Contacts of the helix formed by residues 68 - 84 (chain H) in PDB entry 6C0W
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 68 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LYS* 3.6 24.4 + - - +
96B THR* 4.6 5.9 - - - +
98B TYR* 3.0 27.3 + - + +
64H SER 3.4 15.0 - - - +
65H PHE 2.9 13.0 + - - +
66H VAL 3.2 0.2 - - - -
67H ASN* 1.3 79.3 - - - +
69H ILE* 1.3 66.0 + - - +
70H PHE 3.3 0.7 - - - -
71H GLU* 2.9 21.6 + - - +
72H ARG* 3.0 34.4 + - - +
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Residues in contact with ILE 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 3.9 18.8 - - + -
58G LEU* 4.0 14.1 - - + -
96G LEU* 4.6 15.5 - - + -
97G LEU* 5.0 2.5 - - + -
65H PHE* 3.1 46.3 + - + +
66H VAL* 4.5 1.8 - - - +
68H ASP* 1.3 85.8 - - - +
70H PHE* 1.3 56.4 + - - +
72H ARG* 3.0 26.8 + - + +
73H ILE* 2.9 52.5 + - + +
102H LEU* 5.9 2.0 - - + -
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 4.2 11.0 - - + -
33G LEU* 3.7 51.6 - - + -
34G LEU* 4.2 9.6 - - + -
39G TYR* 4.7 12.1 + + - -
51G LEU* 3.6 36.3 - - + -
55G LEU* 4.3 19.8 - - + +
37H TYR* 5.4 4.5 - - + -
66H VAL 3.8 19.2 + - - +
67H ASN* 5.0 9.0 - - - -
68H ASP 3.3 1.0 - - - +
69H ILE* 1.3 78.4 - - - +
71H GLU* 1.3 62.6 + - + +
73H ILE* 4.8 1.6 - - - +
74H ALA* 3.3 31.3 + - + +
75H GLY 4.0 0.3 + - - -
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Residues in contact with GLU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 3.7 28.6 + - - +
79D ARG* 4.7 14.6 + - - -
39G TYR* 4.8 13.2 + - - +
67H ASN 3.9 14.7 + - - +
68H ASP* 2.9 15.4 + - - +
70H PHE* 1.3 82.0 - - + +
72H ARG* 1.3 71.9 + - - +
75H GLY* 3.3 16.8 + - - -
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Residues in contact with ARG 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 6.1 1.3 - - - +
96B THR* 5.7 3.8 + - - +
98B TYR* 5.1 1.2 + - - -
96G LEU* 3.7 41.6 + - - +
97G LEU* 4.8 7.9 - - - +
99G ARG* 6.1 3.0 - - - +
100G VAL* 5.3 5.3 - - - +
68H ASP* 3.0 30.5 + - - +
69H ILE* 3.0 24.0 + - + +
71H GLU* 1.3 84.4 - - - +
73H ILE* 1.3 55.7 + - + +
75H GLY 3.0 1.6 + - - -
76H GLU* 2.5 42.1 + - - +
101H LEU* 3.9 30.0 - - + +
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Residues in contact with ILE 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 4.1 22.9 - - + -
54G VAL* 4.5 12.6 - - + -
55G LEU* 5.4 1.3 - - + -
58G LEU* 5.3 1.8 - - + -
69H ILE* 2.9 39.3 + - + +
72H ARG* 1.3 71.4 - - + +
74H ALA* 1.3 60.8 + - - +
76H GLU* 3.0 4.0 + - - -
77H ALA* 2.8 33.9 + - - +
94H ILE* 4.2 14.6 - - + -
97H ALA* 3.8 23.5 - - + +
98H VAL* 4.1 20.6 - - + -
101H LEU* 4.3 23.8 - - + -
102H LEU* 5.6 5.8 - - + -
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Residues in contact with ALA 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 3.7 17.6 - - + +
39G TYR* 3.2 29.7 - - + +
51G LEU* 4.1 9.2 - - + +
70H PHE* 3.3 42.3 + - + +
73H ILE* 1.3 77.9 - - - +
75H GLY* 1.3 57.6 - - - +
77H ALA* 4.5 2.2 - - - +
78H SER* 4.2 3.6 + - - -
89H ILE* 5.2 3.0 - - - +
94H ILE* 4.8 10.3 - - + -
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Residues in contact with GLY 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TYR* 4.4 13.9 - - - -
71H GLU* 3.3 17.9 + - - -
72H ARG 3.0 6.9 + - - -
74H ALA* 1.3 77.9 - - - +
76H GLU* 1.3 58.0 + - - +
77H ALA 3.3 0.2 - - - -
78H SER* 3.0 28.1 + - - -
79H ARG* 3.5 3.7 + - - +
