Contacts of the helix formed by residues 86 - 103 (chain B) in PDB entry 1LI5
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 VAL 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ALA* 1.3 65.7 + - - +
88B MET* 3.3 7.0 - - - +
89B VAL* 3.0 40.7 - - - +
90B ASP* 3.3 13.6 - - - +
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Residues in contact with ALA 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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86B VAL* 1.3 78.2 - - - +
88B MET* 1.3 63.9 + - - +
90B ASP* 3.4 10.7 + - - +
91B ARG* 3.3 19.8 + - - +
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL 3.3 4.1 - - - +
87B ALA* 1.3 77.5 - - - +
89B VAL* 1.3 66.3 + - + +
91B ARG* 3.3 7.4 + - - +
92B MET* 3.1 28.5 + - + +
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Residues in contact with VAL 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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32B VAL* 4.7 12.1 - - + +
69B ASP* 3.2 48.7 - - + +
74B ILE* 5.1 8.5 - - + -
86B VAL* 3.0 36.3 - - - +
88B MET* 1.3 75.7 - - + +
90B ASP* 1.3 69.7 + - - +
91B ARG 3.2 0.2 + - - -
92B MET* 3.2 7.1 + - - +
93B ILE* 2.9 39.1 + - + +
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Residues in contact with ASP 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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86B VAL 3.3 17.8 + - - +
87B ALA* 3.7 10.7 - - - +
88B MET 3.3 0.2 - - - -
89B VAL* 1.3 85.7 - - - +
91B ARG* 1.3 62.0 + - - +
93B ILE* 3.9 13.8 + - - +
94B ALA* 3.6 16.5 + - - +
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Residues in contact with ARG 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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87B ALA 3.3 10.0 + - - +
88B MET* 3.6 11.4 - - - +
89B VAL 3.1 0.4 - - - -
90B ASP* 1.3 76.7 - - - +
92B MET* 1.3 75.0 + - + +
94B ALA* 3.0 10.2 + - - +
95B GLU* 2.9 19.4 + - - +
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Residues in contact with MET 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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32B VAL* 3.6 35.4 - - + +
33B TYR 3.9 17.5 - - - +
34B ASP* 4.0 20.0 - - - +
35B LEU* 4.8 5.2 - - + -
88B MET* 3.1 15.5 + - + +
89B VAL 3.2 6.5 + - - +
91B ARG* 1.3 88.9 - - + +
93B ILE* 1.3 53.1 + - - +
95B GLU* 2.8 27.3 + - + +
96B MET* 2.8 35.4 + - - +
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Residues in contact with ILE 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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32B VAL* 4.3 8.0 - - + +
67B ILE* 4.0 42.4 - - + -
69B ASP* 4.9 5.8 - - + +
89B VAL* 2.9 32.4 + - + +
90B ASP* 4.0 15.5 - - - +
92B MET* 1.3 74.7 - - - +
94B ALA* 1.3 56.9 + - - +
96B MET* 3.8 10.1 - - + +
97B HIS* 3.0 47.0 + - + +
113B ARG* 5.4 5.4 - - + -
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Residues in contact with ALA 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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90B ASP 3.6 10.0 + - - +
91B ARG* 3.0 11.5 + - - +
92B MET 3.0 0.8 - - - -
93B ILE* 1.3 74.5 - - - +
95B GLU* 1.3 65.3 + - - +
96B MET 3.1 1.6 - - - -
97B HIS* 3.9 10.1 - - - +
98B LYS* 3.0 22.7 + - - +
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Residues in contact with GLU 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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35B LEU* 4.2 23.3 - - + +
91B ARG 2.9 11.7 + - - +
92B MET* 2.8 29.8 + - + +
94B ALA* 1.3 76.0 - - - +
96B MET* 1.3 60.3 + - - +
98B LYS* 3.2 17.7 - - - +
99B ASP* 3.2 18.0 + - - +
278B ARG* 2.9 38.6 + - - +
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Residues in contact with MET 96 (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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30B ILE* 5.0 19.1 - - - +
