Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 2KSO
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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B GLY 4.7 1.2 + - - +
69B VAL* 3.5 1.0 - - - -
70B GLN* 1.3 77.6 - - - +
72B PRO* 1.3 77.3 - - - +
73B ALA* 2.9 11.9 + - - +
74B HIS* 2.7 53.0 + - + +
75B LYS* 3.0 30.7 + - - +
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Residues in contact with PRO 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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70B GLN 3.5 4.2 - - - +
71B ASP* 1.3 93.9 - - - +
73B ALA* 1.3 58.7 + - + +
75B LYS* 3.4 12.9 + - + +
76B ARG* 3.0 31.2 + - - +
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Residues in contact with ALA 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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71B ASP* 2.9 12.1 + - - +
72B PRO* 1.3 81.7 - - + +
74B HIS* 1.3 61.6 + - + +
76B ARG* 3.5 6.2 + - - +
77B LEU* 2.9 31.6 + - - +
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Residues in contact with HIS 74 (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 LEU* 4.7 11.7 - - + +
41B TYR* 2.8 48.4 + + - -
69B VAL* 3.6 24.8 - - + +
71B ASP* 2.7 43.8 + - + +
72B PRO 3.3 0.2 - - - -
73B ALA* 1.3 77.5 - - + +
75B LYS* 1.3 63.6 + - - +
77B LEU* 3.2 7.6 + - - +
78B LEU* 3.1 23.2 + - - +
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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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61B GLU* 3.4 51.8 - - + +
64B LEU* 3.9 19.5 - - + -
65B GLU* 4.4 3.9 - - + +
69B VAL* 3.1 28.5 - - - +
70B GLN* 3.1 18.7 + - - +
71B ASP 3.0 16.2 + - - +
72B PRO* 3.8 12.1 - - + +
74B HIS* 1.3 75.6 - - - +
76B ARG* 1.3 63.2 + - - +
78B LEU* 3.3 2.8 + - - +
79B LEU* 3.1 30.2 + - - +
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Residues in contact with ARG 76 (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 GLU* 6.1 0.4 - - - -
72B PRO 3.0 18.0 + - - +
73B ALA* 3.7 7.4 - - - +
75B LYS* 1.3 76.4 - - - +
77B LEU* 1.3 62.6 + - + +
79B LEU* 3.4 20.2 + - - +
80B ASP* 3.1 27.2 + - + +
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Residues in contact with LEU 77 (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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36B ILE* 3.7 31.2 - - + +
38B LEU* 3.6 31.4 - - + -
73B ALA 2.9 18.4 + - - +
74B HIS* 3.4 9.0 - - - +
75B LYS 3.2 0.4 - - - -
76B ARG* 1.3 78.0 - - + +
78B LEU* 1.3 59.3 + - - +
80B ASP* 3.1 22.8 + - + +
81B THR* 2.8 18.2 + - - -
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Residues in contact with LEU 78 (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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32B TRP* 4.6 14.8 - - + -
33B LEU* 4.7 11.9 - - + -
38B LEU* 4.6 17.9 - - + +
45B LEU* 3.8 21.3 - - + -
56B LEU* 4.6 9.6 - - + -
59B ILE* 3.8 28.9 - - + -
64B LEU* 3.8 28.3 - - + -
69B VAL* 5.0 6.1 - - + -
74B HIS 3.1 11.2 + - - +
75B LYS 3.8 7.2 - - - +
77B LEU* 1.3 76.3 - - - +
79B LEU* 1.3 62.5 + - - +
81B THR* 3.1 18.6 + - - -
82B LEU* 3.2 14.6 + - + +
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Residues in contact with LEU 79 (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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59B ILE* 4.9 8.1 - - + +
60B THR* 5.6 0.2 - - - -
61B GLU* 3.7 37.9 - - + +
64B LEU* 3.9 20.6 - - + -
75B LYS 3.1 20.0 + - - +
76B ARG* 3.7 22.4 - - - +
77B LEU 3.2 0.2 - - - -
78B LEU* 1.3 78.4 - - + +
80B ASP* 1.3 62.2 + - - +
82B LEU* 3.3 36.3 + - + +
83B GLN* 3.9 9.0 + - - +
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Residues in contact with ASP 80 (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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36B ILE* 4.7 4.0 - - - +
76B ARG* 3.1 18.8 + - + +
77B LEU* 3.2 21.3 - - + +
79B LEU* 1.3 75.8 - - - +
81B THR* 1.3 61.1 + - - +
83B GLN* 3.1 8.5 + - - +
84B LEU* 2.9 44.4 + - - +
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Residues in contact with THR 81 (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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32B TRP* 3.5 30.8 - - + +
36B ILE* 3.0 45.8 - - + +
77B LEU 2.8 16.6 + - - -
78B LEU* 3.1 9.0 + - - -
80B ASP* 1.3 78.0 - - - +
82B LEU* 1.3 58.7 + - - +
84B LEU* 4.0 6.7 - - - -
85B SER* 2.9 42.6 + - - +
86B LYS 3.1 5.7 + - - -
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Residues in contact with LEU 82 (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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32B TRP* 3.6 19.3 - - + -
56B LEU 3.4 23.6 - - - +
57B SER* 3.5 26.9 - - - +
58B ASP* 5.5 0.4 - - - -
59B ILE* 4.2 27.1 - - + +
78B LEU* 3.2 11.6 + - + +
79B LEU* 3.3 31.0 - - + +
80B ASP 3.1 0.6 - - - -
81B THR* 1.3 77.3 - - - +
83B GLN* 1.3 63.8 + - + +
86B LYS* 3.1 26.3 - - - +
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Residues in contact with GLN 83 (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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79B LEU 4.3 9.0 - - - +
80B ASP* 3.1 7.6 + - - +
82B LEU* 1.3 83.5 - - + +
84B LEU* 1.3 66.0 + - - +
85B SER 3.6 0.2 - - - -
86B LYS* 4.3 11.5 + - - +
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Residues in contact with LEU 84 (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 ALA* 5.7 5.2 - - + +
36B ILE* 4.0 26.5 - - + -
80B ASP* 2.9 31.9 + - - +
81B THR* 4.0 3.6 - - - -
83B GLN* 1.3 80.6 - - - +
85B SER* 1.3 65.1 + - - +
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Residues in contact with SER 85 (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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32B TRP* 3.4 33.2 + - - -
35B ALA* 4.7 9.3 - - - +
81B THR* 2.9 25.2 + - - +
84B LEU* 1.3 82.1 - - - +
86B LYS* 1.3 73.7 + - - +
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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