Contacts of the helix formed by residues 63 - 82 (chain A) in PDB entry 2HH3
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 PRO 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY 4.3 9.4 - - - +
61A MET 4.2 4.0 - - - +
62A GLY* 1.3 84.5 - - - +
64A PRO* 1.3 69.7 - - + +
65A ASP* 3.4 1.8 - - + +
66A ARG* 3.2 37.9 - - + +
67A CYS* 2.8 33.2 + - - -
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Residues in contact with PRO 64 (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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12A GLY* 6.2 0.4 - - - -
13A ILE* 5.5 1.0 - - - +
62A GLY 3.9 3.3 - - - +
63A PRO* 1.3 88.6 - - + +
65A ASP* 1.3 73.7 + - - +
67A CYS* 3.5 19.4 - - - +
68A GLU* 3.9 11.7 + - - +
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Residues in contact with ASP 65 (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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63A PRO* 3.4 1.4 - - + +
64A PRO* 1.3 88.0 - - - +
66A ARG* 1.3 66.0 + - - +
68A GLU* 3.0 27.6 + - - +
69A HIS* 3.1 11.2 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP 4.6 4.2 + - - -
40A ALA* 2.8 40.0 + - - +
41A GLY* 4.1 3.8 - - - +
42A VAL* 3.4 19.7 - - + -
63A PRO* 3.2 40.1 + - + +
65A ASP* 1.3 78.1 - - - +
67A CYS* 1.3 59.2 + - - +
69A HIS* 3.1 31.1 + - - +
70A ALA* 2.9 30.0 + - - +
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Residues in contact with CYS 67 (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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12A GLY* 3.5 29.8 - - - -
13A ILE* 3.2 29.4 - - + +
42A VAL* 5.0 0.2 - - - -
60A ILE* 3.7 18.5 - - - +
61A MET* 4.0 14.4 - - - -
62A GLY 4.2 1.1 - - - -
63A PRO 2.8 29.9 + - - -
64A PRO* 3.5 13.0 - - - +
66A ARG* 1.3 77.3 - - - +
68A GLU* 1.3 52.2 + - - +
70A ALA 3.5 0.7 + - - -
71A ALA* 2.8 33.1 + - - +
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Residues in contact with GLU 68 (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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13A ILE* 4.5 8.3 - - + -
64A PRO 3.9 12.5 - - - +
65A ASP* 3.0 19.2 + - - +
67A CYS* 1.3 75.9 - - + +
69A HIS* 1.3 60.2 - - - +
71A ALA* 3.2 10.3 - - + +
72A ARG* 2.9 29.1 + - - +
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP 5.9 2.0 - - - -
40A ALA* 5.6 3.6 - - + -
65A ASP 3.1 11.3 + - - +
66A ARG* 3.3 40.1 + - - +
68A GLU* 1.3 76.9 - - - +
70A ALA* 1.3 62.4 + - - +
72A ARG* 3.3 9.1 + - + +
73A ILE* 3.2 32.0 + - + +
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Residues in contact with ALA 70 (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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36A ILE* 5.3 0.7 - - + -
40A ALA* 3.7 6.3 - - + +
42A VAL* 3.5 44.2 - - + -
44A ILE* 5.1 4.0 - - + -
60A ILE* 3.7 13.5 - - + -
66A ARG 2.9 7.4 + - - +
69A HIS* 1.3 75.2 - - - +
71A ALA* 1.3 65.3 + - - +
73A ILE* 3.2 13.3 + - - +
74A ILE* 3.1 27.5 + - - +
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Residues in contact with ALA 71 (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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13A ILE* 3.5 18.4 - - + -
15A VAL* 4.9 10.9 - - + +
60A ILE* 3.5 10.7 - - + +
67A CYS 2.8 20.5 + - - +
68A GLU* 3.2 11.4 - - - +
69A HIS 3.2 0.2 - - - -
70A ALA* 1.3 76.7 - - - +
72A ARG* 1.3 51.6 + - - +
74A ILE* 3.4 2.4 + - - +
75A ASN* 2.7 38.6 + - - +
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Residues in contact with ARG 72 (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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68A GLU 2.9 12.1 + - - +
69A HIS* 3.6 11.7 - - + +
70A ALA 3.2 0.2 - - - -
71A ALA* 1.3 75.2 - - - +
73A ILE* 1.3 58.1 + - + +
75A ASN* 3.5 24.8 + - - -
76A ASP* 2.7 79.0 + - + +
79A GLN* 4.8 13.5 + - - +
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Residues in contact with ILE 73 (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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36A ILE* 3.6 33.2 - - + +
39A ASP* 5.2 5.2 - - + -
40A ALA* 3.6 35.9 - - + +
69A HIS* 3.4 26.2 - - + +
70A ALA* 3.2 8.3 + - - +
72A ARG* 1.3 79.3 - - + +