32B VAL* 5.9 7.0 - - + -
36B CYS* 5.2 8.5 - - + +
65B ARG* 4.4 3.6 - - - +
67B ILE* 4.2 18.8 - - + -
92B MET 2.8 13.6 + - - +
93B ILE* 3.8 16.4 - - + +
95B GLU* 1.3 74.6 - - - +
97B HIS* 1.3 79.1 + - + +
98B LYS 2.9 1.9 + - - -
99B ASP* 3.0 8.0 + - - +
100B PHE* 2.8 63.0 + - + +
111B GLU* 3.7 23.6 - - - +
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Residues in contact with HIS 97 (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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189A GLU* 5.8 6.8 - - + +
65B ARG* 5.1 3.4 + - - -
67B ILE* 5.0 0.2 - - - +
93B ILE* 3.0 41.9 + - + +
94B ALA* 3.5 8.9 + - - +
96B MET* 1.3 81.5 - - + +
98B LYS* 1.3 57.5 + - - +
100B PHE* 4.5 5.0 - - - +
101B ASP* 2.8 37.2 + - - -
107B ARG* 3.1 44.9 + - - +
111B GLU* 2.8 37.3 + - - -
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Residues in contact with LYS 98 (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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94B ALA 3.0 13.8 + - - +
95B GLU* 3.2 16.2 - - - +
96B MET 2.9 0.4 - - - -
97B HIS* 1.3 78.1 - - - +
99B ASP* 1.3 64.1 + - - +
101B ASP* 3.8 4.1 - - - +
102B ALA* 3.2 22.5 + - - +
278B ARG* 4.6 8.1 - - - +
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Residues in contact with ASP 99 (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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35B LEU* 4.6 14.2 - - - +
36B CYS* 4.7 7.1 + - + +
95B GLU* 3.2 15.9 + - - +
96B MET* 3.0 9.0 + - - +
98B LYS* 1.3 75.4 - - - +
100B PHE* 1.3 70.3 + - + +
102B ALA* 3.0 17.7 + - - +
103B LEU* 3.3 16.7 + - - +
277B VAL* 4.2 19.2 - - + +
278B ARG* 2.8 49.1 + - - +
281B LEU* 6.0 0.9 - - - +
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Residues in contact with PHE 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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30B ILE* 5.4 1.3 - - + -
36B CYS* 4.1 22.2 - - + -
40B HIS 5.1 2.0 - - - -
41B GLY* 5.1 5.6 - - - -
44B PHE* 3.3 41.1 - + + -
65B ARG* 3.9 30.5 - - - -
96B MET* 2.8 56.3 + - + +
97B HIS* 3.9 6.1 - - - +
99B ASP* 1.3 77.4 - - + +
101B ASP* 1.3 66.3 + - - +
103B LEU* 3.1 14.3 + - + +
105B ILE* 3.1 49.4 + - + +
107B ARG* 5.6 1.3 - - - +
277B VAL* 5.5 1.8 - - + -
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Residues in contact with ASP 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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199A GLY* 5.7 0.5 - - - -
200A ALA* 4.1 14.5 + - - +
97B HIS 2.8 25.0 + - - +
98B LYS* 3.8 4.5 - - - +
99B ASP 3.3 0.2 - - - -
100B PHE* 1.3 74.2 - - - +
102B ALA* 1.3 60.7 + - - +
104B ASN* 3.2 13.5 + - - -
105B ILE 4.0 12.8 - - - +
107B ARG* 2.6 45.0 + - - +
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Residues in contact with ALA 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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98B LYS 3.2 12.0 + - - +
99B ASP* 3.0 13.3 + - - +
101B ASP* 1.3 72.4 - - - +
103B LEU* 1.3 60.4 + - + +
104B ASN* 3.1 8.7 + - - +
281B LEU* 6.4 1.6 - - + -
286B ALA* 3.4 28.8 - - + +
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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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41B GLY* 4.7 4.3 - - - -
45B VAL* 4.5 3.8 - - + -
99B ASP 3.3 11.0 + - - +
100B PHE* 3.1 11.3 + - + +
102B ALA* 1.3 77.7 - - + +
104B ASN* 1.3 56.3 + - - +
105B ILE* 3.1 21.3 + - + -
277B VAL* 3.6 33.7 - - + -
281B LEU* 6.4 2.2 - - + -
286B ALA* 4.0 11.7 - - - +
289B VAL* 3.8 33.0 - - + -
290B ARG* 2.7 46.0 + - + +
293B LEU* 4.2 17.9 - - + -
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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