Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 3OJW
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 ILE 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 3.9 2.3 - - - +
78A ARG* 3.6 1.1 - - - +
79A ASN* 1.3 97.9 - - - +
81A ILE* 1.3 63.1 + - - +
82A VAL* 4.2 18.6 - - + -
98A LEU 5.7 1.1 - - - +
99A SER* 5.8 0.4 - - - -
102A ALA* 4.2 9.6 - - + -
107A MET* 4.0 28.7 - - + -
108A ARG 3.2 6.3 + - - +
109A GLY* 2.8 34.3 - - - -
110A MET* 3.0 6.4 + - - +
132A LEU* 3.4 34.5 - - + +
134A VAL* 4.7 3.6 - - + -
224A TRP* 4.0 25.8 - - + -
227A VAL* 4.7 0.9 - - + -
231A PHE* 5.3 0.4 - - + -
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Residues in contact with ILE 81 (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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69A PHE* 3.7 24.0 - - + -
73A MET* 3.8 22.4 - - + -
80A ILE* 1.3 74.5 - - - +
82A VAL* 1.3 66.6 + - - +
83A PHE* 3.7 31.0 - - + -
110A MET* 3.3 38.6 - - + +
112A ALA* 4.0 9.2 - - + -
125A LEU* 4.8 1.8 - - + -
132A LEU 3.0 11.2 + - - +
133A VAL* 3.4 19.5 - - + +
134A VAL 2.9 24.8 + - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.2 12.8 - - + -
81A ILE* 1.3 77.4 - - - +
83A PHE* 1.3 60.4 + - - +
84A TYR 3.9 0.5 + - - -
95A ALA* 3.7 32.6 - - + +
98A LEU* 4.3 12.6 - - + -
99A SER* 4.1 23.1 - - - +
110A MET 2.8 14.0 + - - +
111A SER* 3.1 4.6 - - - -
112A ALA 2.7 30.2 + - - -
134A VAL* 3.2 32.8 - - + +
135A PHE 4.8 0.2 - - - +
136A ALA* 4.9 3.1 - - + +
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Residues in contact with PHE 83 (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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69A PHE* 3.9 22.4 - + - -
81A ILE* 3.7 27.8 - - + -
82A VAL* 1.3 74.6 - - - +
84A TYR* 1.3 61.1 + - - +
112A ALA* 3.2 29.8 - - + -
114A PRO* 3.5 34.3 - - + -
117A TYR* 4.2 9.0 - + - -
119A LEU* 3.8 24.0 - - + -
133A VAL* 3.8 19.3 - - + -
134A VAL 2.8 7.1 + - - -
135A PHE* 3.5 35.0 - + + -
136A ALA* 2.9 27.5 + - - +
137A MET* 4.3 1.9 - - - +
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Residues in contact with TYR 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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83A PHE* 1.3 75.5 - - - +
85A GLY* 1.3 53.7 + - - +
86A SER* 4.2 6.3 - - - -
91A ALA* 3.9 5.2 - - + +
92A GLU* 3.2 64.3 + - + +
95A ALA* 3.8 23.6 - - + -
96A ASN* 4.9 0.4 - - - -
111A SER* 4.3 9.2 - - - -
112A ALA* 3.1 34.8 + - - -
113A ASP* 3.5 35.7 + - + +
114A PRO* 3.2 8.4 - - - +
136A ALA 3.3 3.1 - - - +
137A MET* 4.4 1.3 - - - -
148A ASN* 2.7 34.0 + - - -
279A LYS* 4.2 8.3 + - - -
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Residues in contact with GLY 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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84A TYR* 1.3 70.3 - - - +
86A SER* 1.3 58.9 + - - -
91A ALA* 3.2 7.7 - - - +
136A ALA 2.8 12.2 + - - -
137A MET* 3.6 22.3 - - - -
138A ALA* 2.9 27.1 + - - +
146A THR* 3.3 20.4 - - - -
148A ASN* 3.5 3.1 - - - -
149A ALA* 4.2 2.2 - - - -
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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