Contacts of the helix formed by residues 70 - 88 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS* 2.8 33.0 + - - +
60A ILE* 3.6 26.4 - - + +
66A ALA* 3.7 11.0 - - + -
67A GLU* 2.9 40.9 + - - +
69A ASP* 1.3 78.3 - - - +
71A GLU* 1.3 63.1 + - - +
72A SER 3.3 2.0 - - - -
73A LEU* 3.2 13.5 + - + +
74A LEU* 3.0 28.4 + - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 4.2 0.4 + - - -
68A ASP* 3.3 19.7 + - - +
69A ASP 3.2 2.8 - - - -
70A ASP* 1.3 76.7 - - - +
72A SER* 1.3 58.4 + - - +
74A LEU* 3.3 0.8 + - - -
75A GLY* 2.9 25.6 + - - -
71B GLU 4.1 0.5 - - - +
72B SER* 3.7 16.8 - - - +
75B GLY* 3.2 13.9 + - - -
76B HIS* 2.6 51.1 + - - +
79B ILE* 3.5 30.2 - - + +
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP 4.5 7.9 + - - -
71A GLU* 1.3 79.5 - - - +
73A LEU* 1.3 60.1 + - - +
75A GLY* 3.4 0.9 + - - -
76A HIS* 2.9 28.8 + - - +
71B GLU* 4.0 11.5 - - - +
72B SER* 4.1 23.9 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.7 42.2 - - + +
56A PRO* 3.8 26.7 - - + -
58A LYS* 4.3 19.7 - - + -
60A ILE* 4.0 22.0 - - + -
69A ASP 5.7 0.4 - - - +
70A ASP* 3.2 16.6 + - + +
72A SER* 1.3 81.2 + - - +
74A LEU* 1.3 66.9 + - + +
76A HIS* 3.1 10.0 + - + +
77A LEU* 3.1 27.8 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 6.1 0.4 - - + -
60A ILE* 5.2 9.4 - - + -
63A ILE* 3.5 35.4 - - + -
66A ALA* 4.2 8.1 - - + -
70A ASP* 3.0 22.1 + - + +
71A GLU 3.8 3.1 - - - +
73A LEU* 1.3 77.0 - - + +
75A GLY* 1.3 64.1 + - - +
77A LEU* 3.1 36.6 + - + +
78A MET* 3.5 11.4 + - - +
111A VAL* 4.3 10.5 - - + -
75B GLY* 4.2 4.9 - - - +
78B MET* 4.1 24.3 - - + +
79B ILE* 3.8 30.5 - - + -
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU 2.9 11.3 + - - -
72A SER 3.8 0.7 - - - -
74A LEU* 1.3 76.2 - - - +
76A HIS* 1.3 63.0 + - - +
78A MET* 3.1 13.2 + - - +
79A ILE* 3.0 24.4 + - - +
71B GLU* 3.2 30.7 - - - -
74B LEU* 4.1 1.9 - - - +
75B GLY* 3.6 9.7 - - - -
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 2.7 29.1 + - - -
37A ARG* 3.5 39.6 + - + -
38A CYS* 3.8 23.1 - - + -
72A SER 2.9 14.9 + - - +
73A LEU* 3.1 14.6 + - + +
75A GLY* 1.3 75.2 - - - +
77A LEU* 1.3 57.6 + - - +
79A ILE* 4.4 2.4 - - + +
80A VAL* 2.8 46.4 + - + +
71B GLU* 2.7 36.2 + - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 3.8 17.0 - - + -
54A VAL* 3.8 26.3 - - + +
55A ILE 3.7 6.5 - - - -
56A PRO* 3.7 44.0 - - + -
73A LEU* 3.1 22.4 + - + +
74A LEU* 3.1 22.4 + - + +
76A HIS* 1.3 77.4 - - - +
78A MET* 1.3 56.6 + - - +
80A VAL* 4.7 0.2 - - - -
81A GLY* 2.8 25.8 + - - -
111A VAL* 4.2 16.4 - - + -
112A HIS 5.3 0.2 - - - -
113A LEU* 3.6 21.5 - - + +
78B MET* 6.2 2.2 - - + -
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Residues in contact with MET 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 3.5 10.2 + - - +
75A GLY* 3.1 6.3 + - - +
77A LEU* 1.3 76.9 - - + +
79A ILE* 1.3 60.6 + - - +
81A GLY 3.2 0.5 + - - -
82A LYS* 2.9 29.0 + - - +
96A MET* 3.4 17.7 - - - +
113A LEU* 3.9 24.9 - - + -
63B ILE* 4.6 13.1 - - + +
74B LEU* 3.5 48.7 - - + +
77B LEU* 6.3 0.9 - - - -
78B MET* 3.4 33.7 - - + +
98B VAL* 4.4 22.0 - - - -
113B LEU* 5.6 1.6 - - - -
