Contacts of the helix formed by residues 69 - 89 (chain F) in PDB entry 2H61
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 69 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F PHE* 3.6 6.5 - - - -
25F HIS 4.2 9.4 - - - +
26F LYS* 4.5 19.4 + - + +
63F ASP* 3.8 17.3 - - - +
65F ASP* 5.6 1.1 - - - +
67F GLU 3.9 1.0 + - - -
68F CYS* 1.3 76.6 - - - +
70F PHE* 1.3 60.7 + - - +
71F GLN* 3.2 13.4 + - - +
72F GLU* 2.8 44.0 + - - +
73F PHE* 2.9 26.0 + - - +
812F CA 4.3 0.2 - - - -
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E THR* 3.6 28.3 - - + -
82E THR* 4.0 10.3 - - + -
85E HIS* 3.6 51.5 - + + +
10F LEU 3.7 22.2 - - - -
11F ILE* 3.7 15.0 - - + -
14F PHE* 3.5 34.2 - + + -
25F HIS 4.5 1.0 + - - -
69F ASP* 1.3 77.9 - - - +
71F GLN* 1.3 66.0 + - - +
73F PHE* 3.2 14.2 + + - +
74F MET* 3.0 48.9 + - + +
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Residues in contact with GLN 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ALA* 5.6 0.7 - - + +
82E THR* 3.9 36.9 + - + +
69F ASP* 3.2 12.8 + - - +
70F PHE* 1.3 80.2 - - - +
72F GLU* 1.3 63.6 + - + +
74F MET* 3.2 13.3 + - - +
75F ALA* 3.4 10.0 + - - +
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Residues in contact with GLU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 3.4 29.3 - - - +
62F ASN* 3.0 26.9 + - + +
63F ASP* 3.2 12.9 + - - +
67F GLU 3.0 4.8 - - - +
68F CYS* 3.3 10.7 - - - -
69F ASP* 2.8 40.7 + - - +
71F GLN* 1.3 75.2 - - + +
73F PHE* 1.3 66.1 + - - +
75F ALA* 3.0 18.6 + - - +
76F PHE 3.4 7.8 + - - -
812F CA 2.4 31.2 - - - -
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Residues in contact with PHE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.6 4.9 - - + -
10F LEU* 3.9 21.5 - - + -
13F VAL* 4.2 11.2 - - + -
14F PHE* 3.7 22.4 - + + -
27F LEU* 4.0 15.0 - - + -
32F LEU* 5.2 2.9 - - + -
35F LEU* 3.9 39.5 - - + -
68F CYS* 3.2 11.3 - - - -
69F ASP 2.9 14.2 + - - +
70F PHE* 3.4 22.2 - + - +
72F GLU* 1.3 75.4 - - - +
74F MET* 1.3 59.2 + - - +
76F PHE* 3.1 28.7 + + + +
77F VAL* 2.9 48.6 + - + +
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Residues in contact with MET 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E MET* 4.8 3.8 - - + -
77E VAL* 4.1 5.8 - - + -
78E ALA* 3.5 44.4 - - + +
81E THR* 4.0 10.1 - - - +
82E THR* 4.0 9.2 - - - +
10F LEU* 3.8 32.5 - - + -
70F PHE* 3.0 49.7 + - + +
71F GLN 3.4 11.0 - - - +
72F GLU 3.2 0.4 - - - -
73F PHE* 1.3 78.2 - - - +
75F ALA* 1.3 55.2 + - - +
77F VAL* 3.8 15.6 - - + +
78F ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ALA* 5.4 0.9 - - - +
60F LEU* 4.8 7.4 - - + +
62F ASN* 5.7 7.0 - - - +
71F GLN 3.4 5.5 + - - +
72F GLU* 3.0 14.7 + - - +
74F MET* 1.3 76.2 - - - +
76F PHE* 1.3 57.6 + - - +
78F ALA* 3.3 8.3 + - - +
79F MET* 2.8 28.8 + - - +
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Residues in contact with PHE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 6.2 0.2 - - + -
7E MET* 5.7 0.9 - - + -
32F LEU* 4.7 4.0 - - + -
35F LEU* 5.1 0.9 - - + -
36F ILE* 3.8 29.8 - - + -
40F LEU* 3.7 21.1 - - + -
44F LEU* 4.0 10.8 - - + -
56F VAL* 4.2 15.5 - - + -
60F LEU* 3.6 40.0 - - + +
72F GLU 3.4 2.4 + - - -
73F PHE* 3.1 31.2 + + - +
75F ALA* 1.3 75.0 - - - +
77F VAL* 1.3 68.6 + - + +
79F MET* 3.1 16.2 + - + +
80F VAL* 2.9 44.5 + - + +
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Residues in contact with VAL 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.5 5.6 - - + -
7E MET* 4.5 14.1 - - + -
10E LEU* 4.6 2.9 - - + -
74E MET* 4.1 11.4 - - + -
10F LEU* 4.0 35.7 - - + -
73F PHE* 2.9 53.1 + - + +
74F MET* 3.8 14.1 - - + +
76F PHE* 1.3 73.2 - - + +
78F ALA* 1.3 61.7 + - - +
80F VAL* 3.1 1.4 + - - +
81F THR* 2.7 40.8 + - - +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLN* 5.3 2.9 - - - +
74E MET* 3.7 38.3 - - + +
75E ALA* 5.2 1.1 - - - +
78E ALA* 5.8 1.6 - - + -
74F MET 2.9 15.2 + - - +
75F ALA* 3.4 11.9 - - - +
76F PHE 3.2 0.2 - - - -
77F VAL* 1.3 77.3 - - - +
79F MET* 1.3 64.6 + - - +
81F THR* 4.0 0.3 - - - -
82F THR* 3.0 30.7 + - - +
