Contacts of the helix formed by residues 66 - 86 (chain A) in PDB entry 1RQG
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 SER 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA* 4.1 0.4 - - - -
65A ARG* 1.3 74.2 - - - +
67A PRO* 1.3 75.3 - - - +
68A ARG* 3.7 9.8 + - - +
69A GLU* 2.6 55.4 + - - +
70A ILE* 3.4 6.2 + - - +
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Residues in contact with PRO 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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56A ILE* 4.1 8.1 - - + -
57A SER* 4.3 8.7 - - - -
60A ALA* 3.6 24.5 - - + -
65A ARG 3.7 0.2 - - - -
66A SER* 1.3 85.6 - - - +
68A ARG* 1.3 61.1 + - - +
70A ILE* 3.5 7.7 + - + +
71A VAL* 3.2 28.1 + - - +
235A TRP* 3.5 50.5 - - + +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.0 8.9 - - - +
67A PRO* 1.3 78.8 - - - +
69A GLU* 1.3 66.1 + - - +
71A VAL* 3.2 10.0 - - - +
72A ASP* 3.0 53.8 + - - +
94A ARG* 3.8 12.8 - - - +
96A GLU* 3.0 51.8 + - - +
235A TRP* 3.8 16.8 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.1 31.9 + - + +
66A SER* 2.6 46.3 + - - +
68A ARG* 1.3 80.7 - - - +
70A ILE* 1.3 64.0 + - - +
72A ASP* 3.4 6.4 + - - +
73A GLU* 3.1 22.2 + - - +
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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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13A ALA 3.5 20.6 - - - +
14A ASN* 3.6 10.3 - - - +
56A ILE* 3.7 18.8 - - + +
59A ARG* 3.2 37.2 - - + +
60A ALA* 4.9 9.0 - - + -
65A ARG* 3.6 33.0 - - + +
66A SER 3.4 16.6 - - - +
67A PRO* 3.8 11.4 - - + +
69A GLU* 1.3 76.1 - - - +
71A VAL* 1.3 61.9 + - - +
73A GLU* 3.1 4.4 + - - +
74A PHE* 2.9 33.9 + - + +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 4.0 11.2 - - + +
51A GLU* 3.6 44.2 - - + +
56A ILE* 3.7 22.9 - - + -
67A PRO 3.2 15.0 + - - +
68A ARG* 3.2 22.2 - - - +
70A ILE* 1.3 79.4 - - + +
72A ASP* 1.3 65.4 + - - +
75A HIS* 2.9 33.4 + - - +
94A ARG* 3.9 13.9 - - - +
96A GLU* 4.7 1.1 - - + -
235A TRP* 4.3 7.2 - - + +
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Residues in contact with ASP 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 ARG* 3.0 47.7 + - - +
69A GLU* 3.6 7.0 - - - +
71A VAL* 1.3 79.2 - - - +
73A GLU* 1.3 63.7 + - - +
75A HIS* 4.1 2.7 + - - +
76A GLU* 3.5 19.2 + - - +
94A ARG* 2.6 39.6 + - - +
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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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65A ARG* 2.7 31.4 + - - +
69A GLU 3.1 11.2 + - - +
70A ILE 3.1 9.9 + - - +
72A ASP* 1.3 79.6 - - - +
74A PHE* 1.3 70.7 + - + +
76A GLU* 3.5 4.5 + - - +
77A GLN* 3.1 25.6 + - + +
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Residues in contact with PHE 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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13A ALA* 3.6 29.6 - - + +
14A ASN* 3.4 8.1 - - - -
15A GLY* 3.3 51.6 - - - -
16A PRO* 3.6 14.1 - - + -
49A THR* 4.8 0.7 - - - -
59A ARG* 3.8 26.0 - - - -
65A ARG* 6.2 1.3 - - - -
70A ILE* 2.9 22.8 + - + +
73A GLU* 1.3 84.6 - - + +
75A HIS* 1.3 61.6 + - - +
76A GLU 3.1 1.3 - - - -
77A GLN* 3.7 21.1 - - + -
78A ILE* 2.8 37.4 + - + +
