Contacts of the helix formed by residues 70 - 88 (chain B) in PDB entry 5KM2
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LYS* 2.8 34.9 + - - +
60B ILE* 3.8 22.2 - - + +
66B ALA* 3.6 5.1 - - + -
67B GLU* 2.7 42.7 + - - +
69B ASP* 1.3 79.4 - - - +
71B GLU* 1.3 64.5 + - - +
72B SER 3.3 2.0 - - - -
73B LEU* 3.1 14.0 + - + +
74B LEU* 2.9 32.8 + - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 4.6 6.1 + - - -
72A SER* 4.0 11.7 - - - +
75A GLY* 3.2 18.4 - - - +
76A HIS* 2.7 61.8 + - - +
79A ILE* 3.7 24.3 - - + +
67B GLU 4.0 1.0 + - - -
68B ASP* 3.1 20.8 + - - +
69B ASP 3.2 1.4 - - - -
70B ASP* 1.3 78.6 - - - +
72B SER* 1.3 63.2 + - - +
74B LEU* 3.2 1.6 + - - -
75B GLY 3.0 18.4 + - - -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.7 12.2 - - - +
72A SER* 4.1 27.1 - - - +
69B ASP 4.6 5.7 + - - -
70B ASP 3.3 0.2 - - - -
71B GLU* 1.3 80.7 - - - +
73B LEU* 1.3 58.4 + - - +
75B GLY* 3.3 1.2 + - - -
76B HIS* 2.8 28.9 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.9 45.5 - - + +
56B PRO* 4.0 24.5 - - + -
58B LYS* 4.3 18.8 - - + -
60B ILE* 4.3 18.8 - - + -
69B ASP 5.3 0.8 + - - +
70B ASP* 3.1 16.9 + - - +
72B SER* 1.3 77.7 + - - +
74B LEU* 1.3 68.5 + - + +
76B HIS* 3.1 10.2 + - + +
77B LEU* 3.0 25.9 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY* 4.1 2.9 - - - +
78A MET* 3.5 32.1 - - + +
79A ILE* 3.7 30.7 - - + -
56B PRO* 5.9 0.4 - - + -
60B ILE* 4.9 10.8 - - + -
63B ILE* 3.6 35.0 - - + -
66B ALA* 4.1 6.7 - - + -
70B ASP* 2.9 20.7 + - + +
71B GLU 3.6 5.6 - - - +
73B LEU* 1.3 77.2 - - + +
75B GLY* 1.3 62.5 + - - +
77B LEU* 3.1 36.8 + - + +
78B MET 3.4 3.8 + - - -
111B VAL* 4.8 13.9 - - + -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.2 30.3 - - - -
74A LEU* 4.2 6.9 - - - +
75A GLY* 3.6 10.8 - - - -
78A MET* 4.6 0.2 - - - -
71B GLU 3.0 10.7 + - - -
72B SER 3.7 0.2 - - - -
74B LEU* 1.3 76.5 - - - +
76B HIS* 1.3 56.3 + - - +
78B MET* 3.0 6.7 + - - +
79B ILE* 3.0 30.3 + - - +
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 2.6 35.2 + - - +
35B ASP* 2.7 29.9 + - - -
37B ARG* 3.7 30.7 - - + +
38B CYS* 3.8 15.0 - - + -
72B SER 2.8 14.5 + - - +
73B LEU* 3.2 15.9 - - + +
75B GLY* 1.3 73.8 - - - +
77B LEU* 1.3 60.0 + - - +
79B ILE* 3.8 1.7 - - + +
80B VAL* 2.9 48.3 + - + +
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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
----------------------------------------------------------
78A MET* 6.2 0.9 - - + -
38B CYS* 3.8 18.8 - - + -
54B VAL* 3.7 26.2 - - + +
55B ILE 3.8 6.7 - - - -
56B PRO* 3.7 44.0 - - + -
73B LEU* 3.0 17.5 + - + +
74B LEU* 3.1 30.5 + - + +
76B HIS* 1.3 77.5 - - + +
78B MET* 1.3 57.5 + - + +
80B VAL* 3.6 0.6 + - - -
81B GLY* 2.8 23.0 + - - -
111B VAL* 5.1 5.8 - - + +
113B LEU* 3.5 24.1 - - + +
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.5 34.7 - - + +
74A LEU* 4.1 26.9 - - + +
77A LEU* 6.2 2.2 - - + -
78A MET* 3.4 37.2 - - + +
98A VAL* 4.3 18.6 - - + -
113A LEU* 5.7 2.5 - - - -
74B LEU 3.4 1.5 + - - +
75B GLY 3.0 8.3 + - - +
77B LEU* 1.3 75.7 - - + +
79B ILE* 1.3 61.0 + - - +
81B GLY 3.3 0.3 + - - -
82B LYS* 2.9 27.2 + - - +
96B MET* 3.4 18.7 - - - +
113B LEU* 3.8 23.6 - - + -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.3 1.1 - - + +
66A ALA* 3.9 15.0 - - + +
67A GLU 3.7 21.3 - - - +
68A ASP* 3.9 11.9 - - - +
71A GLU* 3.5 35.9 - - + +
74A LEU* 3.8 22.4 - - + -
