Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 2CUJ
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LYS 5.2 1.2 + - - -
41A LEU* 1.3 83.1 - - - +
43A GLU* 1.3 70.5 + - + +
44A LYS* 3.1 7.1 + - + +
45A GLU* 3.1 22.8 + - - +
46A LYS* 2.9 30.1 + - - +
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Residues in contact with GLU 43 (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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42A ASN* 1.3 79.2 - - + +
44A LYS* 1.3 98.5 + - + +
46A LYS* 3.7 19.9 - - - +
47A GLU* 3.0 27.4 + - - +
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Residues in contact with LYS 44 (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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42A ASN* 3.1 3.9 - - + +
43A GLU* 1.3 106.1 + - + +
45A GLU* 1.3 73.1 + - - +
47A GLU* 3.4 16.9 - - - +
48A LEU* 4.1 6.2 + - - +
98A PHE* 4.6 15.9 - - + -
102A GLU* 3.7 29.9 + - - +
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Residues in contact with GLU 45 (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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41A LEU* 2.9 40.6 - - + +
42A ASN* 3.1 27.3 + - - +
44A LYS* 1.3 86.8 + - + +
46A LYS* 1.3 55.5 + - - +
47A GLU 2.6 16.4 + - - -
48A LEU* 2.7 25.0 + - - +
49A CYS* 3.3 9.1 + - - -
59A TYR* 3.2 37.3 - - + +
98A PHE* 4.7 6.3 - - + -
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Residues in contact with LYS 46 (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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32A LEU* 3.1 40.5 - - + +
38A THR* 3.7 30.9 + - + +
41A LEU* 3.4 17.5 - - + +
42A ASN* 2.9 26.7 + - - +
43A GLU* 3.7 16.5 - - - +
45A GLU* 1.3 76.4 - - - +
47A GLU* 1.3 60.9 + - - +
49A CYS* 3.4 13.2 + - - +
50A GLN* 3.3 10.1 + - - +
56A PRO* 5.6 0.2 - - + -
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Residues in contact with GLU 47 (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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43A GLU* 3.0 15.3 + - - +
44A LYS* 3.4 14.6 - - - +
45A GLU 2.6 4.8 + - - -
46A LYS* 1.3 71.2 - - - +
48A LEU* 1.3 71.2 + - + +
50A GLN* 2.9 23.1 + - - +
51A VAL* 3.0 25.2 + - + +
101A ARG* 5.3 6.2 + - - -
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Residues in contact with LEU 48 (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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44A LYS 4.6 3.4 - - - +
45A GLU* 2.7 17.2 + - - +
47A GLU* 1.3 78.2 - - + +
49A CYS* 1.3 56.6 + - - +
51A VAL* 3.4 9.6 - - + -
52A VAL* 2.6 58.0 + - + +
54A LEU* 5.4 1.8 - - + -
59A TYR* 4.3 20.2 - - + -
94A LYS* 3.8 21.1 - - + +
95A ILE* 4.5 9.6 - - + +
98A PHE* 3.4 48.7 - - + -
101A ARG* 5.8 4.0 - - - +
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Residues in contact with CYS 49 (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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30A LEU* 3.3 6.8 - - - +
32A LEU* 3.2 23.6 - - + -
41A LEU* 4.2 11.2 - - - -
45A GLU 3.8 11.4 - - - -
46A LYS* 3.5 4.3 - - - +
47A GLU 3.2 0.4 - - - -
48A LEU* 1.3 78.9 - - - +
50A GLN* 1.3 56.6 + - - +
53A ARG* 2.9 8.1 - - - -
54A LEU* 2.7 48.9 + - - +
55A VAL 4.2 2.2 - - - -
56A PRO* 3.5 29.6 - - - -
59A TYR* 4.4 10.8 - - - -
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Residues in contact with GLN 50 (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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29A PRO* 3.5 35.3 - - + +
30A LEU 3.9 22.4 + - - +
32A LEU* 3.6 23.8 - - + +
46A LYS* 3.3 17.4 + - - +
47A GLU* 2.9 10.9 + - - +
49A CYS* 1.3 74.9 - - - +
51A VAL* 1.3 66.4 + - - +
53A ARG* 2.9 21.5 + - - +
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Residues in contact with VAL 51 (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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29A PRO* 5.8 0.2 - - - -
47A GLU* 3.0 25.3 + - + +
48A LEU* 3.4 17.9 - - + +
50A GLN* 1.3 77.3 - - - +
52A VAL* 1.3 78.2 + - + +
53A ARG* 3.4 10.6 + - - +
94A LYS* 5.2 10.5 - - + -
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Residues in contact with VAL 52 (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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48A LEU* 2.6 43.7 + - + +
51A VAL* 1.3 75.7 - - + +
53A ARG* 1.3 70.7 + - - +
54A LEU* 4.5 11.7 - - + +
90A ASN 4.9 0.4 - - - +
91A LYS* 3.6 45.0 - - + +
94A LYS* 3.2 35.2 - - + +
95A ILE* 5.1 5.6 - - + +
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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