74A ILE* 1.3 62.2 + - - +
76A ASP* 3.9 3.5 - - - +
77A LEU* 3.3 19.1 + - - +
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Residues in contact with ILE 74 (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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15A VAL* 5.7 5.6 - - + -
17A VAL* 4.8 6.1 - - + -
25A VAL* 4.4 20.0 - - + -
36A ILE* 4.3 14.4 - - + -
44A ILE* 3.5 41.5 - - + -
46A PHE* 6.1 0.2 - - + -
58A ALA* 4.7 8.1 - - + -
60A ILE* 3.6 30.3 - - + -
70A ALA 3.1 9.3 + - - +
71A ALA* 3.9 2.9 - - - +
73A ILE* 1.3 73.7 - - - +
75A ASN* 1.3 54.6 + - - +
77A LEU* 3.1 8.5 + - - +
78A LEU* 2.8 59.6 + - + +
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Residues in contact with ASN 75 (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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15A VAL* 5.6 9.0 - - + +
71A ALA* 2.7 25.0 + - + +
72A ARG* 3.5 28.1 + - - +
74A ILE* 1.3 72.0 - - - +
76A ASP* 1.3 53.3 + - - +
78A LEU* 2.9 11.4 + - - +
79A GLN* 2.7 41.8 + - - +
82A ARG* 5.0 14.5 - - - +
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Residues in contact with ASP 76 (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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72A ARG* 2.7 61.4 + - + +
73A ILE* 3.9 4.3 - - - +
75A ASN* 1.3 71.7 + - - +
77A LEU* 1.3 61.2 + - - +
79A GLN* 3.2 19.0 - - - +
80A SER* 4.3 3.1 + - - -
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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
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24A VAL* 4.2 23.3 - - + +
25A VAL* 4.1 34.3 - - + -
32A MET* 4.7 18.8 - - + -
36A ILE* 4.9 7.6 - - + -
73A ILE* 3.3 11.8 + - + +
74A ILE* 3.1 10.6 + - - +
76A ASP* 1.3 80.6 - - - +
78A LEU* 1.3 59.2 + - - +
79A GLN 3.2 0.9 + - - -
80A SER* 4.0 7.1 + - - -
81A LEU* 3.5 22.1 - - + +
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Residues in contact with LEU 78 (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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15A VAL* 6.4 0.9 - - + -
16A PRO 3.7 19.3 - - - +
17A VAL* 3.6 21.8 - - + -
18A PRO* 3.8 7.6 - - + -
21A SER* 3.6 29.4 - - - -
25A VAL* 3.7 22.4 - - + -
74A ILE* 2.8 33.0 + - + +
75A ASN* 2.9 10.1 + - - +
77A LEU* 1.3 75.8 - - - +
79A GLN* 1.3 56.3 + - - +
80A SER 3.3 0.4 - - - -
81A LEU* 3.5 7.4 - - + -
82A ARG* 2.7 49.0 + - - +
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Residues in contact with GLN 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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72A ARG* 4.8 11.2 + - - +
75A ASN* 2.7 19.2 + - - +
76A ASP* 3.2 18.8 - - - +
77A LEU 3.2 0.8 - - - -
78A LEU* 1.3 78.3 - - - +
80A SER* 1.3 64.9 + - - +
82A ARG* 3.8 22.4 + - - +
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Residues in contact with SER 80 (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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76A ASP 4.3 2.3 + - - -
77A LEU 4.0 6.3 + - - -
78A LEU 3.3 0.2 - - - -
79A GLN* 1.3 80.2 - - - +
81A LEU* 1.3 66.5 + - - +
82A ARG 3.6 2.8 + - - -
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Residues in contact with LEU 81 (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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18A PRO* 5.2 0.5 - - - +
20A HIS* 5.6 6.1 - - - +
21A SER* 3.2 41.5 + - - +
24A VAL* 3.8 42.2 - - + -
25A VAL* 5.0 0.2 - - + -
77A LEU* 3.5 22.4 - - + +
78A LEU* 3.0 18.3 + - + +
80A SER* 1.3 84.0 - - - +
82A ARG* 1.3 58.0 + - - +
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Residues in contact with ARG 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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16A PRO* 2.9 25.6 + - - +
18A PRO* 3.4 21.4 - - + +
55A GLU* 2.6 46.2 + - - -
75A ASN* 5.0 11.5 - - - +
78A LEU* 2.7 34.5 + - - +
79A GLN* 4.0 22.4 - - - +
80A SER 3.4 2.7 - - - -
81A LEU* 1.3 77.0 - - - +
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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
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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