Contacts of the helix formed by residues 69 - 86 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.6 4.9 - - - -
25C HIS 4.4 1.6 - - - +
26C LYS* 3.9 30.3 - - + +
63C ASP* 4.3 11.1 - - - +
65C ASP* 5.9 0.2 - - - +
67C GLU 4.0 1.0 - - - -
68C CYS* 1.3 74.5 - - - +
70C PHE* 1.3 59.7 + - - +
71C GLN* 3.9 9.8 - - - +
72C GLU* 2.9 44.7 + - - +
73C PHE* 2.9 26.3 + - - +
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Residues in contact with PHE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU 4.1 3.1 - - - -
11C ILE* 3.8 20.0 - - + -
14C PHE* 3.4 51.1 - + + -
25C HIS 4.3 2.1 + - - +
69C ASP* 1.3 76.6 - - - +
71C GLN* 1.3 62.6 + - - +
73C PHE* 3.1 11.5 + + - +
74C MET* 2.8 46.7 + - + +
81D THR* 3.7 26.5 - - + -
82D THR* 4.1 14.6 - - - -
85D HIS* 3.6 49.1 - + + -
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Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 3.3 10.8 + - - +
70C PHE* 1.3 83.1 - - + +
72C GLU* 1.3 59.7 + - + +
74C MET* 3.3 9.0 + - - +
75C ALA* 3.1 26.2 + - - +
78D ALA* 4.8 4.7 - - - +
79D MET* 5.8 0.7 - - - -
82D THR* 2.4 50.9 + - - +
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.2 28.3 - - - +
62C ASN* 3.2 11.0 + - + +
63C ASP* 3.0 28.4 + - - +
67C GLU 2.9 6.3 - - - +
68C CYS* 3.2 10.8 - - - -
69C ASP* 2.9 36.6 + - - +
71C GLN* 1.3 74.1 - - + +
73C PHE* 1.3 60.8 + - - +
75C ALA* 3.5 7.6 + - - +
76C PHE* 3.0 27.0 + - - +
806C CA 2.4 31.1 - - - -
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.7 24.0 - - - -
13C VAL* 3.7 20.9 - - + -
14C PHE* 3.5 29.4 - + + -
27C LEU* 4.0 15.7 - - + -
32C LEU* 5.5 0.7 - - + -
35C LEU* 3.8 29.6 - - + -
40C LEU* 5.7 0.2 - - + -
68C CYS* 3.4 8.7 - - - -
69C ASP 2.9 14.7 + - - +
70C PHE* 3.4 15.3 - + - +
72C GLU* 1.3 75.0 - - - +
74C MET* 1.3 65.7 + - - +
76C PHE* 3.2 17.8 + + - +
77C VAL* 2.9 53.9 + - + +
3D LEU* 4.4 6.5 - - + -
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.4 39.5 - - + -
70C PHE* 2.8 52.0 + - + +
71C GLN* 3.3 13.4 + - - +
73C PHE* 1.3 79.8 - - - +
75C ALA* 1.3 56.6 + - - +
77C VAL* 3.3 14.8 + - + +
78C ALA* 2.8 30.1 + - - +
74D MET* 4.8 4.7 - - + -
77D VAL* 4.7 4.0 - - + -
78D ALA* 3.8 45.0 - - + +
81D THR* 4.2 4.9 - - + +
82D THR* 4.6 0.4 - - - +
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU 6.1 0.4 - - - +
62C ASN* 5.6 7.9 - - - +
71C GLN 3.1 12.5 + - - +
72C GLU* 3.7 10.1 - - - +
73C PHE 3.3 0.2 - - - -
74C MET* 1.3 77.2 - - - +
76C PHE* 1.3 56.9 + - - +
78C ALA* 3.2 8.3 + - - +
79C MET* 2.9 30.0 + - - +
78D ALA* 5.3 1.1 - - - +
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Residues in contact with PHE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.6 4.7 - - + -
35C LEU* 5.1 0.7 - - + -
36C ILE* 3.8 28.5 - - + -
40C LEU* 3.8 21.3 - - + -
44C LEU* 3.9 18.6 - - + -
56C VAL* 4.1 15.5 - - + -
60C LEU* 3.3 36.6 - - + +
72C GLU 3.0 15.6 + - - +
73C PHE* 3.3 28.7 - + - +
75C ALA* 1.3 76.9 - - - +
77C VAL* 1.3 61.8 + - + +
79C MET* 3.2 18.8 + - + +
80C VAL* 3.0 44.7 + - + +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.1 20.6 - - + -
40C LEU* 6.1 2.0 - - + -
73C PHE* 2.9 53.9 + - + +
74C MET* 3.6 15.0 - - + +
76C PHE* 1.3 72.9 - - + +
78C ALA* 1.3 56.2 + - - +
80C VAL* 3.2 4.4 + - - -
81C THR* 2.8 51.7 + - - +
3D LEU* 4.3 10.1 - - + -
7D MET* 4.4 11.9 - - + -
