Contacts of the helix formed by residues 43 - 51 (chain C) in PDB entry 1KYZ
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 ASP 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ALA 3.0 0.8 + - - -
40C LEU* 3.0 19.2 + - - +
41C GLU 3.2 2.4 - - - +
42C LEU* 1.3 81.2 - - - +
44C LEU* 1.3 63.8 + - - +
45C LEU 3.4 2.9 - - - -
46C GLU* 2.9 34.0 + - - +
47C ILE* 3.1 27.8 + - + +
50C LYS* 5.6 3.6 + - - -
117C LYS* 4.5 8.5 + - - -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 2.9 37.4 + - + +
42C LEU* 3.7 21.5 - - + +
43C ASP* 1.3 74.0 - - - +
45C LEU* 1.3 68.9 + - + +
47C ILE* 3.3 5.6 + - + +
48C ILE* 3.1 27.7 + - + +
62C ILE* 3.8 23.7 - - + +
66C LEU* 4.0 11.2 - - + -
77C LEU* 3.8 25.6 - - + -
80C MET* 4.5 9.6 - - + -
81C LEU* 3.8 31.2 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.4 7.9 - - + -
39C ALA* 4.4 3.5 + - + -
40C LEU* 3.7 28.6 - - + +
43C ASP 3.4 0.8 - - - -
44C LEU* 1.3 81.9 - - + +
46C GLU* 1.3 58.6 + - + +
48C ILE* 3.4 6.3 + - + +
49C ALA* 2.9 26.2 + - - +
81C LEU* 5.8 0.2 - - + -
84C LEU* 4.8 12.1 - - + -
89C ILE* 4.8 6.3 - - + -
90C LEU* 3.8 30.3 - - + -
108C LEU* 4.0 14.2 - - + +
112C ALA* 5.6 0.4 - - + -
115C LEU* 3.6 43.5 - - + +
116C VAL* 4.1 14.6 - - + +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ASP* 2.9 40.2 + - - +
45C LEU* 1.3 76.1 - - + +
47C ILE* 1.3 66.4 + - - +
49C ALA* 2.8 17.2 + - - +
50C LYS* 2.9 32.9 + - - +
115C LEU 4.6 1.2 - - - +
116C VAL* 2.9 20.7 - - - +
117C LYS* 2.8 53.2 + - + +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU 4.1 3.4 - - - +
43C ASP* 3.1 21.2 + - + +
44C LEU* 3.3 7.8 + - + +
46C GLU* 1.3 76.5 - - + +
48C ILE* 1.3 64.4 + - - +
50C LYS* 3.3 23.9 + - + +
51C ALA* 3.6 6.4 + - - +
57C ILE* 4.3 7.6 - - + +
62C ILE* 4.0 29.6 - - + +
65C GLN* 3.8 42.4 - - + +
66C LEU* 3.4 33.0 - - + -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU 3.1 20.0 + - - +
45C LEU* 3.7 7.0 - - + +
47C ILE* 1.3 75.7 - - - +
49C ALA* 1.3 63.0 + - - +
51C ALA* 3.2 18.1 + - + +
52C GLY 4.1 4.7 + - - +
55C ALA* 4.5 4.2 - - - +
57C ILE* 4.0 11.4 - - + -
62C ILE* 3.8 32.8 - - + -
81C LEU* 4.8 4.7 - - + -
90C LEU* 4.2 27.4 - - + -
106C TYR* 4.0 18.6 - - + +
107C GLY* 3.9 18.4 - - - -
108C LEU* 3.7 22.8 - - + +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU 2.9 14.4 + - - +
46C GLU* 2.8 19.5 + - - +
48C ILE* 1.3 77.7 - - - +
50C LYS* 1.3 60.4 + - + +
52C GLY* 2.9 18.9 + - - -
108C LEU* 3.9 16.4 - - + -
116C VAL* 4.1 19.1 - - + -
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ASP* 5.6 3.5 + - - -
46C GLU* 2.9 37.1 + - - +
47C ILE* 3.3 17.0 + - + +
49C ALA* 1.3 76.0 - - + +
51C ALA* 1.3 61.8 + - - +
52C GLY* 3.0 2.5 + - - -
65C GLN* 6.1 1.1 - - - +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE 3.6 2.2 + - - +
48C ILE 3.2 13.6 + - - +
49C ALA 3.0 1.0 + - - -
50C LYS* 1.3 78.3 - - - +
52C GLY* 1.3 57.2 + - - +
55C ALA* 3.4 23.4 - - + +
57C ILE* 3.9 32.5 - - + -
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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