Contacts of the helix formed by residues 66 - 75 (chain B) in PDB entry 3KYB
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B THR* 3.0 22.1 + - - +
65B ASP* 1.3 75.7 - - - +
67B GLU* 1.3 64.2 + - - +
68B THR* 3.2 15.5 + - - -
69B VAL* 3.0 36.5 + - + +
70B TRP 3.1 17.2 + - - -
190B PHE* 4.6 0.2 - - - -
353B ASP* 5.1 1.3 - - - +
357B ALA* 4.2 13.1 - - + +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP 3.5 4.2 + - - +
66B ASN* 1.3 73.6 + - - +
68B THR* 1.3 54.2 + - - +
70B TRP* 3.1 4.7 + - + -
71B ASN* 2.7 58.6 + - - +
189B LYS* 4.9 7.5 + - - -
190B PHE* 3.5 36.1 - - + -
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Residues in contact with THR 68 (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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66B ASN* 3.2 11.8 + - - -
67B GLU* 1.3 79.2 - - - +
69B VAL* 1.3 56.8 + - + +
71B ASN* 3.5 8.3 + - - +
72B TYR* 3.0 27.5 + - + +
360B LEU* 5.0 13.9 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.8 26.9 - - + -
64B THR* 4.6 0.9 - - - +
66B ASN* 3.0 36.2 + - + +
68B THR* 1.3 73.6 - - + +
70B TRP* 1.3 66.4 + - - +
72B TYR* 3.0 15.8 + - - +
73B ILE* 3.0 14.2 + - - +
353B ASP* 3.9 20.6 - - + +
356B ILE* 4.2 13.0 - - + -
357B ALA* 3.8 29.8 - - + +
360B LEU* 4.6 8.7 - - + -
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Residues in contact with TRP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.0 17.9 - + - -
64B THR* 4.2 4.8 - - + +
66B ASN 3.1 11.9 + - - +
67B GLU* 3.4 14.1 - - + +
69B VAL* 1.3 73.7 - - - +
71B ASN* 1.3 75.6 + - - +
72B TYR 3.1 0.2 + - - -
73B ILE* 3.2 24.9 - - + +
74B ASN* 2.9 47.4 + - - +
79B MET* 3.8 30.7 - - + -
80B MET 6.2 0.4 - - - -
190B PHE* 3.5 50.7 - + + -
191B GLN 4.0 29.6 - - - -
192B GLY* 4.1 2.0 - - - -
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Residues in contact with ASN 71 (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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67B GLU* 2.7 46.5 + - - +
68B THR* 3.9 7.5 - - - +
70B TRP* 1.3 81.8 - - - +
72B TYR* 1.3 63.4 + - - +
74B ASN* 3.4 8.4 + - - +
75B LYS* 3.3 37.5 + - - +
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Residues in contact with TYR 72 (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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17B VAL* 3.8 27.1 - - + +
20B ARG* 4.7 7.1 - - + +
21B GLN* 4.1 11.5 + - - -
68B THR* 3.0 18.9 + - + +
69B VAL* 3.0 9.6 + - - +
71B ASN* 1.3 77.6 - - - +
73B ILE* 1.3 74.5 + - + +
75B LYS* 3.1 31.9 + - + +
76B HIS* 3.4 29.2 + + - -
201B MET* 5.1 0.2 - - + -
205B ILE* 3.5 35.7 - - + +
356B ILE* 4.1 10.1 - - + -
360B LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 73 (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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62B PHE* 3.7 31.4 - - + -
69B VAL 3.0 10.6 + - - +
70B TRP* 3.2 21.5 - - + +
72B TYR* 1.3 80.4 - - + +
74B ASN* 1.3 56.2 + - - +
75B LYS 3.0 0.4 - - - -
76B HIS* 2.6 26.6 + - - +
77B ALA* 3.0 15.0 + - - +
79B MET* 3.7 33.7 - - + -
201B MET* 2.8 37.9 - - + -
356B ILE* 3.6 23.1 - - + -
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TRP* 2.9 61.8 + - - +
71B ASN* 3.7 9.8 + - - +
72B TYR 3.2 0.2 - - - -
73B ILE* 1.3 76.8 - - - +
75B LYS* 1.4 58.6 + - - +
76B HIS 3.2 0.2 - - - -
77B ALA 3.0 16.6 - - - +
78B GLU* 4.6 0.5 - - - -
79B MET* 3.3 33.4 + - - +
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Residues in contact with LYS 75 (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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71B ASN* 3.3 27.3 + - - +
72B TYR* 3.1 22.6 + - + +
73B ILE 3.0 1.2 - - - -
74B ASN* 1.4 77.2 - - - +
76B HIS* 1.3 76.5 + - + +
77B ALA 3.6 0.4 - - - -
204B SER* 4.5 1.0 + - - -
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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