Contacts of the helix formed by residues 87 - 95 (chain A) in PDB entry 4LAX
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A VAL* 1.3 77.0 - - - +
88A LYS* 1.3 66.5 + - - +
89A ALA* 4.4 5.2 - - + -
90A TRP* 3.0 36.5 + - + +
91A ASP* 3.5 3.6 + - - +
107A CYS* 5.0 0.4 - - - -
111A TYR 3.8 9.2 - - - +
112A ALA* 3.7 37.2 - - + +
113A TYR* 3.5 30.5 - - + -
128A LEU* 4.4 2.5 - - + -
130A PHE* 3.9 31.4 - - + -
301A FK5 2.9 34.3 + - + +
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Residues in contact with LYS 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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27A PRO* 5.6 5.1 - - - +
86A VAL 3.7 1.5 + - - -
87A ILE* 1.3 72.9 - - - +
89A ALA* 1.3 63.3 + - - +
90A TRP 3.1 0.5 + - - -
91A ASP* 3.1 23.1 + - + +
92A ILE* 3.0 55.8 + - + +
110A GLU 5.2 2.2 - - - +
111A TYR* 3.5 25.7 + - + +
112A ALA 5.3 0.6 + - - -
302A DMS 5.2 9.2 - - + +
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Residues in contact with ALA 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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33A VAL* 4.0 25.9 - - + +
87A ILE* 3.3 6.9 - - + -
88A LYS* 1.3 75.7 - - - +
90A TRP* 1.3 57.6 + - - +
92A ILE* 3.8 2.2 - - - +
93A ALA* 2.9 31.4 + - - +
105A ILE* 4.2 0.8 - - + +
107A CYS* 3.4 37.7 - - + -
111A TYR* 2.9 20.2 + - + +
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Residues in contact with TRP 90 (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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55A VAL* 3.8 22.0 - - + -
57A TYR* 3.6 45.1 - + + -
77A PHE* 3.9 7.0 - + - -
79A PHE* 3.8 21.1 - + - -
81A LEU* 4.9 0.4 - - - -
86A VAL* 3.6 13.7 - - + -
87A ILE* 3.0 32.9 + - + +
89A ALA* 1.3 76.0 - - - +
91A ASP* 1.3 60.9 + - - +
93A ALA* 4.6 3.4 - - - -
94A ILE* 2.9 50.2 + - + +
105A ILE* 4.1 13.4 - - + +
130A PHE* 3.5 36.0 - + - +
132A VAL* 3.9 12.8 - - + -
301A FK5 3.5 30.4 - - + +
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Residues in contact with ASP 91 (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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79A PHE* 4.2 1.0 - - - -
80A ASP 4.8 0.5 - - - +
81A LEU* 3.6 13.4 - - + +
82A GLY* 3.0 39.1 + - - +
83A LYS 4.4 0.5 + - - -
84A GLY* 3.8 17.8 + - - -
86A VAL* 3.4 24.3 - - - +
87A ILE 3.5 2.3 + - - -
88A LYS* 3.1 27.7 + - - +
90A TRP* 1.3 79.5 - - - +
92A ILE* 1.3 63.4 + - - +
95A ALA* 3.5 21.0 + - - +
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Residues in contact with ILE 92 (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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25A ILE* 3.4 39.5 - - + +
26A SER* 4.5 0.7 - - - -
27A PRO* 3.9 22.2 - - + -
33A VAL* 4.0 12.1 - - + -
88A LYS* 3.0 41.0 + - + +
89A ALA* 3.8 3.4 - - - +
91A ASP* 1.3 77.5 - - - +
93A ALA* 1.3 60.7 + - - +
95A ALA* 3.8 8.2 + - - +
96A THR* 3.7 16.2 - - + +
111A TYR* 3.7 34.5 - - + -
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Residues in contact with ALA 93 (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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25A ILE* 3.8 15.3 - - + -
33A VAL* 4.6 1.3 - - + -
35A LYS* 5.9 0.4 - - + -
89A ALA 2.9 22.2 + - - +
90A TRP* 4.2 1.6 - - - +
92A ILE* 1.3 72.2 - - - +
94A ILE* 1.3 70.1 + - + +
95A ALA 3.2 1.6 - - - -
96A THR* 2.8 23.1 + - - +
97A MET* 3.5 9.0 - - - +
103A CYS* 5.6 2.2 - - - -
105A ILE* 3.7 38.1 - - + -
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Residues in contact with ILE 94 (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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47A PRO* 3.3 24.5 - - + +
53A VAL* 3.7 29.8 - - + -
55A VAL* 4.7 3.4 - - + -
79A PHE* 3.6 19.3 - - + -
81A LEU* 3.9 11.2 - - + -
90A TRP* 2.9 39.6 + - + +
93A ALA* 1.3 76.1 - - + +
95A ALA* 1.3 62.2 + - - +
96A THR 3.0 1.8 + - - -
97A MET* 3.1 33.6 + - - +
105A ILE* 6.0 0.4 - - + -
132A VAL* 3.8 23.3 - - + -
134A LEU* 4.9 5.6 - - + -
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Residues in contact with ALA 95 (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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46A MET* 3.6 22.2 - - - +
47A PRO 3.7 20.0 - - - +
48A MET* 5.7 3.8 - - - -
81A LEU* 4.3 8.8 - - + +
91A ASP 3.5 18.8 + - - +
92A ILE* 3.9 6.7 - - - +
93A ALA 3.2 1.0 - - - -
94A ILE* 1.3 77.9 - - - +
96A THR* 1.3 60.4 + - + +
97A MET 3.5 0.2 - - - -
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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