Contacts of the helix formed by residues 83 - 98 (chain B) in PDB entry 3LKB
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 ALA 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP* 5.8 2.0 + - - +
58B TYR* 3.3 37.9 - - + -
60B ASN* 4.6 4.3 - - - +
63B THR* 5.8 1.9 - - - +
82B TYR* 1.3 78.8 - - + +
84B THR* 1.3 66.6 + - - +
85B GLY* 4.2 1.6 - - - +
86B ALA* 3.9 24.9 - - + +
87B ASN* 2.9 26.9 + - - +
393B VAL* 3.2 8.1 - - - -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR 3.6 0.2 + - - -
83B ALA* 1.3 71.4 - - - +
85B GLY* 1.3 56.7 + - - +
87B ASN* 3.1 3.2 + - - +
88B LEU* 2.9 31.1 + - - +
105B SER* 2.8 20.0 - - - +
107B HIS* 4.3 16.2 + - + -
110B LEU* 4.5 0.7 - - - +
126B TYR* 3.6 14.6 - - + -
154B PRO* 3.2 10.1 + - - +
155B PHE* 3.0 28.2 + - - -
158B ALA* 5.1 0.2 - - + -
393B VAL* 2.4 60.5 - - + +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 5.1 2.0 + - - -
60B ASN* 3.8 14.6 + - - -
83B ALA* 3.2 3.4 - - - +
84B THR* 1.3 80.6 + - - +
86B ALA* 1.3 60.4 + - - +
88B LEU* 3.5 6.2 + - - +
89B GLN* 3.1 23.6 + - - +
154B PRO* 3.9 28.1 - - - +
155B PHE 4.8 0.8 - - - +
393B VAL* 4.8 0.2 - - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASN* 3.4 29.0 + - + +
63B THR* 3.9 32.5 - - + +
81B SER* 6.6 0.2 - - - -
82B TYR 6.0 0.4 - - - +
83B ALA* 3.4 21.0 + - + +
84B THR 3.4 0.2 - - - -
85B GLY* 1.3 74.8 - - - +
87B ASN* 1.3 58.1 + - - +
89B GLN* 3.1 4.1 + - - +
90B LEU* 2.9 37.9 + - + +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 5.2 0.8 - - - -
81B SER* 2.8 38.8 + - - -
82B TYR 3.5 10.9 + - - +
83B ALA 2.9 24.5 + - - +
84B THR 3.5 3.1 - - - +
86B ALA* 1.3 74.8 - - - +
88B LEU* 1.3 65.5 + - - +
90B LEU* 3.2 5.7 + - - +
91B LYS* 3.1 27.0 + - - +
94B ILE* 4.3 9.7 - - - +
101B THR* 3.9 14.5 - - - +
103B PRO* 3.7 13.6 - - - +
105B SER* 4.3 0.3 - - - -
110B LEU* 3.6 24.0 - - + +
119B ILE* 5.3 3.2 - - + +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 2.9 19.6 + - - +
85B GLY* 3.8 6.1 - - - +
86B ALA 3.4 0.2 - - - -
87B ASN* 1.3 76.5 - - - +
89B GLN* 1.3 61.4 + - - +
91B LYS* 3.7 22.1 + - + +
92B PRO* 4.3 3.1 - - - +
107B HIS* 4.3 19.1 - - + +
109B GLU* 4.0 27.8 - - + +
110B LEU* 3.8 18.6 - - + +
154B PRO* 4.1 23.8 - - + -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASN* 3.4 40.1 - - - +
61B ALA* 5.7 0.5 - - - -
64B GLN* 3.9 18.5 - - - +
85B GLY 3.1 15.1 + - - +
86B ALA* 3.1 5.8 + - - +
88B LEU* 1.3 77.8 - - - +
90B LEU* 1.3 65.7 + - + +
92B PRO* 3.5 12.6 - - - +
93B LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASN 5.9 0.2 - - - +
63B THR* 4.4 18.6 - - + -
64B GLN* 3.8 41.5 - - + +
67B PHE* 4.5 9.0 - - + -
79B PHE* 4.3 22.2 - - + -
86B ALA* 2.9 25.1 + - + +
87B ASN* 3.2 3.8 + - - +
89B GLN* 1.3 81.1 - - + +
91B LYS* 1.3 65.8 + - - +
92B PRO* 3.2 3.8 - - - -
93B LEU* 3.0 26.3 + - + +
94B ILE* 2.8 36.7 + - + +
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Residues in contact with LYS 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 ASN 3.1 21.2 + - - +
