Contacts of the helix formed by residues 68 - 76 (chain D) in PDB entry 3KWO
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 CYS 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D ILE* 3.7 1.8 - - - +
67D THR* 1.3 81.0 + - - +
69D GLN* 1.3 66.4 + - - +
70D LYS* 3.4 26.0 - - - -
71D VAL* 3.1 22.8 + - + +
72D LEU* 3.0 24.8 + - - +
155D ACY 3.4 3.8 - - - -
156D ACY 3.8 3.1 - - - -
164D ZN 2.4 32.5 - - - -
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Residues in contact with GLN 69 (chain D).
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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15D HIS* 5.4 10.8 - - + +
67D THR 4.0 1.0 + - - -
68D CYS* 1.3 71.6 - - - +
70D LYS* 1.3 58.1 + - - +
72D LEU* 3.2 16.3 + - + +
73D MSE 2.9 29.5 + - - +
155D ACY 2.7 27.8 + - + +
156D ACY 3.6 18.3 - - - +
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Residues in contact with LYS 70 (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 CYS* 3.1 15.7 - - - -
69D GLN* 1.3 80.9 - - - +
71D VAL* 1.3 59.0 + - + +
73D MSE 3.2 16.7 + - + +
74D GLU* 3.0 60.3 + - + +
156D ACY 4.1 18.8 + - + +
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Residues in contact with VAL 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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66D ILE* 3.7 25.4 - - + -
68D CYS* 3.1 26.4 + - + +
70D LYS* 1.3 74.8 - - + +
72D LEU* 1.3 64.7 + - - +
74D GLU* 3.3 11.8 + - - +
75D ASN* 3.0 45.5 + - - +
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Residues in contact with LEU 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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11D GLN* 4.4 2.5 - - - +
12D ALA* 3.8 30.5 - - - +
15D HIS* 3.7 42.1 + - + +
51D PHE* 4.0 27.1 - - + -
66D ILE* 3.5 28.5 - - + +
67D THR* 5.6 1.3 - - - -
68D CYS 3.0 20.3 + - - +
69D GLN* 3.2 15.0 + - + +
71D VAL* 1.3 75.5 - - - +
73D MSE 1.3 62.9 + - - +
76D ALA* 3.2 23.7 + - - +
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Residues in contact with MSE 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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15D HIS* 5.3 5.1 + - + -
69D GLN 2.9 17.0 + - - +
70D LYS* 3.6 16.6 - - + +
71D VAL 3.2 0.4 - - - -
72D LEU* 1.3 78.6 - - - +
74D GLU* 1.3 83.3 + - + +
75D ASN 3.2 0.9 + - - -
76D ALA* 3.4 16.3 + - - +
80D LYS* 4.6 13.5 + - - +
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Residues in contact with GLU 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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70D LYS* 3.0 53.5 + - - +
71D VAL* 3.9 14.2 - - - +
73D MSE 1.3 89.9 - - + +
75D ASN* 1.3 69.8 + - - +
76D ALA 4.4 2.9 - - - +
77D LYS* 4.9 2.3 + - - -
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Residues in contact with ASN 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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8D LEU* 5.6 2.8 + - - +
9D GLN* 3.0 15.3 + - - +
12D ALA* 3.9 15.3 - - + -
66D ILE* 4.2 10.1 - - - +
71D VAL* 3.0 38.9 + - - +
74D GLU* 1.3 87.6 - - - +
76D ALA* 1.3 63.8 + - - +
77D LYS* 2.9 30.1 + - - +
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Residues in contact with ALA 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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12D ALA* 4.0 6.7 - - - +
13D ASP* 3.5 7.0 - - - -
16D HIS* 3.8 38.8 - - + +
72D LEU 3.2 12.4 + - - +
73D MSE 3.4 16.2 + - - +
74D GLU 4.4 3.6 - - - +
75D ASN* 1.3 78.2 - - - +
77D LYS* 1.3 63.2 + - - +
78D SER 3.9 0.7 - - - -
80D LYS* 4.7 13.1 + - - +
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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