Contacts of the helix formed by residues 87 - 95 (chain B) in PDB entry 4LAV
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 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B VAL* 1.3 77.2 - - - +
88B LYS* 1.3 68.3 + - - +
89B ALA* 4.2 3.4 - - + -
90B TRP* 2.9 39.2 + - + +
91B ASP* 3.3 8.1 + - - +
111B TYR 3.8 9.9 - - - +
112B ALA* 3.6 37.2 - - + +
113B TYR* 3.6 33.0 - - + +
130B PHE* 3.6 36.6 - - + -
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Residues in contact with LYS 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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86B VAL 3.7 1.0 + - - -
87B ILE* 1.3 71.9 - - - +
89B ALA* 1.3 57.3 + - - +
90B TRP 3.2 0.2 + - - -
91B ASP* 3.2 10.1 + - - +
92B ILE* 2.9 36.8 + - + +
110B GLU 4.0 20.3 + - - +
111B TYR* 3.4 30.1 + - + +
112B ALA 5.2 0.8 + - - -
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Residues in contact with ALA 89 (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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33B VAL* 3.8 23.3 - - + +
87B ILE* 3.2 5.8 - - + -
88B LYS* 1.3 75.5 - - - +
90B TRP* 1.3 61.5 + - + +
92B ILE* 3.7 1.7 - - - +
93B ALA* 2.9 31.0 + - - +
105B ILE* 4.1 3.9 - - + +
107B CYS* 3.5 34.3 - - + -
111B TYR* 2.9 19.1 + - - +
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Residues in contact with TRP 90 (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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55B VAL* 5.2 2.5 - - + -
57B TYR* 3.4 46.9 - + + -
77B PHE* 3.7 28.7 - + - -
79B PHE* 4.5 7.2 - + - -
86B VAL* 3.6 28.9 - - + -
87B ILE* 2.9 29.7 + - + +
89B ALA* 1.3 77.1 - - + +
91B ASP* 1.3 67.4 + - - +
92B ILE 3.1 0.9 - - - -
93B ALA* 4.3 3.1 - - - +
94B ILE* 2.9 42.8 + - + +
105B ILE* 4.1 13.5 - - + -
113B TYR* 6.0 1.3 - - - -
130B PHE* 3.5 48.6 - + + +
132B VAL* 4.9 7.8 - - + +
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Residues in contact with ASP 91 (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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79B PHE* 3.8 6.9 - - - -
80B ASP 4.5 0.5 - - - +
81B LEU* 3.7 8.9 - - - +
82B GLY* 2.9 33.5 + - - +
83B LYS 3.7 1.6 + - - -
84B GLY* 3.1 31.0 + - - -
85B GLU 5.1 0.2 + - - -
86B VAL* 3.5 21.3 - - - +
87B ILE 3.3 3.6 + - - +
88B LYS* 3.2 12.1 + - - +
90B TRP* 1.3 79.1 - - - +
92B ILE* 1.3 64.5 + - + +
95B ALA* 3.5 20.1 + - - +
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Residues in contact with ILE 92 (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 ILE* 3.6 40.2 - - + +
27B PRO* 3.6 29.2 - - + -
33B VAL* 3.9 14.1 - - + -
88B LYS* 2.9 22.7 + - + +
89B ALA* 3.7 4.0 - - - +
91B ASP* 1.3 81.6 - - + +
93B ALA* 1.3 62.7 + - - +
95B ALA* 3.6 10.2 + - - +
96B THR* 3.6 13.3 - - - +
111B TYR* 3.6 32.8 - - + -
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Residues in contact with ALA 93 (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 ILE* 3.6 14.4 - - + -
33B VAL* 4.7 0.4 - - + -
35B LYS* 4.9 0.2 - - - -
89B ALA 2.9 22.3 + - - +
90B TRP* 4.1 2.9 - - - +
92B ILE* 1.3 71.6 - - - +
94B ILE* 1.3 65.9 + - + +
96B THR* 2.7 27.4 + - - +
97B MET* 3.4 9.7 - - - +
103B CYS* 4.8 6.7 - - - -
105B ILE* 3.9 35.0 - - + -
132B VAL* 5.7 1.8 - - + -
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Residues in contact with ILE 94 (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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47B PRO* 3.3 24.1 - - + +
53B VAL* 4.1 13.7 - - + -
55B VAL* 4.1 13.2 - - + -
79B PHE* 3.4 33.0 - - + -
81B LEU* 3.8 15.7 - - + -
90B TRP* 2.9 31.7 + - + +
93B ALA* 1.3 80.7 - - + +
95B ALA* 1.3 60.7 + - - +
97B MET* 3.1 21.5 + - - +
132B VAL* 4.0 24.0 - - + -
134B LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 95 (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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46B MET* 3.0 28.1 - - - +
47B PRO 4.1 9.3 - - - +
48B MET* 6.1 0.2 - - - -
81B LEU* 4.0 18.7 - - + +
91B ASP 3.5 17.3 + - - +
92B ILE* 3.8 6.7 - - - +
93B ALA 3.2 0.4 - - - -
94B ILE* 1.3 78.1 - - - +
96B THR* 1.3 58.1 + - + +
97B MET 3.5 0.7 - - - -
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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