Contacts of the helix formed by residues 61 - 73 (chain B) in PDB entry 3KTC
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 THR 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B PHE* 4.3 3.4 - - - -
59B GLY 4.0 9.9 - - - +
60B VAL* 1.3 75.5 - - - +
62B LEU* 1.3 66.1 + - - +
63B SER* 3.6 9.4 + - - -
64B GLU* 3.0 36.0 + - - +
65B VAL* 3.0 23.7 + - - +
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Residues in contact with LEU 62 (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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56B PHE* 3.9 30.8 - - + -
61B THR* 1.3 74.0 - - - +
63B SER* 1.3 57.3 + - - +
65B VAL* 3.2 4.1 + - + +
66B LYS* 2.9 42.1 + - - +
114B ILE* 4.3 20.6 - - + -
117B GLU* 3.9 32.1 - - + -
118B LEU* 4.0 29.6 - - + -
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Residues in contact with SER 63 (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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61B THR* 3.2 8.6 + - - -
62B LEU* 1.3 80.7 - - - +
64B GLU* 1.3 61.8 + - - +
66B LYS* 3.5 13.2 + - - +
67B ASP* 3.1 31.6 + - - -
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Residues in contact with GLU 64 (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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35B ILE* 3.6 15.8 - - + +
59B GLY 3.6 6.0 - - - +
60B VAL* 3.4 13.3 - - - +
61B THR* 3.0 42.4 + - - +
63B SER* 1.3 74.7 - - - +
65B VAL* 1.3 60.2 + - - +
67B ASP* 3.4 7.9 + - - +
68B ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 65 (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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34B THR* 3.9 11.2 - - + -
35B ILE* 3.9 6.7 - - + -
38B ILE* 4.2 2.0 - - + -
52B LEU* 3.7 28.3 - - + -
56B PHE* 3.8 29.2 - - + -
60B VAL* 3.5 21.3 - - + -
61B THR 3.0 16.8 + - - +
62B LEU* 3.2 9.6 + - - +
64B GLU* 1.3 74.5 - - - +
66B LYS* 1.3 59.7 + - - +
68B ALA* 3.2 1.6 + - - +
69B LEU* 2.8 42.1 + - + +
118B LEU* 4.5 7.4 - - + -
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Residues in contact with LYS 66 (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 LEU* 2.9 37.7 + - + +
63B SER* 3.7 12.0 + - - +
64B GLU 3.4 0.2 - - - -
65B VAL* 1.3 76.3 - - - +
67B ASP* 1.3 65.5 + - - +
69B LEU* 3.5 8.0 + - - +
70B LYS* 3.0 25.4 + - - +
117B GLU* 3.0 36.9 + - - -
118B LEU* 3.5 25.8 - - + -
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Residues in contact with ASP 67 (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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63B SER* 3.1 25.0 + - - +
64B GLU* 3.7 7.5 - - - +
65B VAL 3.2 0.2 - - - -
66B LYS* 1.3 78.2 - - - +
68B ALA* 1.3 58.1 + - - +
70B LYS* 3.4 16.9 + - - +
71B ASP* 3.0 40.0 + - - +
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Residues in contact with ALA 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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35B ILE* 3.8 30.7 - - + -
38B ILE* 3.4 17.7 - - + +
39B ASN* 4.7 8.0 - - - +
64B GLU 2.9 18.3 + - - +
65B VAL 3.8 2.9 - - - +
67B ASP* 1.3 74.3 - - - +
69B LEU* 1.3 60.7 + - - +
71B ASP* 3.4 5.4 + - - +
72B ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 69 (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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38B ILE* 3.9 23.5 - - + +
50B VAL* 3.7 29.4 - - + -
52B LEU* 4.4 12.8 - - + -
65B VAL* 2.8 36.4 + - + +
66B LYS* 3.8 4.5 - - - +
68B ALA* 1.3 75.9 - - - +
70B LYS* 1.3 63.8 + - - +
72B ALA* 3.2 1.7 + - - -
73B GLY 3.1 4.3 + - - -
74B LEU* 3.0 50.8 + - + +
75B LYS* 4.9 1.1 - - - -
76B ALA* 4.5 11.2 - - + +
118B LEU* 4.5 16.8 - - + -
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Residues in contact with LYS 70 (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 LYS 3.0 17.9 + - - +
67B ASP* 3.6 16.8 - - - +
69B LEU* 1.3 75.4 - - - +
71B ASP* 1.3 79.4 + - - +
73B GLY* 3.2 13.4 + - - -
74B LEU 4.7 2.0 - - - +
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Residues in contact with ASP 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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39B ASN* 6.2 0.2 - - - +
42B LYS* 3.5 23.7 + - - +
67B ASP* 3.0 25.0 + - - +
68B ALA* 4.0 5.2 - - - +
70B LYS* 1.3 98.9 + - - +
72B ALA* 1.3 57.3 + - - +
73B GLY 3.6 0.3 + - - -
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Residues in contact with ALA 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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38B ILE* 3.7 20.4 - - + +
39B ASN* 5.3 1.8 - - - +
42B LYS* 3.8 37.9 - - + +
47B LEU 5.2 1.0 - - - +
68B ALA 2.9 18.5 + - - +
69B LEU 3.2 2.9 + - - +
71B ASP* 1.3 75.6 - - - +
73B GLY* 1.3 61.7 + - - +
74B LEU* 3.6 21.2 + - + +
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Residues in contact with GLY 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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47B LEU 3.8 9.2 - - - +
48B SER* 3.9 6.8 - - - +
69B LEU 3.1 3.8 + - - -
70B LYS 3.2 10.9 + - - -
71B ASP 3.3 1.8 + - - -
72B ALA* 1.3 78.3 - - - +
74B LEU* 1.3 64.5 + - - +
345B EDO 4.8 3.5 + - - -
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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