Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 4OA8
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 HIS 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B HIS 3.0 7.2 + - - +
59B SER* 3.4 7.4 - - - +
60B ILE 2.9 25.6 + - - +
78B LEU* 3.9 2.3 - - - +
81B LYS 3.9 2.9 + - - +
82B GLY* 1.3 74.7 + - - +
84B ILE* 1.3 85.0 + - - +
85B TYR* 3.5 37.7 - + + +
107B GLU 5.3 0.7 - - - -
108B ASP 3.1 28.6 + - - -
109B LYS* 3.2 20.3 + - - -
110B ILE 3.8 1.1 - - - -
111B THR* 2.9 30.0 + - - -
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Residues in contact with ILE 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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60B ILE* 3.3 24.0 - - + +
62B GLU* 4.6 5.4 - - + -
71B ALA* 3.2 37.2 - - + +
74B MET* 3.5 16.2 - - + -
75B ALA* 3.4 25.6 - - + +
78B LEU* 3.5 17.0 - - + -
83B HIS* 1.3 80.8 - - - +
85B TYR* 1.3 70.2 + - - +
86B THR* 4.3 12.1 - - - -
109B LYS 2.8 13.0 + - - +
110B ILE* 3.4 6.9 - - + -
111B THR 2.9 27.0 + - - +
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Residues in contact with TYR 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 SER* 5.1 4.0 - - - -
60B ILE 2.9 16.3 + - - +
61B VAL* 3.4 5.8 - - + +
62B GLU 2.8 26.6 + - - +
83B HIS* 3.5 43.0 - + + +
84B ILE* 1.3 71.7 - - - +
86B THR* 1.3 60.2 + - - +
87B ILE* 5.0 2.0 - - - +
111B THR* 3.4 20.4 - - + +
113B LEU* 4.9 5.6 - - + -
124B LEU* 3.9 33.3 - - + +
127B MET* 4.2 28.0 - - + -
130B PHE* 3.9 27.0 - + - -
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Residues in contact with THR 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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62B GLU* 2.6 40.0 + - - +
65B THR* 2.8 29.7 + - + +
71B ALA* 4.4 2.5 - - + -
84B ILE* 4.3 4.5 - - - -
85B TYR* 1.3 76.3 - - - +
87B ILE* 1.3 56.9 + - - +
110B ILE* 3.9 16.2 - - + -
111B THR 2.9 16.3 + - - +
112B VAL* 3.3 22.8 - - + -
113B LEU* 2.7 34.1 + - - +
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Residues in contact with ILE 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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61B VAL* 4.7 1.6 - - + -
62B GLU 2.9 16.7 + - - +
63B VAL* 4.6 8.4 - - + +
64B GLY* 2.8 30.1 + - - -
65B THR* 3.1 4.9 + - - -
85B TYR 5.0 0.2 - - - +
86B THR* 1.3 79.3 + - - +
88B GLU* 1.3 65.0 + - - +
89B LYS 5.3 0.2 - - - +
113B LEU* 3.4 16.6 - - + +
115B GLY 3.9 15.7 - - - +
117B ALA* 4.0 15.7 - - + +
120B GLN* 3.9 33.7 - - + -
121B LEU* 3.7 39.0 - - + +
124B LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 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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64B GLY* 3.8 5.1 - - - -
65B THR* 3.2 23.4 + - - +
66B CYS* 2.9 25.6 + - - +
87B ILE* 1.3 77.4 - - - +
89B LYS* 1.3 64.0 + - - +
90B ASP* 3.1 31.0 + - - +
93B ASN* 3.1 33.4 + - + -
94B VAL* 3.7 17.0 - - + +
112B VAL* 4.6 1.3 - - + -
113B LEU 2.9 6.6 + - - +
114B HIS* 3.4 9.0 + - - -
115B GLY 3.1 22.4 + - - -
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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