88B LEU* 4.0 16.4 - - + +
89B GLN 3.5 0.2 - - - -
90B LEU* 1.3 75.2 - - - +
92B PRO* 1.3 71.2 - - + +
94B ILE* 3.7 8.7 - - - +
95B GLN* 2.9 24.6 + - - +
109B GLU* 2.9 24.3 + - - +
110B LEU* 3.4 24.9 + - + +
112B ASP 2.8 27.3 + - - -
113B PRO 4.8 1.4 - - - -
114B PRO* 3.2 20.6 + - - +
115B ASN* 3.4 22.1 - - + +
119B ILE* 3.8 13.0 - - + -
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Residues in contact with PRO 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU 4.3 3.4 - - - +
89B GLN 3.5 14.1 - - - +
90B LEU 3.4 4.3 - - - -
91B LYS* 1.3 95.4 - - + +
93B LEU* 1.3 52.5 + - - +
95B GLN* 3.3 2.8 + - - +
96B GLU* 2.8 38.4 + - + +
115B ASN* 3.9 23.7 - - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 4.6 4.5 - - - +
67B PHE* 4.1 16.6 - - + -
68B GLU* 4.0 28.9 - - + +
89B GLN 5.4 0.4 + - - +
90B LEU* 3.0 32.4 + - + +
92B PRO* 1.3 77.7 - - - +
94B ILE* 1.3 60.3 + - - +
96B GLU* 3.3 11.1 - - + +
97B LEU* 2.8 60.1 + - + +
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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
----------------------------------------------------------
67B PHE* 4.5 13.9 - - + -
79B PHE* 4.6 5.2 - - + -
87B ASN* 4.3 10.5 - - - +
90B LEU* 2.8 41.8 + - + +
91B LYS* 3.7 4.3 - - - +
93B LEU* 1.3 72.5 - - - +
95B GLN* 1.3 57.7 + - - +
97B LEU 3.3 0.3 + - - -
98B ARG* 2.9 24.1 + - - -
99B ILE* 3.4 23.8 + - + +
101B THR* 3.2 48.0 - - + +
115B ASN 6.1 0.2 - - - +
118B TYR* 4.1 11.4 - - + +
119B ILE* 4.2 22.2 - - + -
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Residues in contact with GLN 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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91B LYS 2.9 17.7 + - - +
92B PRO 3.5 3.8 - - - +
94B ILE* 1.3 76.6 - - - +
96B GLU* 1.3 64.1 + - - +
98B ARG* 3.2 19.9 + - - -
115B ASN* 3.3 38.7 + - + +
117B ASP* 2.8 48.9 + - - +
118B TYR* 3.6 23.6 + - - -
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Residues in contact with GLU 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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92B PRO 2.8 21.0 + - - +
93B LEU* 3.3 18.3 - - + +
95B GLN* 1.3 76.1 - - - +
97B LEU* 1.3 68.6 + - + +
98B ARG* 3.2 29.0 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.1 10.3 - - + -
68B GLU* 6.3 1.1 - - + -
71B VAL* 4.1 37.5 - - + -
93B LEU* 2.8 49.0 + - + +
95B GLN 3.3 0.2 - - - -
96B GLU* 1.3 83.4 - - + +
98B ARG* 1.3 70.6 + - - +
99B ILE* 3.3 15.3 + - + +
313B ASN* 3.1 12.6 + - - -
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Residues in contact with ARG 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 ILE 2.9 7.8 + - - -
95B GLN 3.2 12.2 + - - -
96B GLU* 3.2 33.7 + - - +
97B LEU* 1.3 80.9 - - - +
99B ILE* 1.3 58.4 + - - +
100B PRO* 3.8 3.6 - - - +
118B TYR* 3.1 47.0 + - + +
313B ASN* 2.9 27.6 + - - +
314B GLU* 5.4 12.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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