Contacts of the helix formed by residues 57 - 68 (chain B) in PDB entry 2LUC
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 PRO 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 5.3 2.6 - - + +
44B ASN* 4.8 9.9 - - - +
51B THR* 5.1 4.3 - - + -
56B ASP* 1.3 84.0 - - + +
58B GLY* 1.3 60.0 + - - +
59B VAL* 3.0 6.7 - - + -
60B LEU* 3.0 40.7 + - + +
61B ASP* 3.7 2.4 + - - +
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Residues in contact with GLY 58 (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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56B ASP* 2.9 19.1 + - - -
57B PRO* 1.3 79.7 - - - +
59B VAL* 1.3 57.4 + - - +
60B LEU 3.3 0.2 - - - -
61B ASP* 3.0 28.6 - - - +
62B ARG* 3.2 15.2 - - - +
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Residues in contact with VAL 59 (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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50B PHE* 4.4 11.2 - - + -
51B THR* 4.6 7.6 - - + +
54B GLN* 3.8 36.1 - - + +
56B ASP* 3.0 23.5 + - - +
57B PRO* 4.3 0.7 - - + -
58B GLY* 1.3 74.9 - - - +
60B LEU* 1.3 75.8 + - + +
61B ASP 2.9 4.7 - - - -
62B ARG* 2.8 19.6 + - + +
63B MET* 2.8 48.7 + - + +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.1 4.1 - - + -
40B LEU* 3.6 37.5 - - + +
43B MET* 3.3 34.3 - - + -
44B ASN* 3.1 32.5 - - - +
51B THR* 3.3 27.4 - - + +
57B PRO* 3.0 21.5 + - + +
59B VAL* 1.3 84.9 - - + +
61B ASP* 1.3 57.8 + - - +
63B MET* 3.6 7.4 - - - +
64B MET* 2.9 30.3 + - - +
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Residues in contact with ASP 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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36B LYS* 2.7 38.0 + - - +
40B LEU* 5.0 0.6 - - + +
57B PRO 3.7 1.9 + - - +
58B GLY* 3.0 23.2 + - - +
60B LEU* 1.3 79.6 - - - +
62B ARG* 1.3 63.0 + - - +
64B MET* 3.7 1.0 - - - +
65B LYS* 3.2 32.6 + - - +
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Residues in contact with ARG 62 (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 GLN* 5.8 3.8 - - - +
58B GLY 3.2 17.7 - - - +
59B VAL* 2.8 19.2 + - + +
61B ASP* 1.3 78.8 - - + +
63B MET* 1.3 65.8 + - - +
65B LYS* 3.6 2.7 + - - +
66B LYS* 3.0 26.5 + - - +
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Residues in contact with MET 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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39B PHE* 3.8 12.8 - - + -
43B MET* 3.8 11.7 - - + -
50B PHE* 3.9 25.1 - - + -
59B VAL* 2.8 37.5 + - + +
60B LEU* 3.6 13.9 - - - +
62B ARG* 1.3 74.5 - - - +
64B MET* 1.3 67.0 + - - +
66B LYS* 3.0 27.5 + - - +
67B LEU* 2.9 35.0 + - + +
83B LEU* 3.6 26.0 - - + +
86B GLY* 6.4 1.6 - - - -
87B LEU* 5.2 4.0 - - + +
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Residues in contact with MET 64 (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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34B LEU 3.4 23.6 - - - +
36B LYS* 3.7 36.1 - - + -
39B PHE* 3.6 30.9 - - + -
60B LEU 2.9 17.5 + - - +
61B ASP 3.7 4.9 - - - +
63B MET* 1.3 76.7 - - - +
65B LYS* 1.3 67.1 + - + +
68B ASP* 2.6 40.2 + - + +
73B GLY* 3.6 23.8 - - - +
74B GLN 3.7 0.7 - - - -
75B LEU* 3.6 28.7 - - + +
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Residues in contact with LYS 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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36B LYS* 5.7 4.0 - - + +
61B ASP* 3.2 29.4 + - - +
62B ARG* 4.4 2.9 - - - +
64B MET* 1.3 89.4 - - + +
66B LYS* 1.3 60.8 + - - +
68B ASP* 2.7 39.1 + - - +
71B SER* 4.9 4.4 - - - +
72B ASP 5.4 0.4 - - - -
73B GLY* 4.5 9.8 - - - +
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Residues in contact with LYS 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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62B ARG 3.0 16.8 + - - +
63B MET* 3.0 28.0 + - - +
65B LYS* 1.3 81.2 - - - +
67B LEU* 1.3 80.7 + - + +
68B ASP 3.5 1.8 - - - -
69B THR* 4.8 3.6 + - - -
86B GLY* 5.8 5.5 - - - -
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Residues in contact with LEU 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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39B PHE* 4.1 1.6 - - + -
63B MET* 2.9 26.5 + - + +
66B LYS* 1.3 97.5 - - + +
68B ASP* 1.3 54.2 + - - +
69B THR* 2.6 24.1 + - - -
75B LEU* 3.3 28.9 - - + -
79B GLU* 3.2 24.9 - - - +
82B ASN* 3.8 15.9 + - + +
83B LEU* 3.3 58.8 - - + +
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Residues in contact with ASP 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 MET* 2.6 29.7 + - - +
65B LYS* 2.7 41.1 + - - +
66B LYS 3.5 1.5 - - - -
67B LEU* 1.3 66.7 - - - +
69B THR* 1.3 60.3 + - - +
70B ASN 3.2 1.1 - - - -
71B SER* 3.1 22.6 + - - -
72B ASP 2.7 10.0 + - - -
73B GLY* 2.7 29.3 + - - -
74B GLN 3.2 14.3 - - - +
75B LEU* 3.2 5.3 - - + +
79B GLU* 3.2 5.8 - - - -
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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