Contacts of the helix formed by residues 55 - 66 (chain A) in PDB entry 2LMC
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 THR 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.2 2.9 - - - -
53A ALA* 4.1 1.0 - - - +
54A GLU* 1.3 79.1 - - - +
56A LEU* 1.3 70.1 + - - +
57A ASP* 4.3 9.6 - - + +
58A GLU* 2.8 29.0 + - - +
59A ALA* 2.9 23.7 + - - +
56B PRO* 4.9 15.5 - - + -
58B GLU* 4.7 4.7 - - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.4 6.1 - - + +
36A PHE* 3.6 32.8 - - + -
54A GLU 5.6 0.9 - - - +
55A THR* 1.3 75.7 - - + +
57A ASP* 1.3 59.6 + - - +
59A ALA* 2.9 7.3 + - - +
60A LEU* 2.8 26.0 + - - +
79A PRO* 3.9 16.8 - - + -
81A VAL* 4.0 20.0 - - + -
56B PRO* 3.8 20.2 - - + +
57B TYR* 4.0 6.1 - - + -
58B GLU* 3.1 48.7 - - - +
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 3.5 5.7 - - + +
56A LEU* 1.3 71.5 - - - +
58A GLU* 1.3 53.1 + - - +
60A LEU* 3.2 4.0 - - - +
61A GLU* 2.8 49.5 + - - +
45B ARG* 2.6 30.8 + - - -
47B VAL* 3.5 18.7 - - - +
58B GLU* 2.8 34.9 + - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER* 4.0 9.5 - - - -
53A ALA* 3.3 11.2 - - + +
54A GLU* 2.9 38.7 + - - +
55A THR* 2.8 38.7 + - - +
56A LEU 3.1 0.4 - - - -
57A ASP* 1.3 80.5 + - - +
59A ALA* 1.3 60.8 + - - +
61A GLU* 3.4 17.8 + - - +
62A LEU* 3.1 33.3 + - + +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.4 44.4 - - + -
51A ILE* 3.7 13.3 - - + +
53A ALA* 3.6 12.5 - - + +
55A THR 2.9 5.7 + - - +
56A LEU 2.9 8.3 + - - +
58A GLU* 1.3 73.6 - - - +
60A LEU* 1.3 57.9 + - - +
62A LEU* 3.1 1.9 + - - +
63A ALA* 2.8 37.2 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 2.8 12.2 + - - +
57A ASP* 3.2 10.5 - - - +
59A ALA* 1.3 77.9 - - - +
61A GLU* 1.3 63.7 + - - +
63A ALA* 3.7 9.3 + - - +
64A GLU* 3.7 11.4 + - - +
77A VAL* 5.7 0.2 - - + -
38B LYS* 4.8 5.8 + - - +
45B ARG* 3.4 42.8 - - + +
47B VAL* 3.8 5.8 - - + -
58B GLU* 3.6 29.4 - - + +
59B GLU* 3.5 30.7 - - - +
60B MET* 3.5 20.6 - - + +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASP* 2.8 30.4 + - - +
58A GLU* 3.5 23.4 - - - +
60A LEU* 1.3 75.0 - - - +
62A LEU* 1.3 58.4 + - + +
64A GLU* 3.4 1.6 + - - +
65A TRP* 2.7 43.2 + - + +
38B LYS* 5.0 8.9 - - - +
45B ARG* 3.7 22.2 + - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.2 31.2 - - - +
29A LEU* 4.5 3.4 - - + +
30A SER* 5.2 2.5 - - - +
51A ILE* 4.2 8.3 - - + -
52A TYR 4.0 10.1 - - - +
53A ALA* 3.8 23.6 - - + -
58A GLU* 3.1 22.4 + - + +
59A ALA* 3.1 5.3 + - - +
61A GLU* 1.3 78.2 - - + +
63A ALA* 1.3 63.7 + - - +
65A TRP* 4.6 6.1 - - + -
66A GLN* 2.7 43.3 + - + +
67A TYR* 3.8 1.5 - - + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 4.4 8.1 - - + -
51A ILE* 3.8 31.4 - - + +
59A ALA 2.8 21.4 + - - +
60A LEU* 4.0 5.4 - - - +
61A GLU 3.4 0.2 - - - -
62A LEU* 1.3 71.6 - - - +
64A GLU* 1.3 59.2 + - - +
67A TYR* 2.9 22.5 - - - +
74A VAL* 3.2 15.1 - - - +
77A VAL* 4.4 5.4 - - + -
60B MET* 3.8 16.6 - - + -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU 3.7 2.6 + - - +
61A GLU 3.4 5.2 + - - +
62A LEU 3.1 0.2 - - - -
63A ALA* 1.3 78.6 - - - +
65A TRP* 1.3 69.5 + - + +
67A TYR 3.0 2.6 + - - -
68A VAL* 2.9 38.3 + - + +
74A VAL* 4.1 4.9 - - + -
38B LYS* 2.6 46.4 + - - +
39B GLU* 3.7 3.3 - - - -
40B THR* 2.8 55.1 + - + +
43B LYS* 4.8 1.0 - - - +
60B MET* 3.7 26.4 - - + +
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Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 2.7 29.5 + - + +
62A LEU* 4.6 6.1 - - + -
64A GLU* 1.3 81.9 - - - +
66A GLN* 1.3 59.2 + - - +
68A VAL* 4.0 8.3 - - + -
69A PRO* 3.1 28.7 - - + +
38B LYS* 5.9 6.3 - - + -
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR 5.3 0.2 + - - -
27A GLY* 3.6 24.4 + - - +
28A SER* 3.4 28.2 + - - +
29A LEU* 5.7 4.0 - - + -
62A LEU* 2.7 38.2 + - + +
65A TRP* 1.3 78.2 - - - +
67A TYR* 1.3 69.7 + - + +
69A PRO* 3.4 10.7 - - - +
70A ALA* 4.4 8.1 - - - +
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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