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Residues in contact with MET 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLN* 5.6 1.6 - - - -
44F LEU* 5.8 6.5 - - + -
75F ALA 2.8 14.9 + - - +
76F PHE* 3.1 17.9 + - - +
78F ALA* 1.3 79.7 - - - +
80F VAL* 1.3 78.0 + - + +
82F THR* 3.7 5.1 - - - -
83F ALA* 3.2 32.6 + - + +
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E MET* 3.7 28.5 - - + -
40F LEU* 4.7 4.5 - - + -
43F PHE* 4.3 19.5 - - + -
44F LEU* 4.3 16.8 - - + -
76F PHE* 2.9 49.9 + - + +
77F VAL 3.9 2.5 - - - +
79F MET* 1.3 87.1 - - + +
81F THR* 1.3 59.1 + - - +
83F ALA* 3.2 9.9 - - + +
84F CYS* 2.9 24.7 + - + +
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Residues in contact with THR 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E MET* 3.4 36.3 - - + +
10E LEU* 4.4 2.9 - - + +
11E ILE* 3.7 15.5 - - + -
70E PHE* 3.5 24.5 - - + -
74E MET* 4.1 13.8 - - - +
77F VAL* 2.7 23.8 + - - +
78F ALA 4.0 2.2 - - - -
80F VAL* 1.3 75.2 - - - +
82F THR* 1.3 55.6 + - - +
84F CYS* 2.9 7.5 + - + +
85F HIS* 2.7 34.0 + - - +
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Residues in contact with THR 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E PHE* 3.6 23.3 - - + -
71E GLN* 2.8 44.2 + - + +
74E MET* 4.1 6.2 - - - +
78F ALA 3.0 21.8 + - - -
79F MET* 3.7 4.9 - - - -
81F THR* 1.3 75.5 - - - +
83F ALA* 1.3 57.5 + - - +
85F HIS* 3.3 4.1 + - - +
86F GLU* 3.0 47.3 + - + +
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F MET* 3.2 23.5 + - + +
80F VAL* 3.2 14.1 - - + +
82F THR* 1.3 80.9 - - - +
84F CYS* 1.3 60.7 + - - +
86F GLU* 3.4 20.0 + - - +
87F PHE* 3.3 25.3 + - + -
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Residues in contact with CYS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E MET* 5.7 0.7 - - + -
8E VAL* 4.9 5.8 - - - -
11E ILE* 5.0 7.2 - - + -
43F PHE* 4.0 37.5 - - + -
80F VAL* 2.9 11.5 + - + +
81F THR* 2.9 13.1 + - + +
83F ALA* 1.3 71.4 - - - +
85F HIS* 1.3 66.3 + - - +
86F GLU 3.1 1.6 - - - -
87F PHE* 3.0 25.1 + - - +
88F PHE* 3.4 38.2 + - - -
87G PHE* 6.5 1.1 - - - -
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Residues in contact with HIS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 4.3 15.8 - - + +
14E PHE* 4.3 12.5 - + - -
15E HIS* 3.8 20.5 + + - -
25E HIS* 5.6 2.7 - - + -
70E PHE* 3.5 53.8 - + + +
81F THR 2.7 15.9 + - - +
82F THR* 3.3 10.4 + - - +
84F CYS* 1.3 72.4 - - - +
86F GLU* 1.3 65.7 + - + +
88F PHE* 3.4 3.2 + - - +
89F GLU* 3.1 59.9 + - + +
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Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLN* 5.6 1.6 - - - +
82F THR* 3.0 33.4 + - + +
83F ALA* 3.7 13.5 - - - +
84F CYS 3.1 0.6 - - - -
85F HIS* 1.3 85.0 - - + +
87F PHE* 1.3 64.1 + - - +
89F GLU* 3.2 25.6 - - + +
90F HIS* 5.2 0.5 - - - +
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Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ALA* 3.3 27.0 + - + -
84F CYS* 3.0 15.3 + - - +
86F GLU* 1.3 77.9 - - - +
88F PHE* 1.3 67.9 + - + +
90F HIS* 3.6 23.7 + - - +
87G PHE* 3.3 45.3 - + + -
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Residues in contact with PHE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 4.9 9.9 - - + -
11E ILE* 3.5 28.7 - - + -
15E HIS* 4.6 4.5 - - + -
84F CYS* 3.4 35.7 + - - -
85F HIS* 3.4 7.2 + - - +
86F GLU 3.3 0.4 - - - -
87F PHE* 1.3 84.1 - - + +
89F GLU* 1.3 61.8 + - - +
90F HIS* 3.4 3.8 + + - -
41G SER 4.3 0.9 - - - +
42G HIS* 3.2 38.4 - - - +
43G PHE* 3.5 32.8 - + - -
84G CYS* 6.1 0.7 - - - -
87G PHE* 5.3 5.6 - + - -
88G PHE* 4.2 30.7 - + - -
0H MET* 3.5 21.3 - - + -
8H VAL* 5.6 3.6 - - + -
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E PHE* 5.8 0.2 - - - -
15E HIS* 3.9 8.7 + - - -
24E LYS 5.4 0.2 - - - +
25E HIS* 2.3 47.9 + - + +
85F HIS* 3.1 49.6 + - + +
86F GLU* 3.2 18.0 + - + +
88F PHE* 1.3 74.5 - - - +
90F HIS* 1.3 63.5 + - - +
42G HIS* 3.9 21.1 + - - -
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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