Contacts of the strand formed by residues 99 - 106 (chain B) in PDB entry 4OBP
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 ASP 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ASP* 3.4 7.4 - - - +
58B VAL* 2.9 32.5 + - + +
60B GLU* 5.2 5.4 + - - +
63B GLU* 3.1 34.8 - - - +
90B ILE* 4.0 5.1 - - + +
91B LYS 3.8 8.5 - - - +
92B LYS* 3.3 26.5 - - - +
93B SER* 3.5 23.7 + - - +
97B HIS 3.2 14.7 - - - +
98B ASP* 1.3 74.8 - - - +
100B GLN* 1.3 64.8 + - - +
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Residues in contact with GLN 100 (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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27B LEU* 5.2 2.8 - - - +
55B VAL* 3.6 21.7 - - + +
56B MET 3.4 2.5 - - - +
57B ASP* 3.3 24.7 + - - +
58B VAL* 3.9 3.8 - - - -
89B PHE 3.7 0.2 - - - +
90B ILE* 3.2 4.7 - - - -
91B LYS* 2.8 52.8 + - + +
98B ASP 5.6 0.2 - - - +
99B ASP* 1.3 76.9 - - - +
101B LEU* 1.4 60.0 + - - +
102B TRP* 3.3 23.9 + - - +
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Residues in contact with LEU 101 (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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54B LYS 3.4 1.2 - - - +
55B VAL* 3.3 6.1 - - - -
56B MET* 2.7 50.9 + - + +
58B VAL* 3.7 16.6 - - + +
66B ILE* 3.7 32.3 - - + -
88B ALA* 4.4 10.3 - - + -
89B PHE 3.5 15.0 - - - +
90B ILE* 3.8 9.4 - - + -
100B GLN* 1.4 70.7 - - - +
102B TRP* 1.3 67.0 + - - +
103B LEU* 4.2 26.9 - - + -
178B LEU* 4.4 6.7 - - + +
182B VAL* 4.1 24.7 - - + -
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Residues in contact with TRP 102 (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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21B PRO* 3.5 28.7 - - + -
25B PHE* 3.5 35.7 - - + -
26B GLU* 4.3 1.1 - - - -
27B LEU* 3.5 42.4 - - + -
53B ILE* 3.8 26.7 - - + -
54B LYS 3.3 3.6 - - - -
55B VAL* 3.9 12.4 - - + +
87B GLY 3.9 0.3 - - - +
88B ALA* 3.3 5.0 - - - +
89B PHE* 2.7 47.1 + - + +
91B LYS* 3.8 31.7 - - + +
100B GLN* 3.3 29.4 + - - -
101B LEU* 1.3 81.6 - - - +
103B LEU* 1.3 63.4 + - - +
104B VAL* 4.0 4.9 - - + -
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Residues in contact with LEU 103 (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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53B ILE* 3.3 3.6 - - - -
54B LYS* 2.8 37.4 + - + +
56B MET* 4.5 6.5 - - - -
85B TYR* 3.7 19.7 - - + +
87B GLY 3.7 0.7 - - - -
88B ALA* 3.8 15.0 - - + -
101B LEU* 4.2 18.4 - - + -
102B TRP* 1.3 73.7 - - - +
104B VAL* 1.3 60.5 + - - +
172B PHE* 3.5 38.8 - - + +
178B LEU* 3.8 16.2 - - + -
179B ASP* 3.6 43.5 - - + +
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Residues in contact with VAL 104 (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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25B PHE* 3.6 41.1 - - + -
51B ALA* 3.8 8.3 - - + -
52B ALA 3.6 1.6 - - - -
53B ILE* 3.8 27.8 - - + -
85B TYR* 3.4 8.1 - - - -
86B TYR* 2.6 39.3 + - + -
87B GLY 2.8 15.1 + - - +
89B PHE* 3.7 32.1 - - + -
102B TRP* 4.5 2.0 - - + -
103B LEU* 1.3 77.5 - - - +
105B MET* 1.3 59.7 + - - +
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Residues in contact with MET 105 (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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51B ALA* 3.5 5.9 - - - +
52B ALA* 2.7 43.8 + - + -
83B ALA* 3.4 19.3 - - + +
84B THR 3.1 13.9 - - - +
86B TYR* 3.7 7.0 - - - -
104B VAL* 1.3 75.5 - - - +
106B GLU* 1.4 74.1 + - - +
160B LEU* 4.2 20.9 - - + -
170B VAL* 4.0 4.0 - - + -
171B ASP 3.2 46.9 - - - +
172B PHE* 3.6 35.4 - - + -
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Residues in contact with GLU 106 (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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49B GLN* 5.8 3.6 - - - +
50B LEU 4.9 1.6 - - - -
52B ALA* 4.0 1.0 - - - +
82B ILE 3.7 1.0 - - - +
83B ALA* 3.5 10.9 - - - +
84B THR* 2.8 42.6 + - - +
86B TYR* 3.4 27.2 - - - +
105B MET* 1.4 92.2 - - - +
107B PHE* 1.3 72.5 + - - +
108B CYS* 3.8 3.2 + - - -
162B THR* 4.8 3.5 - - - +
168B LYS* 3.2 39.0 + - - +
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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