75B GLY 3.0 12.2 + - - +
76B HIS* 3.3 4.2 + - + +
78B MET* 1.3 72.3 - - - +
80B VAL* 1.3 68.5 + - + +
82B LYS* 3.3 13.9 + - + +
83B LYS* 3.0 50.3 + - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.7 33.7 - - + -
38B CYS* 3.9 7.6 - - - -
40B ALA* 4.6 2.2 - - + -
54B VAL* 3.9 20.9 - - + -
76B HIS* 2.9 50.6 + - + +
77B LEU 3.9 2.7 - - - +
79B ILE* 1.3 76.4 - - + +
81B GLY* 1.3 57.6 - - - +
83B LYS* 3.3 8.3 + - + +
84B CYS* 2.9 39.8 + - - -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.5 11.4 - - - -
54B VAL* 3.8 16.8 - - - +
77B LEU 2.8 17.6 + - - -
78B MET 3.3 2.4 + - - -
79B ILE 3.2 0.2 - - - -
80B VAL* 1.3 77.8 - - - +
82B LYS* 1.3 55.9 + - - +
84B CYS 3.4 0.2 + - - -
85B ALA* 2.9 30.3 + - - +
96B MET* 3.8 13.0 - - - -
115B VAL* 4.4 3.1 - - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.5 18.4 - - + +
64A SER* 3.1 32.0 + - - +
65A VAL* 4.5 0.8 - - - +
66A ALA 3.3 25.8 + - - +
68A ASP* 5.3 0.8 + - - -
78B MET 2.9 15.8 + - - +
79B ILE* 3.7 22.2 - - + +
81B GLY* 1.3 74.7 - - - +
83B LYS* 1.3 83.8 + - + +
85B ALA* 3.3 3.6 + - - +
86B ALA* 3.1 22.7 + - + +
94B TYR* 3.6 24.4 + - - +
96B MET* 3.6 5.0 - - + +
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Residues in contact with LYS 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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68A ASP* 2.9 39.2 + - - -
79B ILE* 3.0 32.6 + - + +
80B VAL* 3.8 7.6 - - + +
82B LYS* 1.3 95.0 - - - +
84B CYS* 1.3 60.3 + - - +
86B ALA* 3.3 7.2 + - - +
87B ASP* 3.0 36.1 + - - +
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Residues in contact with CYS 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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32B ILE* 3.8 18.4 - - + -
33B PHE* 3.7 32.5 - - - -
40B ALA* 4.1 7.9 - - - -
52B PHE* 3.6 22.7 - - + -
80B VAL* 2.9 30.4 + - - +
83B LYS* 1.3 77.3 - - - +
85B ALA* 1.3 58.2 + - - +
87B ASP* 3.2 9.5 + - - +
88B LEU* 2.9 33.6 + - - +
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Residues in contact with ALA 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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52B PHE* 3.8 6.4 - - - -
81B GLY 2.9 17.6 + - - +
82B LYS 3.5 5.8 - - - +
83B LYS 3.3 0.2 - - - -
84B CYS* 1.3 77.0 - - - +
86B ALA* 1.3 60.7 + - - +
88B LEU* 3.3 1.9 + - - -
89B GLY 3.2 4.7 + - - -
90B LEU* 3.0 42.1 + - + +
94B TYR* 3.5 36.1 - - + -
115B VAL* 4.4 6.3 - - + -
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Residues in contact with ALA 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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82B LYS* 3.1 13.2 + - + +
83B LYS* 3.6 10.5 - - - +
85B ALA* 1.3 75.3 - - - +
87B ASP* 1.3 62.1 + - - +
89B GLY* 3.0 19.1 + - - -
90B LEU* 4.7 5.2 - - - +
94B TYR* 5.4 0.4 - - - -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 6.1 2.2 - - + -
83B LYS* 3.0 25.2 + - - +
84B CYS* 3.2 9.5 + - - +
86B ALA* 1.3 79.6 - - - +
88B LEU* 1.3 61.5 + - + +
89B GLY* 3.2 3.0 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 4.0 26.5 - - + -
42B HIS* 4.2 18.2 - - + +
50B THR* 4.1 21.3 + - + +
52B PHE* 3.7 31.0 - - + -
84B CYS 2.9 21.3 + - - +
85B ALA* 3.9 4.5 - - - +
86B ALA 3.2 0.4 - - - -
87B ASP* 1.3 79.2 - - + +
89B GLY* 1.3 60.3 + - - +
90B LEU* 3.4 9.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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