4.7 10.1 - - + +
82A LYS* 1.4 78.9 - - - +
84A PRO* 1.3 79.2 - - + +
116A GLY* 3.6 27.1 - - - +
117A VAL 4.1 4.0 - - - -
118A VAL* 4.0 8.0 - - + +
157A PHE 2.9 13.6 + - - +
158A ALA* 3.5 4.3 - - - -
159A ASP* 2.7 27.4 + - - -
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Residues in contact with PRO 84 (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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82A LYS 4.6 1.8 - - - +
83A LEU* 1.3 89.8 - - + +
85A LEU* 1.3 59.4 + - - +
116A GLY 3.5 13.9 - - - +
117A VAL* 3.5 9.9 - - + +
118A VAL 3.0 25.1 + - - +
159A ASP* 4.3 7.1 - - + +
162A ASN* 3.4 23.8 - - + +
164A PHE* 4.1 8.7 - - + -
327A VAL* 3.4 38.1 - - + +
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Residues in contact with LEU 85 (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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83A LEU 3.5 0.4 + - - -
84A PRO* 1.3 73.2 - - - +
86A VAL* 1.3 70.3 + - - +
87A VAL* 4.6 1.8 - - + -
118A VAL* 3.5 29.8 - - + +
120A ALA* 4.3 11.7 - - + +
146A ILE* 3.9 31.0 - - + -
154A LEU* 4.2 13.7 - - + -
158A ALA* 4.3 15.3 - - + -
159A ASP 4.1 11.6 + - - +
160A PHE* 4.7 8.5 - - + -
162A ASN 3.1 7.0 + - - +
163A CYS* 3.2 12.7 - - + -
164A PHE* 2.8 26.9 + - - +
192A LEU* 4.1 16.2 - - + -
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Residues in contact with VAL 86 (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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85A LEU* 1.3 75.5 - - - +
87A VAL* 1.4 61.8 + - - +
88A TYR* 4.4 7.4 - - + -
111A MET* 4.7 8.3 - - + -
117A VAL* 3.8 32.5 - - + -
118A VAL 2.9 12.5 + - - +
119A ILE* 3.2 10.7 - - + +
120A ALA 2.8 31.2 + - - -
164A PHE* 3.4 22.0 - - + +
166A MET* 3.7 37.7 - - + -
198A VAL* 6.3 0.7 - - + -
323A LEU* 5.8 2.9 - - + -
327A VAL* 5.0 5.2 - - + -
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Residues in contact with VAL 87 (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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85A LEU* 4.6 5.4 - - + -
86A VAL* 1.4 70.6 - - - +
88A TYR* 1.3 60.4 + - - +
89A PHE* 3.9 26.7 - - + -
120A ALA* 3.4 10.1 - - + +
122A VAL* 4.0 9.6 - - + -
142A ALA* 5.1 2.5 - - + -
143A LEU* 4.1 20.6 - - + -
146A ILE* 3.5 29.8 - - + -
163A CYS* 3.9 23.6 - - - -
164A PHE 2.8 11.2 + - - +
165A ILE* 3.5 6.7 - - + -
166A MET 2.8 27.4 + - - +
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Residues in contact with TYR 88 (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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86A VAL* 4.4 3.1 - - + -
87A VAL* 1.3 72.5 - - - +
89A PHE* 1.3 78.1 + - - +
90A HIS* 3.8 18.6 - - + -
104A PHE* 3.5 21.8 - + + -
107A PHE* 4.1 14.6 - + - -
108A CYS* 3.6 21.3 - - - -
111A MET* 3.9 13.9 - - + -
119A ILE* 3.7 22.2 - - + -
120A ALA 2.8 8.6 + - - +
121A SER* 3.4 18.0 + - - -
122A VAL* 2.9 27.4 + - - +
166A MET* 3.2 42.6 - - + +
167A GLY* 4.3 3.8 - - - -
168A GLU* 3.5 21.9 - - + +
310A LEU* 4.9 0.9 - - - +
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Residues in contact with PHE 89 (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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87A VAL* 3.9 21.1 - - + -
88A TYR* 1.3 76.7 - - - +
90A HIS* 1.3 65.1 + - - +
122A VAL* 3.5 39.7 - - + -
124A TYR* 3.9 17.5 - + + -
135A ALA 5.2 0.4 - - - -
139A ALA* 3.4 40.6 - - + -
143A LEU* 5.9 1.3 - - + -
165A ILE* 3.9 18.4 - - + -
166A MET 2.9 18.9 + - - -
167A GLY* 3.2 1.2 - - - -
168A GLU 3.1 23.2 + - - -
171A GLY* 3.4 21.5 - - - +
174A ILE* 3.7 14.4 - - + -
175A ALA* 4.3 13.0 - - + -
178A ALA* 5.0 1.1 - - + -
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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