Contacts of the helix formed by residues 66 - 82 (chain A) in PDB entry 2HRB
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLN* 5.8 0.5 + - - -
63A ASP* 3.0 23.2 + - + +
64A ILE 4.6 0.4 - - - -
65A ASP* 1.3 76.9 - - - +
67A LEU* 1.3 59.9 + - - +
68A GLN* 3.1 22.2 + - - +
69A SER* 2.9 36.4 + - - -
70A ILE* 3.0 14.1 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASP 4.0 3.4 + - - -
66A ASP* 1.3 73.4 + - - +
68A GLN* 1.3 62.6 + - + +
70A ILE* 3.3 9.2 + - + +
71A ARG* 2.9 61.8 + - - +
120A ASN* 4.5 25.8 - - + +
124A GLU* 4.0 31.4 - - + +
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Residues in contact with GLN 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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66A ASP* 3.1 12.3 + - - +
67A LEU* 1.3 82.0 - - - +
69A SER* 1.3 57.6 + - - +
71A ARG* 3.9 29.7 - - - +
72A ALA* 2.9 30.7 + - - +
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Residues in contact with SER 69 (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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60A HIS* 5.3 0.2 - - - -
61A GLN* 2.8 30.9 + - - +
62A LEU* 3.3 5.5 - - - +
63A ASP 2.9 27.1 + - - -
66A ASP* 2.9 25.7 + - - -
68A GLN* 1.3 76.7 - - - +
70A ILE* 1.3 65.6 + - - +
72A ALA* 3.4 6.6 + - - +
73A LEU* 3.0 23.4 + - - +
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Residues in contact with ILE 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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62A LEU* 3.8 13.2 - - + -
64A ILE* 3.4 24.7 - - - +
66A ASP 3.0 13.2 + - - +
67A LEU* 3.6 13.5 - - + +
69A SER* 1.3 75.0 - - - +
71A ARG* 1.3 57.0 + - - +
73A LEU* 3.2 6.3 + - - +
74A ARG* 2.9 24.9 + - - +
117A ALA 4.2 0.2 - - - +
120A ASN* 3.8 15.3 - - + +
121A MET* 3.7 48.9 - - + +
124A GLU* 3.4 34.3 - - + -
125A LEU* 4.5 5.3 - - + +
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Residues in contact with ARG 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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67A LEU* 2.9 48.6 + - - +
68A GLN* 4.0 23.7 - - - +
70A ILE* 1.3 75.4 - - - +
72A ALA* 1.3 59.8 + - - +
74A ARG* 3.3 26.5 + - - +
75A ASP* 2.9 38.3 + - - +
124A GLU* 3.0 44.1 + - + +
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Residues in contact with ALA 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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60A HIS* 4.1 12.8 + - + -
61A GLN* 6.1 0.2 - - - +
68A GLN 2.9 22.0 + - - +
69A SER* 3.8 7.2 - - - +
71A ARG* 1.3 71.1 - - - +
73A LEU* 1.3 63.1 + - - +
75A ASP* 3.5 8.4 + - - +
76A PHE* 3.0 24.3 + - - +
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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
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9A LEU* 3.4 40.2 - - + -
36A THR* 4.5 1.3 - - + -
60A HIS* 3.9 37.8 - - + +
61A GLN 4.7 0.4 - - - +
62A LEU* 3.7 35.4 - - + -
69A SER 3.0 14.2 + - - +
70A ILE 3.2 8.7 + - - +
72A ALA* 1.3 72.7 - - - +
74A ARG* 1.3 60.2 - - - +
76A PHE* 3.3 13.6 + - + +
77A LEU* 2.9 34.7 + - + +
121A MET* 4.6 0.4 - - + -
125A LEU* 4.4 14.8 - - + -
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Residues in contact with ARG 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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70A ILE 2.9 11.6 + - - +
71A ARG* 3.4 30.9 - - - +
73A LEU* 1.3 76.1 - - - +
75A ASP* 1.3 81.4 + - - +
77A LEU* 3.2 4.9 + - - +
