Contacts of the helix formed by residues 59 - 75 (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 ASN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY* 3.6 27.5 + - - +
56B ASP* 3.0 13.9 + - - +
57B GLN* 3.2 4.5 - - + +
58B TYR* 1.3 76.9 - - - +
60B ASN* 1.3 63.6 + - - +
61B ALA* 2.8 25.4 + - - +
62B ASN* 2.9 33.6 + - - +
63B THR* 3.1 14.0 + - - -
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Residues in contact with ASN 60 (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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58B TYR 3.7 8.7 + - - +
59B ASN* 1.3 73.3 + - - +
61B ALA* 1.3 57.8 + - - +
63B THR* 3.3 7.8 + - - -
64B GLN* 2.9 31.0 + - - +
83B ALA* 4.6 4.2 - - - +
85B GLY* 3.8 17.1 + - - -
86B ALA* 3.4 28.7 + - - +
89B GLN* 3.4 34.7 - - - +
90B LEU* 5.9 0.3 - - - +
154B PRO* 6.1 0.4 - - - +
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Residues in contact with ALA 61 (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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59B ASN* 2.8 18.0 + - - +
60B ASN* 1.3 72.3 - - - +
62B ASN* 1.3 66.3 + - - +
64B GLN* 4.0 4.4 - - - +
65B ARG* 3.1 23.2 + - - +
89B GLN* 5.7 0.4 - - - -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TYR 3.8 16.2 + - - +
276A GLY* 4.2 10.4 + - - -
277A ARG* 6.3 0.2 - - - +
55B ASP 5.0 1.6 + - - -
56B ASP* 3.2 33.4 + - + +
57B GLN* 5.0 5.9 + - - +
59B ASN* 2.9 26.7 + - - +
61B ALA* 1.3 77.2 - - - +
63B THR* 1.3 54.9 + - - +
65B ARG* 3.1 24.7 + - - +
66B PHE* 2.7 53.1 + - + -
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Residues in contact with THR 63 (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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13B SER* 3.7 23.5 + - - +
56B ASP* 2.6 31.3 + - - +
58B TYR 5.2 0.5 - - - -
59B ASN 3.1 12.9 + - - -
60B ASN* 3.3 8.4 + - - -
62B ASN* 1.3 75.6 - - - +
64B GLN* 1.3 57.2 + - - +
66B PHE* 3.2 2.4 + - - +
67B PHE* 2.7 31.8 + - - +
79B PHE* 4.8 8.3 - - + -
81B SER* 6.1 1.1 - - - -
82B TYR* 5.9 3.1 - - + +
83B ALA* 5.8 1.2 - - - +
86B ALA* 3.9 26.6 - - + +
90B LEU* 4.4 11.7 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASN 2.9 16.9 + - - +
61B ALA* 4.0 5.3 - - - +
63B THR* 1.3 78.2 - - - +
65B ARG* 1.3 57.3 + - - +
67B PHE* 3.2 6.4 + - - +
68B GLU* 2.9 59.9 + - + +
89B GLN* 3.9 16.8 - - - +
90B LEU* 3.8 28.0 - - + +
93B LEU* 4.6 5.6 - - + +
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Residues in contact with ARG 65 (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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36A LYS* 6.0 4.0 - - - +
275A TYR* 5.0 19.7 + - - +
54B ARG* 5.0 3.6 - - - +
61B ALA 3.1 16.8 + - - +
62B ASN* 3.1 25.7 + - - +
64B GLN* 1.3 73.7 - - - +
66B PHE* 1.3 90.5 - - + +
68B GLU* 3.4 8.0 + - - +
69B GLU* 3.2 25.3 + - + +
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Residues in contact with PHE 66 (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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32A GLU* 6.2 0.4 - - - -
11B PHE* 3.6 21.7 - - + -
13B SER* 3.7 12.3 - - - +
54B ARG* 3.4 57.2 - - + +
55B ASP 3.7 23.8 - - - -
56B ASP* 3.9 9.6 - - + -
62B ASN* 2.7 35.7 + - + +
63B THR 3.8 3.1 - - - +
65B ARG* 1.3 102.9 - - + +
67B PHE* 1.3 63.0 + - - +
69B GLU* 3.5 5.4 + - + +
70B ALA* 3.2 23.4 + - - +
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Residues in contact with PHE 67 (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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11B PHE* 3.9 11.0 - + + -