10D LEU* 5.0 0.9 - - + -
74D MET* 4.2 12.8 - - + -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C MET 2.8 20.8 + - - +
75C ALA* 3.2 9.6 + - - +
77C VAL* 1.3 72.1 - - - +
79C MET* 1.3 57.0 + - - +
82C THR* 2.8 37.3 + - - +
71D GLN 5.5 0.7 - - - +
74D MET* 3.7 40.7 - - + +
75D ALA* 5.0 2.0 - - - +
78D ALA* 5.6 2.0 - - + -
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Residues in contact with MET 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 6.2 0.7 - - + -
59C THR* 5.3 9.9 - - + -
60C LEU* 4.6 8.5 - - + -
75C ALA 2.9 13.6 + - - +
76C PHE* 3.5 35.7 - - + +
78C ALA* 1.3 75.0 - - - +
80C VAL* 1.3 66.0 + - + +
82C THR* 3.9 3.8 - - - -
83C ALA* 2.9 37.1 + - - +
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.9 5.6 - - + -
43C PHE* 4.3 11.4 - - + +
44C LEU* 4.2 28.0 - - + -
76C PHE* 3.0 48.0 + - + +
77C VAL* 3.9 4.9 - - - +
79C MET* 1.3 88.7 - - + +
81C THR* 1.3 57.4 + - - +
83C ALA* 3.7 5.2 - - + +
84C CYS* 3.0 27.3 + - + +
7D MET* 3.8 20.9 - - + -
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Residues in contact with THR 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 2.8 31.9 + - - +
78C ALA 4.2 1.3 - - - -
80C VAL* 1.3 71.0 - - - +
82C THR* 1.4 59.0 + - - -
84C CYS* 3.1 8.2 + - - -
85C HIS* 2.8 28.6 + - - +
7D MET* 3.4 49.4 - - + +
10D LEU* 4.8 1.1 - - + -
11D ILE* 4.0 8.3 - - + -
70D PHE* 3.7 24.2 - - + -
74D MET* 4.2 14.2 - - + +
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Residues in contact with THR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ALA* 2.8 28.1 + - - +
79C MET* 3.9 4.9 - - - -
81C THR* 1.4 72.8 - - - +
83C ALA* 1.3 61.9 + - - +
85C HIS* 3.3 5.5 + - - +
86C GLU* 3.1 32.8 + - + +
70D PHE* 3.8 11.9 - - + -
71D GLN* 3.5 50.9 - - + +
74D MET* 3.7 9.2 - - - +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C MET* 2.9 27.1 + - + +
80C VAL* 3.7 6.1 - - - +
82C THR* 1.3 74.8 - - - +
84C CYS* 1.3 62.8 + - - +
86C GLU* 3.2 30.6 + - - +
90E HIS* 3.7 11.5 + - + -
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Residues in contact with CYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE* 3.6 41.1 - - + -
80C VAL* 3.0 17.0 + - + +
81C THR* 3.1 20.1 + - - -
83C ALA* 1.3 77.4 - - - +
85C HIS* 1.3 60.5 + - - +
87C PHE* 3.2 22.3 - - - +
7D MET* 4.8 2.5 - - - -
11D ILE* 3.8 9.0 - - - -
87E PHE* 3.4 22.6 - - + -
90E HIS* 3.5 17.7 + - + +
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Residues in contact with HIS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C THR 2.8 16.5 + - - +
82C THR* 3.3 6.4 + - - +
84C CYS* 1.3 73.7 - - - +
86C GLU* 1.3 55.9 + - - +
87C PHE 3.0 5.8 - - - -
88C PHE* 2.8 36.4 + + - +
89C GLU* 3.2 33.6 + - + -
11D ILE* 4.0 17.9 - - + -
14D PHE* 4.5 4.3 - + - -
15D HIS* 2.6 41.7 + + - -
25D HIS* 4.6 4.3 - - + -
70D PHE* 3.4 44.6 - + + +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C THR* 3.1 26.0 + - + +
83C ALA* 3.2 18.7 + - - +
85C HIS* 1.3 72.2 - - - +
87C PHE* 1.3 58.6 + - - +
88C PHE 3.1 0.2 - - - -
89C GLU* 2.9 52.7 + - + +
90E HIS* 4.4 1.6 - - - +
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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
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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