78A ARG* 2.9 29.7 + - + +
124A GLU* 3.1 46.4 + - + +
125A LEU* 3.6 22.9 - - + +
128A ILE* 3.8 22.5 - - + +
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Residues in contact with ASP 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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71A ARG* 2.9 20.2 + - - +
72A ALA* 3.7 7.3 - - - +
73A LEU 3.3 0.2 - - - -
74A ARG* 1.3 102.7 + - - +
76A PHE* 1.3 65.5 + - - +
78A ARG* 3.4 6.6 + - - +
79A LYS* 3.0 26.7 + - - +
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Residues in contact with PHE 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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34A VAL* 4.4 13.0 - - + -
58A ARG* 3.7 31.6 - - + -
59A PHE 5.3 4.0 - - - -
60A HIS* 3.4 40.8 - + + +
72A ALA 3.0 14.5 + - - +
73A LEU* 3.5 11.4 - - + +
75A ASP* 1.3 75.7 - - - +
77A LEU* 1.3 78.6 + - + +
79A LYS* 3.3 5.4 + - - +
80A GLU* 3.0 62.1 + - + +
81A TYR* 4.3 7.9 - + - -
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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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7A VAL* 4.4 9.4 - - + -
9A LEU* 4.0 24.5 - - + -
34A VAL* 4.7 0.9 - - + -
73A LEU* 2.9 27.9 + - + +
74A ARG 3.5 6.3 - - - +
76A PHE* 1.3 88.6 - - + +
78A ARG* 1.3 65.7 + - - +
81A TYR* 3.0 35.5 + - + -
82A GLY 3.2 5.2 + - - -
83A GLY 3.2 11.5 + - - +
84A LEU* 3.9 37.0 - - + -
125A LEU* 4.4 6.1 - - + -
128A ILE* 3.6 21.3 - - + -
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Residues in contact with ARG 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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74A ARG* 2.9 17.1 + - + +
75A ASP* 3.8 6.5 - - - +
77A LEU* 1.3 76.7 - - - +
79A LYS* 1.3 60.2 - - - +
82A GLY* 3.1 33.6 + - - -
83A GLY 3.8 2.9 - - - +
128A ILE* 3.6 26.0 - - + +
2003A GOL 2.7 52.1 + - - -
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Residues in contact with LYS 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 ASP 3.0 18.2 + - - +
76A PHE* 3.7 5.2 - - - +
77A LEU 3.3 0.2 - - - -
78A ARG* 1.3 79.3 - - - +
80A GLU* 1.3 69.4 + - + +
82A GLY 4.6 1.0 + - - -
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Residues in contact with GLU 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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58A ARG* 2.8 40.2 + - - -
76A PHE* 3.0 35.5 + - + +
79A LYS* 1.3 87.4 - - + +
81A TYR* 1.3 84.3 + - + +
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Residues in contact with TYR 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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5A SER* 3.7 32.2 - - - +
6A ARG 4.3 2.0 - - - -
7A VAL* 3.5 39.1 - - + +
32A ASP* 2.6 35.1 + - + +
34A VAL* 4.7 0.7 - - + -
58A ARG* 2.7 34.3 + - - -
76A PHE* 4.3 12.8 - + - -
77A LEU* 3.0 14.6 + - + +
80A GLU* 1.3 97.1 - - + +
82A GLY* 1.3 56.8 + - - +
83A GLY 3.2 17.9 - - - +
130A LYS* 3.2 21.6 + - - +
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Residues in contact with GLY 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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77A LEU 3.2 0.2 + - - -
78A ARG* 3.1 34.7 + - - -
79A LYS 4.5 0.8 + - - -
80A GLU 3.8 0.6 - - - -
81A TYR* 1.3 77.1 - - - +
83A GLY* 1.3 55.1 + - - +
130A LYS* 3.9 6.2 - - - -
2003A GOL 2.9 23.4 + - - -
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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