Contacts of the helix formed by residues 63 - 77 (chain A) in PDB entry 2HR3
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 ARG 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA* 4.7 0.7 - - - -
61A ARG 5.0 0.2 - - - +
62A MSE 1.3 74.6 - - - +
64A SER* 1.3 67.5 + - - +
65A SER* 4.1 16.6 + - - +
66A ASN* 2.9 24.4 + - + +
67A LEU* 3.2 12.3 + - - +
32B PRO* 3.4 26.0 - - + +
33B VAL* 3.7 26.3 + - + +
36B SER* 3.1 32.3 + - - -
70B LEU* 4.0 9.1 - - - +
73B GLU* 2.9 40.8 + - - -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 5.6 3.3 + - - -
57A ALA* 4.4 12.8 - - - +
62A MSE 3.6 4.0 + - - -
63A ARG* 1.3 70.7 - - - +
65A SER* 1.3 65.0 + - - +
66A ASN 2.9 1.7 + - - -
67A LEU* 3.6 3.1 + - - +
68A ALA* 3.2 21.2 + - - +
32B PRO* 5.7 0.2 - - - +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 4.1 15.1 + - - +
64A SER* 1.3 79.1 - - - +
66A ASN* 1.3 63.2 + - - +
68A ALA* 3.7 14.9 + - - +
69A ALA* 4.0 7.1 + - - +
72A ARG* 5.0 1.7 + - - -
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MSE 3.1 20.3 - - + +
63A ARG* 2.9 22.9 + - + +
65A SER* 1.3 78.7 + - - +
67A LEU* 1.3 65.5 + - - +
68A ALA 3.2 1.3 - - - -
69A ALA* 3.3 9.2 + - - +
70A LEU* 3.3 28.4 + - - +
66B ASN* 3.5 26.4 + - - +
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Residues in contact with LEU 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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40A VAL* 3.9 30.5 - - + -
53A PRO* 3.1 35.2 - - + +
56A LEU* 3.8 16.2 - - + -
57A ALA* 3.5 20.2 - - + +
62A MSE 3.5 19.4 - - + +
63A ARG 3.2 12.4 + - - +
64A SER* 3.8 4.7 - - - +
66A ASN* 1.3 75.8 - - - +
68A ALA* 1.3 65.8 + - - +
69A ALA 3.1 0.4 - - - -
70A LEU* 4.5 2.0 - - + +
71A LEU* 2.9 49.6 + - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 3.2 15.1 + - - +
65A SER* 3.7 10.1 - - - +
66A ASN 3.2 1.2 - - - -
67A LEU* 1.3 77.5 - - - +
69A ALA* 1.3 58.3 + - - +
71A LEU* 3.6 8.6 - - - +
72A ARG* 3.0 42.4 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER 4.0 5.1 + - - +
66A ASN* 3.3 9.8 + - - +
67A LEU 3.1 0.2 - - - -
68A ALA* 1.3 79.8 - - - +
70A LEU* 1.3 59.9 + - + +
72A ARG* 3.1 36.3 + - - +
73A GLU* 3.2 32.8 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.8 25.6 - - - +
37A GLN* 4.6 5.5 - - + +
40A VAL* 3.7 31.6 - - + -
62A MSE 3.8 22.4 - - + -
66A ASN* 3.3 16.3 + - - +
67A LEU 3.4 3.1 + - - +
69A ALA* 1.3 74.3 - - + +
71A LEU* 1.3 60.4 + - - +
73A GLU* 3.3 15.0 + - - +
74A LEU* 3.1 33.6 + - + +
63B ARG* 3.4 29.4 - - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.6 29.4 - - + -
44A ILE* 4.7 0.4 - - + -
53A PRO* 3.9 31.2 - - + -
56A LEU* 4.1 9.2 - - + -
67A LEU* 2.9 42.9 + - + +
68A ALA* 3.6 7.0 - - - +
70A LEU* 1.3 73.3 - - - +
72A ARG* 1.3 66.7 + - - +
73A GLU 3.4 0.2 + - - -
74A LEU 3.4 0.7 + - - -
75A GLU* 3.2 22.9 + - - +
80A ILE* 3.6 27.8 - - + +
94A VAL* 4.5 14.6 - - + -
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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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65A SER 5.0 2.4 + - - -
68A ALA* 3.0 23.1 + - - +
69A ALA* 3.1 59.8 + - - +
71A LEU* 1.3 77.5 - - - +
73A GLU* 1.3 62.3 + - + +
75A GLU* 3.6 4.2 + - - +
76A ARG* 3.3 26.2 + - + +
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Residues in contact with GLU 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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33A VAL* 5.3 2.3 - - - +
37A GLN* 3.2 24.7 - - - +
69A ALA* 3.2 19.8 + - - +
70A LEU* 3.3 21.3 + - - +
72A ARG* 1.3 76.3 - - + +
74A LEU* 1.3 57.5 + - - +
76A ARG* 3.4 8.6 + - - +
77A GLY* 3.1 24.8 + - - -
63B ARG* 3.2 39.0 + - - -
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Residues in contact with LEU 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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37A GLN* 3.9 28.3 - - + +
40A VAL* 3.4 38.8 - - + -
41A LEU* 3.8 23.6 - - + -
70A LEU 3.1 16.8 + - - +
71A LEU* 4.4 0.4 - - + -
73A GLU* 1.3 77.4 - - - +
75A GLU* 1.3 63.4 + - - +
77A GLY* 3.5 2.6 + - - -
78A GLY 3.2 2.9 + - - -
79A LEU* 2.9 58.1 + - + +
80A ILE* 3.5 27.6 - - + -
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Residues in contact with GLU 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 LEU 3.2 11.7 + - - +
72A ARG* 4.0 5.2 - - - +
74A LEU* 1.3 74.1 - - - +
76A ARG* 1.3 57.8 + - + +
78A GLY* 2.7 25.3 + - - -
80A ILE* 3.6 31.3 - - + +
81A VAL* 4.7 1.6 - - - +
82A ARG* 3.3 41.2 + - + +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.3 16.1 + - + +
73A GLU* 3.4 9.8 + - - +
75A GLU* 1.3 77.3 - - + +
77A GLY* 1.3 57.0 + - - +
78A GLY 3.4 2.1 + - - -
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Residues in contact with GLY 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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73A GLU 3.1 14.1 + - - -
74A LEU* 3.5 2.7 - - - -
75A GLU 3.1 0.4 - - - -
76A ARG* 1.3 75.4 - - - +
78A GLY* 1.3 60.3 + - - +
79A LEU* 3.2 13.4 + - - +
99A GLU* 3.5 19.6 - - - +
8C GLN* 5.6 0.2 - - - +
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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