Contacts of the helix formed by residues 78 - 89 (chain B) in PDB entry 2K42
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 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.0 0.9 - - - +
35A ARG* 2.7 37.3 + - - +
68A GLU 3.9 3.8 - - - -
69A MET* 3.8 23.7 - - - +
72A GLN* 3.8 12.9 - - - +
76B LEU* 3.9 3.1 - - - +
77B PRO* 1.3 94.2 - - + +
79B VAL* 1.3 70.3 + - - +
80B ALA* 3.0 27.5 + - - +
81B GLN* 3.2 23.2 + - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.3 23.1 - - + -
55A PHE* 3.3 30.2 - - + -
65A VAL* 3.1 33.4 - - + +
68A GLU* 3.3 39.6 + - + +
69A MET* 3.9 9.4 - - + -
72A GLN* 5.4 0.7 - - - -
78B ASP* 1.3 81.0 - - - +
80B ALA* 1.3 56.5 + - - +
81B GLN 3.2 0.2 - - - -
82B ARG* 2.9 26.6 + - + +
83B LEU 3.4 3.5 + - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.2 21.3 - - + +
35A ARG* 3.3 34.1 - - + -
36A ALA* 3.5 15.1 - - - +
76B LEU* 3.4 10.8 - - + -
78B ASP* 3.0 15.5 + - - +
79B VAL* 1.3 78.9 - - - +
81B GLN* 1.3 61.3 + - - +
83B LEU* 3.2 16.9 + - - +
84B MET* 3.5 4.3 + - - +
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 4.1 21.9 + - + +
74B HIS* 2.9 69.2 + - + +
75B MET* 4.7 1.2 - - - +
76B LEU* 2.9 36.1 + - + +
78B ASP 3.2 17.1 + - - +
80B ALA* 1.3 78.3 - - - +
82B ARG* 1.3 77.7 + - + +
83B LEU 3.1 1.4 + - - -
84B MET* 3.2 14.8 + - - +
85B GLN* 3.6 3.1 + - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.2 24.5 - - + -
59A GLN* 3.5 18.2 + - - +
68A GLU* 2.7 39.6 + - - +
71A ARG* 3.7 9.1 - - - +
72A GLN* 3.9 23.5 + - - +
74B HIS* 4.7 4.0 - - - -
79B VAL* 2.9 19.4 + - + +
81B GLN* 1.3 91.8 + - + +
83B LEU* 1.3 59.4 - - - +
85B GLN* 3.8 6.6 + - - +
86B HIS* 3.5 15.9 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 11.2 - - + -
33A PHE* 3.7 19.1 - - + -
36A ALA* 3.4 23.6 - - + -
38A ILE* 3.3 23.6 - - + -
52A ILE* 4.2 8.7 - - + -
55A PHE* 3.4 51.5 - - + -
79B VAL 3.4 0.4 + - - -
80B ALA 3.2 3.7 + - - +
81B GLN 3.0 0.8 - - - -
82B ARG* 1.3 78.0 - - - +
84B MET* 1.3 64.1 + - - +
85B GLN 3.1 1.8 - - - -
86B HIS* 3.0 12.3 + - + -
87B LEU* 3.1 45.4 + - + +
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Residues in contact with MET 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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35A ARG 3.4 20.0 - - - +
36A ALA 3.2 28.7 - - - +
37A GLY* 5.2 0.7 - - - -
73B GLY* 3.0 51.6 - - - +
74B HIS* 3.9 4.7 - - + +
76B LEU* 3.4 17.0 - - + -
80B ALA 3.7 7.2 - - - +
81B GLN* 3.2 7.8 + - - +
83B LEU* 1.3 77.2 - - - +
85B GLN* 1.3 70.0 + - - +
87B LEU* 3.9 4.6 + - - +
88B ALA* 3.2 25.3 + - - +
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Residues in contact with GLN 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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74B HIS* 3.5 49.3 + - + +
81B GLN 3.6 2.0 + - - +
82B ARG* 4.0 7.9 - - - +
83B LEU 3.1 0.4 - - - -
84B MET* 1.3 83.9 - - - +
86B HIS* 1.3 57.5 + - - +
88B ALA* 3.3 5.3 + - - +
89B GLU* 2.8 38.5 + - + +
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Residues in contact with HIS 86 (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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51A LEU* 3.2 30.9 + - + +
54A ASP* 2.7 28.8 + - - -
55A PHE* 3.5 26.3 + + + -
58A ASP* 5.4 9.0 - - - -
82B ARG 3.5 13.6 + - - +
83B LEU* 3.0 7.6 + - + +
85B GLN* 1.3 81.1 - - - +
87B LEU* 1.3 61.0 + - + +
89B GLU* 2.7 45.3 + - - +
90B HIS* 3.3 22.9 - - - -
92B ILE* 4.5 0.3 - - - +
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Residues in contact with LEU 87 (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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36A ALA* 5.5 0.7 - - + +
38A ILE* 3.8 23.8 - - + -
42A GLN* 5.8 0.7 - - - +
48A THR* 3.8 18.4 - - + +
51A LEU* 4.1 10.1 - - + +
52A ILE* 4.0 8.1 - - + +
83B LEU* 3.1 47.9 + - + +
84B MET* 4.6 4.5 - - - +
86B HIS* 1.3 78.6 - - + +
88B ALA* 1.3 64.8 + - - +
89B GLU 3.2 0.4 - - - -
90B HIS 3.2 1.4 + - - -
91B GLY 3.2 21.0 + - - -
92B ILE* 3.2 54.1 + - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET 3.2 19.3 + - - +
85B GLN* 3.3 6.8 + - - +
87B LEU* 1.3 77.1 - - - +
89B GLU* 1.3 56.9 + - - +
90B HIS 3.0 10.5 + - - -
91B GLY* 4.2 4.9 + - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN* 2.8 18.9 + - - +
86B HIS* 2.7 48.3 + - - +
88B ALA* 1.3 75.3 - - - +
90B HIS* 1.3 74.8 + - + +
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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