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Residues in contact with GLU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 3.4 14.2 + - - -
92F ARG* 4.9 9.0 - - + +
72H ARG 2.5 19.1 + - - +
73H ILE 3.9 1.8 - - - +
75H GLY* 1.3 73.7 - - - +
77H ALA* 1.3 57.6 + - - +
79H ARG* 3.0 51.9 + - - +
80H LEU* 3.2 27.6 + - - +
97H ALA* 3.4 26.2 - - - +
100H LEU* 3.6 8.7 - - - +
101H LEU* 3.9 24.2 - - + +
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ILE 2.8 20.3 + - - +
74H ALA* 4.8 1.3 - - - -
76H GLU* 1.3 74.4 + - - +
78H SER* 1.3 65.3 + - - +
80H LEU* 3.0 20.3 + - - +
81H ALA 3.2 8.5 + - - -
89H ILE* 4.9 4.9 - - + -
93H GLU* 3.8 21.4 - - + +
94H ILE* 3.7 27.1 - - + -
97H ALA* 3.8 13.7 - - + -
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Residues in contact with SER 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ASN 4.8 0.5 + - - -
39G TYR* 2.3 54.5 + - - +
74H ALA 4.2 3.4 + - - -
75H GLY 3.0 18.3 + - - -
77H ALA* 1.3 78.6 - - - +
79H ARG* 1.3 55.0 + - - +
81H ALA* 3.0 26.8 + - - +
82H HIS* 3.5 6.8 + - - +
89H ILE* 4.5 6.7 - - - +
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Residues in contact with ARG 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 4.8 12.4 + - - -
72F TYR* 5.4 2.7 + - - -
91F LYS* 4.9 13.7 - - - +
92F ARG* 5.0 14.6 - - - +
75H GLY 3.5 2.3 + - - +
76H GLU* 3.0 39.7 + - - +
78H SER* 1.3 78.9 - - - +
80H LEU* 1.3 57.3 + - + +
82H HIS* 2.9 22.4 + - + +
83H TYR* 3.2 54.5 + - + +
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F THR* 5.9 1.1 - - + -
72F TYR* 3.6 35.4 - - + -
75F HIS* 4.2 20.0 - - + +
76H GLU* 3.2 38.4 - - - +
77H ALA* 3.0 12.5 + - - +
79H ARG* 1.3 80.5 - - + +
81H ALA* 1.3 57.4 + - - +
82H HIS 3.2 2.0 + - - -
83H TYR* 4.3 5.6 - - + +
84H ASN* 3.5 28.3 + - - +
93H GLU* 4.0 17.3 - - + +
96H THR* 3.4 31.6 - - - +
97H ALA* 5.8 0.4 - - + -
100H LEU* 4.6 4.7 - - + -
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Residues in contact with ALA 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G TYR 5.0 0.7 - - - +
40G ALA* 4.6 15.0 - - + -
77H ALA 3.2 3.4 + - - +
78H SER* 3.0 17.7 + - - +
80H LEU* 1.3 76.5 - - - +
82H HIS* 1.3 57.3 + - - +
84H ASN 4.7 0.4 - - - -
86H ARG* 3.0 40.1 + - + +
87H SER* 5.0 0.7 - - - -
88H THR 3.7 22.4 - - - +
89H ILE* 4.7 0.7 - - + -
93H GLU* 3.9 11.4 - - - +
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Residues in contact with HIS 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 4.8 5.6 + - - -
37C GLY* 4.5 28.1 - - - -
39C TYR* 5.6 4.2 + - - -
78H SER 3.5 6.7 + - - +
79H ARG* 2.9 12.3 + - + +
81H ALA* 1.3 79.7 - - - +
83H TYR* 1.3 78.7 + + + +
84H ASN 3.3 1.6 - - - -
85H LYS* 3.5 12.0 + - - +
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Residues in contact with TYR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TYR* 4.3 23.6 - + + -
88F TYR* 3.4 71.6 - + + -
91F LYS* 4.6 13.0 + - - +
79H ARG* 3.2 49.2 + - + +
80H LEU* 4.3 4.2 - - + -
82H HIS* 1.3 91.5 - + - +
84H ASN* 1.3 67.3 + - - +
85H LYS* 3.3 2.4 + - - +
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Residues in contact with ASN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TYR* 5.3 3.1 + - - +
75F HIS* 3.1 33.0 + - + +
76F ALA* 3.3 28.4 - - + +
78F ARG* 4.9 2.4 + - - -
80H LEU* 3.5 26.5 + - - +
82H HIS 3.3 0.2 - - - -
83H TYR* 1.3 81.7 - - - +
85H LYS* 1.3 70.8 + - - +
86H ARG* 3.5 26.0 + - + +
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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