63B THR 2.7 21.6 + - - +
64B GLN* 3.6 6.1 - - - +
65B ARG 3.2 0.2 - - - -
66B PHE* 1.3 74.6 - - - +
68B GLU* 1.3 62.7 + - - +
70B ALA* 3.2 2.3 + - - +
71B VAL* 3.0 32.6 + - + +
76B ILE* 3.8 17.7 - - + -
79B PHE* 3.4 56.3 - + + -
90B LEU* 4.5 9.9 - - + -
93B LEU* 4.1 23.8 - - + -
94B ILE* 4.5 10.8 - - + -
97B LEU* 4.1 17.9 - - + -
99B ILE* 3.8 23.1 - - + -
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Residues in contact with GLU 68 (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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64B GLN* 2.9 52.1 + - - +
65B ARG* 4.1 7.1 - - - +
67B PHE* 1.3 76.2 - - + +
69B GLU* 1.3 57.1 + - - +
71B VAL* 3.3 7.3 + - - +
72B ASP* 2.9 35.9 + - - +
93B LEU* 4.0 24.1 - - + +
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Residues in contact with GLU 69 (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 ARG* 5.9 5.4 - - - +
65B ARG* 3.2 20.1 + - + +
66B PHE* 3.7 6.7 - - + +
68B GLU* 1.3 76.6 - - - +
70B ALA* 1.3 59.1 + - - +
72B ASP* 4.5 7.3 - - - +
73B ARG* 3.0 60.2 + - + +
74B PHE* 5.9 2.7 - - + -
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Residues in contact with ALA 70 (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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11B PHE* 3.9 35.2 - - + -
52B VAL* 5.8 0.7 - - + -
66B PHE 3.2 15.8 + - - +
67B PHE 3.2 4.0 + - - +
69B GLU* 1.3 77.1 - - + +
71B VAL* 1.3 65.7 + - - +
74B PHE* 3.2 37.5 + - + +
75B LYS 3.4 2.8 + - - -
76B ILE* 3.8 13.9 + - + +
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Residues in contact with VAL 71 (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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67B PHE* 3.0 46.9 + - + +
68B GLU* 3.7 9.0 - - - +
70B ALA* 1.3 77.1 - - - +
72B ASP* 1.3 71.3 + - - +
75B LYS* 3.0 27.5 + - - +
76B ILE* 4.1 15.3 - - + +
97B LEU* 4.1 28.3 - - + -
99B ILE* 5.0 2.2 - - + -
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Residues in contact with ASP 72 (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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68B GLU* 2.9 22.3 + - - +
69B GLU* 4.2 10.1 - - - +
71B VAL* 1.3 85.0 - - - +
73B ARG* 1.3 61.5 + - + +
75B LYS* 3.4 18.5 + - - +
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Residues in contact with ARG 73 (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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69B GLU* 3.0 41.3 + - - +
72B ASP* 1.3 79.4 - - + +
74B PHE* 1.3 97.3 + - + +
75B LYS* 3.7 5.2 - - - +
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Residues in contact with PHE 74 (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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7B GLN* 4.4 13.0 - - - -
9B THR* 3.5 39.8 + - + -
50B ASN* 3.8 19.7 - - - -
52B VAL* 4.1 20.2 - - + -
69B GLU* 5.4 3.1 - - + -
70B ALA* 3.2 28.7 + - + +
73B ARG* 1.3 119.3 - - + +
75B LYS* 1.3 76.2 + - - +
76B ILE* 3.2 3.4 + - + +
77B PRO* 5.5 0.2 - - - +
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Residues in contact with LYS 75 (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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70B ALA 3.4 0.6 + - - -
71B VAL* 3.0 21.4 + - - +
72B ASP* 3.4 24.0 + - - +
73B ARG 4.1 6.1 - - - +
74B PHE* 1.3 81.2 - - - +
76B ILE* 1.3 65.7 + - - +
77B PRO* 3.6 5.9 - - - +
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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