Contacts of the helix formed by residues 36 - 46 (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 LYS 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B SER* 1.3 80.1 + - - +
37B THR* 1.3 59.7 + - - +
39B PHE* 3.0 1.7 + - - +
40B LEU* 2.8 53.0 + - + +
61B ASP* 2.7 46.8 + - - +
64B MET* 3.7 31.9 - - + -
65B LYS* 5.7 4.9 - - + +
73B GLY* 3.4 12.5 + - - +
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Residues in contact with THR 37 (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 SER* 3.4 0.6 + - - -
36B LYS* 1.3 80.8 - - - +
38B GLU* 1.3 72.0 + - - +
40B LEU* 3.4 16.5 - - + +
41B SER* 2.9 41.1 + - - +
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Residues in contact with GLU 38 (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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24B TYR* 3.3 30.4 - - + +
27B LYS* 3.7 23.7 - - + +
28B ASP* 4.0 14.3 - - + +
34B LEU* 3.3 14.8 - - + +
35B SER* 3.0 34.9 + - - +
37B THR* 1.3 92.4 - - - +
39B PHE* 1.3 58.5 + - - +
41B SER* 3.6 3.5 + - - -
42B PHE* 2.8 28.1 + - - +
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Residues in contact with PHE 39 (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 22.8 - - + +
35B SER 2.7 16.5 + - - +
36B LYS 3.4 4.0 - - - +
38B GLU* 1.3 74.3 - - - +
40B LEU* 1.3 59.0 + - + +
42B PHE* 3.7 8.5 - + - -
43B MET* 2.7 72.0 + - + +
60B LEU* 4.1 11.7 - - + -
63B MET* 3.8 14.8 - - + -
64B MET* 3.6 26.5 - - + -
67B LEU* 4.1 0.9 - - + -
75B LEU* 3.4 25.8 - - + -
80B PHE* 4.5 3.8 - + - -
83B LEU* 3.5 33.4 - - + -
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Residues in contact with LEU 40 (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* 2.8 57.6 + - + +
37B THR* 3.4 21.3 - - + +
39B PHE* 1.3 80.3 - - + +
41B SER* 1.3 61.3 + - - +
44B ASN* 2.7 36.2 + - - +
57B PRO* 5.3 2.2 - - + +
60B LEU* 3.6 34.8 - - + +
61B ASP 5.0 0.4 - - - +
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Residues in contact with SER 41 (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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24B TYR* 3.9 13.9 - - - -
27B LYS* 5.3 3.6 - - - -
37B THR* 2.9 24.3 + - - +
38B GLU* 3.8 5.2 + - - -
40B LEU* 1.3 74.0 - - - +
42B PHE* 1.3 59.0 + - - +
44B ASN* 3.3 4.8 + - - +
45B THR* 2.6 39.9 + - - +
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Residues in contact with PHE 42 (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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10A THR* 3.7 11.9 - - + -
20B VAL* 3.5 31.9 - - + -
24B TYR* 3.3 33.1 - + + -
34B LEU* 4.2 6.5 - - + -
38B GLU 2.8 19.9 + - - +
39B PHE* 3.4 23.8 - + - +
41B SER* 1.3 74.9 - - - +
43B MET* 1.3 62.8 + - - +
45B THR* 2.9 5.5 + - - -
46B GLU* 2.6 48.1 + - + +
47B LEU* 3.6 25.4 - - + -
80B PHE* 3.2 35.4 - + - -
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Residues in contact with MET 43 (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* 2.7 64.0 + - + +
42B PHE* 1.3 74.6 - - + +
44B ASN* 1.3 57.5 + - - +
47B LEU* 2.8 51.1 - - + -
50B PHE* 3.9 21.5 - - + -
51B THR* 2.7 33.1 + - - +
60B LEU* 3.3 27.1 - - + -
63B MET* 3.8 22.9 - - + -
83B LEU* 4.6 1.1 - - + -
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Residues in contact with ASN 44 (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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40B LEU* 2.7 33.7 + - - +
41B SER* 3.9 5.1 - - - +
43B MET* 1.3 76.2 - - - +
45B THR* 1.3 60.7 + - + +
48B ALA* 3.0 19.5 - - - +
51B THR* 3.4 16.1 - - - +
52B LYS* 2.8 36.0 + - - +
57B PRO* 4.8 10.3 - - - +
60B LEU* 3.1 18.8 - - - +
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Residues in contact with THR 45 (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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3A LYS* 5.7 1.2 + - - -
8A THR* 3.7 9.7 - - - +
24B TYR* 2.7 26.2 + - - +
41B SER* 2.6 25.4 + - - +
42B PHE 2.9 2.9 + - - -
44B ASN* 1.3 82.7 - - + +
46B GLU* 1.3 75.4 + - - +
47B LEU 3.2 1.8 + - - -
48B ALA* 3.6 11.5 + - - +
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Residues in contact with GLU 46 (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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8A THR* 2.5 43.0 + - - +
9A GLU* 4.8 2.3 + - - +
10A THR* 3.8 16.2 - - + -
11A GLU* 3.2 2.3 - - - -
20B VAL* 4.1 9.4 - - - +
23B LYS* 2.7 32.0 + - - -
24B TYR* 3.5 27.5 + - + -
42B PHE* 2.6 29.4 + - + +
45B THR* 1.3 85.8 + - - +
47B LEU* 1.3 65.9 + - - +
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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