Contacts of the helix formed by residues 70 - 79 (chain D) in PDB entry 1KLU
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 70 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D TRP* 3.7 16.8 - - - +
68D LEU* 3.2 2.7 - - - +
69D LEU* 1.3 99.4 - - - +
71D GLU* 1.3 64.7 + - - +
72D ASP* 3.3 13.3 + - - +
73D LEU* 2.9 39.6 + - - +
74D ALA 3.3 8.5 + - - -
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS* 3.6 58.9 + - + +
47D TRP* 4.0 3.2 - - - +
70D ASN* 1.3 71.8 - - - +
72D ASP* 1.3 62.9 + - - +
74D ALA* 3.0 4.3 + - - +
75D LYS* 2.8 61.1 + - + +
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Residues in contact with ASP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ASN* 3.3 10.9 + - - +
71D GLU* 1.3 79.1 - - - +
73D LEU* 1.3 58.9 + - + +
75D LYS* 3.2 23.7 + - - +
76D LYS* 2.8 31.5 + - - +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.7 15.0 - - + +
69D LEU* 4.0 29.8 - - + +
70D ASN* 2.9 24.4 + - - +
71D GLU 3.2 0.2 - - - -
72D ASP* 1.3 76.3 - - + +
74D ALA* 1.3 62.8 + - - +
76D LYS* 3.3 34.3 + - - +
77D TYR* 3.3 31.0 - - + -
218D ASN 4.0 4.9 - - - +
219D ASP* 3.7 25.6 - - - +
220D ASN* 4.3 7.6 - - + -
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS 3.3 26.7 - - - +
47D TRP* 3.8 20.2 - - - -
48D ASP 4.1 9.2 - - - +
49D LEU* 3.5 8.1 - - + +
68D LEU* 3.5 14.3 - - + +
70D ASN 3.3 2.0 + - - -
71D GLU 3.0 4.1 + - - +
73D LEU* 1.3 74.7 - - - +
75D LYS* 1.3 60.5 + - - +
77D TYR 3.3 1.0 + - - -
78D LYS* 2.8 33.6 + - - +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLU* 2.8 46.2 + - + +
72D ASP* 3.2 27.6 + - - +
74D ALA* 1.3 74.8 - - + +
76D LYS* 1.3 65.1 + - - +
77D TYR 3.3 0.2 + - - -
78D LYS* 3.4 21.0 + - + +
79D ASP* 4.5 2.9 + - - +
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Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ASP 2.8 12.7 + - - +
73D LEU* 3.3 35.2 - - - +
74D ALA 3.2 0.2 - - - -
75D LYS* 1.3 78.0 - - - +
77D TYR* 1.3 92.2 + - + +
79D ASP 4.8 1.2 + - - -
80D GLU* 3.8 20.3 - - - +
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Residues in contact with TYR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 5.2 0.3 + - - -
49D LEU* 3.8 16.3 - - + +
51D TYR* 4.2 7.0 + - - +
68D LEU* 4.9 1.1 - - + -
73D LEU* 3.3 21.3 - - + -
74D ALA 3.3 2.0 + - - -
76D LYS* 1.3 106.5 + - + +
78D LYS* 1.3 68.7 + - - +
79D ASP 3.2 3.1 - - - -
80D GLU* 3.1 38.1 + - - +
82D VAL* 3.9 8.0 - - + +
115D ILE* 3.4 41.5 + - + -
116D THR* 5.1 0.9 - - - -
117D LYS* 4.1 17.5 - - + -
220D ASN* 3.6 28.1 + - - -
222D THR* 5.4 3.6 - - - +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 3.5 8.7 + - - +
40D SER* 2.8 31.2 + - - +
42D ASP 6.5 0.7 - - - -
43D SER* 5.7 7.9 - - - -
49D LEU* 3.6 19.0 - - + +
74D ALA 2.8 19.2 + - - +
75D LYS* 3.4 16.0 + - + +
77D TYR* 1.3 77.7 - - - +
79D ASP* 1.3 80.5 + - - +
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 2.5 27.5 + - - +
75D LYS 4.5 3.9 + - - +
76D LYS 4.8 1.2 + - - -
77D TYR 3.2 0.6 - - - -
78D LYS* 1.3 103.8 + - - +
80D GLU* 1.3 61.9 + - - +
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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