Contacts of the helix formed by residues 42 - 55 (chain B) in PDB entry 6CDS
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS 4.5 4.7 - - - +
41B TRP* 1.3 77.2 - - - +
43B GLY* 1.3 66.5 + - - +
44B LYS* 3.1 5.2 - - + +
45B ASP* 2.9 25.9 + - - +
46B LEU 3.4 8.7 + - - -
77B MET 3.3 11.9 - - - +
78B ASP* 3.4 28.6 + - - +
79B LYS 3.2 13.5 - - - +
80B LYS* 3.9 6.1 - - + +
81B VAL* 3.7 7.6 - - - +
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Residues in contact with GLY 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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42B LYS* 1.3 72.4 - - - +
44B LYS* 1.3 55.0 + - - +
46B LEU* 3.6 2.6 + - - +
47B PHE* 2.9 31.0 + - - +
75B LEU* 3.8 24.1 - - - +
76B LYS 3.6 16.6 - - - -
77B MET* 3.3 9.9 + - - +
79B LYS 2.8 13.5 + - - -
81B VAL* 4.1 3.5 - - - +
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 3.1 5.3 - - + -
43B GLY* 1.3 77.3 - - - +
45B ASP* 1.3 58.3 + - - +
47B PHE* 5.8 0.2 - - + -
48B ASP* 2.8 66.4 + - - +
77B MET* 3.1 38.1 + - + +
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Residues in contact with ASP 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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41B TRP* 3.4 44.7 + - + -
42B LYS* 2.9 34.2 + - - +
44B LYS* 1.3 77.9 - - - +
46B LEU* 1.3 63.4 + - - +
48B ASP* 3.9 5.0 - - - +
49B LEU* 3.1 23.4 + - - +
52B ARG* 5.0 2.1 + - - -
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Residues in contact with LEU 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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24B VAL* 4.0 17.0 - - + -
26B ILE* 4.5 4.9 - - + -
35B PHE* 4.9 5.2 - - + -
37B CYS* 4.5 18.4 - - + -
41B TRP* 4.1 6.4 - - + -
42B LYS 3.4 2.2 + - - -
43B GLY 3.9 5.8 - - - +
44B LYS 3.4 0.2 - - - -
45B ASP* 1.3 75.6 - - - +
47B PHE* 1.3 66.6 + - - +
49B LEU* 3.3 16.5 + - + +
50B VAL* 3.1 38.3 + - + +
64B LEU* 4.1 7.4 - - + -
75B LEU* 4.1 8.1 - - + -
81B VAL* 3.9 26.5 - - + -
94B PHE* 3.5 37.5 - - + -
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Residues in contact with PHE 47 (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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43B GLY 2.9 19.9 + - - +
44B LYS* 3.7 3.4 - - + +
46B LEU* 1.3 76.6 - - - +
48B ASP* 1.3 69.4 + - - +
50B VAL* 3.2 5.7 + - - +
51B CYS* 3.0 44.0 + - - -
59B THR* 3.5 24.5 - - + -
62B PHE* 3.5 30.1 - - + -
63B GLY* 3.9 6.3 - - - -
64B LEU* 3.7 24.4 - - + +
77B MET* 3.8 22.7 - - + -
96B PHE* 3.5 26.0 - + - -
500B PIO 3.4 20.2 - - - -
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Residues in contact with ASP 48 (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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44B LYS* 2.8 64.1 + - - +
45B ASP* 3.9 4.6 - - - +
47B PHE* 1.3 85.1 - - - +
49B LEU* 1.4 51.7 + - - +
51B CYS* 3.7 6.8 - - - +
52B ARG* 2.8 54.9 + - + +
59B THR* 5.9 1.2 - - - +
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Residues in contact with LEU 49 (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 PHE* 3.5 40.4 - - + -
36B ASN 4.7 2.9 - - - +
41B TRP* 3.8 29.6 - - + -
45B ASP 3.1 14.6 + - - +
46B LEU* 3.3 12.5 + - + +
48B ASP* 1.4 71.0 - - - +
50B VAL* 1.3 57.7 + - - +
52B ARG* 3.4 28.4 + - + +
53B THR* 2.7 44.1 + - - +
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Residues in contact with VAL 50 (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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26B ILE* 3.9 31.4 - - + -
28B THR* 5.3 0.4 - - + -
33B MET* 5.6 1.1 - - - -
35B PHE* 3.9 29.2 - - + -
46B LEU* 3.1 21.0 + - + +
47B PHE* 3.2 7.8 + - - +
49B LEU* 1.3 75.5 - - + +
51B CYS* 1.3 62.5 + - - +
53B THR* 3.3 3.5 + - - -
54B LEU* 3.0 40.3 + - + +
64B LEU* 4.5 5.6 - - + -
96B PHE* 3.5 31.0 - - + -
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Residues in contact with CYS 51 (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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47B PHE* 3.0 47.2 + - - +
48B ASP* 3.7 7.4 - - - +
50B VAL* 1.3 76.5 - - - +
52B ARG* 1.4 61.4 + - + +
54B LEU* 3.3 3.9 + - - -
55B GLY 3.0 3.5 + - - -
56B LEU* 2.9 49.1 + - - +
59B THR* 3.5 26.9 - - + -
96B PHE* 3.9 13.9 - - - -
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Residues in contact with ARG 52 (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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41B TRP* 5.7 4.6 - - - -
45B ASP 5.0 1.2 + - - -
48B ASP* 2.8 45.7 + - + +
49B LEU* 3.7 34.6 - - + +
51B CYS* 1.4 70.3 - - + +
53B THR* 1.3 63.6 + - - +
55B GLY* 3.0 15.5 + - - -
56B LEU 5.2 0.2 - - - -
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Residues in contact with THR 53 (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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33B MET* 4.3 13.0 - - - -
35B PHE* 3.2 33.9 - - + -
49B LEU* 2.7 26.3 + - - +
50B VAL 3.5 4.7 - - - -
52B ARG* 1.3 75.9 - - - +
54B LEU* 1.4 61.5 + - + +
55B GLY 3.4 0.9 + - - -
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Residues in contact with LEU 54 (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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28B THR* 4.3 11.7 - - + +
30B ASP* 6.1 1.6 - - + +
33B MET* 4.2 26.0 - - + -
50B VAL* 3.0 34.6 + - + +
51B CYS* 3.8 4.5 - - - +
53B THR* 1.4 76.4 - - + +
55B GLY* 1.3 61.1 + - - +
56B LEU* 3.5 9.8 + - + -
96B PHE* 3.7 35.4 - - + -
113B ILE* 3.8 29.2 - - + +
117B LEU* 4.5 9.0 - - + -
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Residues in contact with GLY 55 (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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51B CYS 3.0 0.4 + - - -
52B ARG* 3.0 16.9 + - - -
53B THR 3.2 1.4 + - - -
54B LEU* 1.3 77.9 - - - +
56B LEU* 1.4 57.2 + - - +
57B ARG* 4.0 4.4 + - - +
111B GLN* 3.1 21.1 + - - -
113B ILE* 3.8 4.5 - - - +
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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