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY 3.0 18.0 + - - +
76A HIS* 3.3 3.6 + - + +
78A MET* 1.3 75.4 - - - +
80A VAL* 1.3 65.9 + - + +
82A LYS* 3.3 11.3 - - + +
83A LYS* 3.0 50.6 + - + +
63B ILE* 5.3 0.4 - - + -
66B ALA* 3.9 19.1 - - + +
67B GLU 3.6 22.9 - - - +
68B ASP* 3.8 9.6 - - - +
71B GLU* 3.7 31.4 - - + +
74B LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 35.0 - - + -
38A CYS* 3.7 18.2 - - - -
40A ALA* 4.6 3.1 - - + -
54A VAL* 4.0 11.2 - - + -
76A HIS* 2.8 51.2 + - + +
77A LEU 4.0 2.2 - - - +
79A ILE* 1.3 76.7 - - + +
81A GLY* 1.3 55.1 + - - +
83A LYS* 3.2 9.1 + - + +
84A CYS* 2.8 41.0 + - - -
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.6 7.8 - - - -
54A VAL* 3.9 17.5 - - - +
77A LEU 2.8 21.6 + - - -
78A MET 3.2 2.0 + - - -
80A VAL* 1.3 74.5 - - - +
82A LYS* 1.3 56.3 + - - +
85A ALA* 2.9 29.6 + - - +
96A MET* 3.8 13.7 - - - -
115A VAL* 4.2 6.5 - - - +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET 2.9 15.1 + - - +
79A ILE* 3.3 24.0 - - + +
81A GLY* 1.3 75.5 - - - +
83A LYS* 1.3 83.4 + - + +
85A ALA* 3.4 2.6 + - - +
86A ALA* 3.1 21.5 + - - +
94A TYR* 3.2 26.0 + - - +
96A MET* 3.5 8.0 - - + +
63B ILE* 3.6 25.4 - - + +
64B SER* 3.3 21.9 + - - +
65B VAL* 4.6 0.6 - - - +
66B ALA 3.1 27.1 + - - -
68B ASP* 5.7 0.2 + - - -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.0 34.0 + - + +
80A VAL* 3.7 9.0 - - + +
82A LYS* 1.3 92.8 - - + +
84A CYS* 1.3 61.5 + - - +
86A ALA* 3.3 6.8 + - - +
87A ASP* 3.0 37.5 + - - +
68B ASP* 2.8 36.6 + - - -
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Residues in contact with CYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.8 18.8 - - + -
33A PHE* 3.7 31.6 - - - -
40A ALA* 3.9 8.7 - - - -
52A PHE* 3.7 22.4 - - + -
80A VAL* 2.8 33.4 + - - +
83A LYS* 1.3 73.7 - - - +
85A ALA* 1.3 57.2 + - - +
87A ASP* 3.1 11.2 + - - +
88A LEU* 2.9 35.0 + - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.9 5.1 - - - -
81A GLY 2.9 17.7 + - - +
82A LYS 3.7 2.7 - - - +
83A LYS 3.3 0.4 - - - -
84A CYS* 1.3 76.2 - - - +
86A ALA* 1.3 62.6 + - - +
88A LEU* 3.3 2.8 + - - -
89A GLY 3.2 4.7 + - - -
90A LEU* 3.0 42.3 + - + +
94A TYR* 3.5 40.2 - - + -
115A VAL* 4.4 5.6 - - + -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 3.1 14.0 + - + +
83A LYS* 3.6 8.7 - - - +
84A CYS 3.2 0.2 - - - -
85A ALA* 1.3 77.6 - - - +
87A ASP* 1.3 59.5 + - - +
89A GLY* 3.0 19.9 + - - +
90A LEU* 4.8 3.8 - - - +
94A TYR* 5.3 1.3 - - - -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 5.9 3.4 - - + -
33A PHE* 6.1 1.4 - - - -
83A LYS* 3.0 24.2 + - - +
84A CYS* 3.1 13.7 + - - +
86A ALA* 1.3 78.3 - - - +
88A LEU* 1.3 62.9 + - + +
89A GLY 3.3 1.0 + - - -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.1 26.0 - - + -
42A HIS* 4.3 15.5 - - + +
50A THR* 4.1 14.9 + - + +
52A PHE* 3.7 31.9 - - + -
84A CYS 2.9 21.2 + - - +
85A ALA 3.8 4.0 - - - +
86A ALA 3.1 0.4 - - - -
87A ASP* 1.3 80.0 - - + +
89A GLY* 1.3 61.9 + - - +
90A LEU* 3.4 15.3 + - + +
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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