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Residues in contact with HIS 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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49A THR* 2.9 34.5 - - - +
51A GLU* 3.9 4.5 - - - +
71A VAL 2.9 19.0 + - - +
72A ASP 4.1 3.6 - - - +
73A GLU 3.3 0.2 - - - -
74A PHE* 1.3 77.2 - - - +
76A GLU* 1.3 61.2 + - - +
78A ILE* 4.1 0.3 - - - +
79A LYS* 2.8 53.1 + - + +
92A PHE* 3.5 27.1 + + - -
93A GLY 3.4 19.6 + - - -
94A ARG* 3.8 30.6 + - + +
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Residues in contact with GLU 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 ASP 3.5 10.0 + - - +
73A GLU* 3.7 8.7 - - - +
74A PHE 3.1 0.2 - - - -
75A HIS* 1.3 81.2 + - - +
77A GLN* 1.3 66.5 + - - +
79A LYS* 4.3 16.5 + - + +
80A ILE* 3.0 61.8 + - - +
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Residues in contact with GLN 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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16A PRO* 3.7 24.7 - - - +
17A ILE 4.9 0.8 - - - +
73A GLU* 3.1 16.5 + - + +
74A PHE* 3.9 18.8 - - + +
75A HIS 3.4 0.2 - - - -
76A GLU* 1.3 81.5 + - - +
78A ILE* 1.3 64.4 + - - +
80A ILE* 3.7 4.0 + - - +
81A THR* 2.6 44.7 + - - -
356A HIS* 3.4 35.2 + - - +
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Residues in contact with ILE 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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11A PRO* 4.1 9.4 - - + -
12A TYR 4.2 10.1 - - - +
15A GLY 3.3 25.4 - - - +
17A ILE* 3.9 22.9 - - + -
49A THR* 4.1 16.6 - - + -
74A PHE* 2.8 26.9 + - + +
75A HIS 4.1 1.1 - - - +
77A GLN* 1.3 88.1 - - - +
79A LYS* 1.3 59.2 + - - +
81A THR* 3.1 4.9 + - - -
82A PHE* 2.9 57.1 + - + -
92A PHE* 3.8 10.3 - - + -
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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 HIS* 2.8 40.1 + - + +
76A GLU* 4.0 20.9 + - + +
78A ILE* 1.3 74.6 - - - +
80A ILE* 1.3 61.7 + - + +
82A PHE* 3.4 6.1 + - - +
83A GLN* 2.7 51.9 + - - +
92A PHE* 3.6 31.4 - - + +
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Residues in contact with ILE 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 GLU* 3.0 47.8 + - - +
77A GLN* 4.0 4.0 - - - +
79A LYS* 1.3 78.8 - - + +
81A THR* 1.3 63.7 + - - +
83A GLN* 3.0 23.9 + - + +
84A ARG* 2.8 48.0 + - + +
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Residues in contact with THR 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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17A ILE* 4.3 18.6 - - + +
77A GLN* 2.6 41.2 + - - +
78A ILE* 3.1 8.9 + - - -
80A ILE* 1.3 77.2 - - - +
82A PHE* 1.3 51.9 + - - +
84A ARG* 2.9 13.7 + - + +
85A ALA* 2.7 31.9 + - - +
355A VAL* 3.7 32.5 - - + -
356A HIS* 3.8 15.4 - - + +
359A LEU* 4.7 0.2 - - - +
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Residues in contact with PHE 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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11A PRO* 4.0 5.8 - - + -
17A ILE* 3.3 30.7 - - + -
22A LEU* 4.2 1.6 - - + -
26A TYR* 3.6 47.6 - + + -
78A ILE* 2.9 40.7 + - + +
79A LYS* 3.7 5.2 - - - +
80A ILE 3.2 0.2 - - - -
81A THR* 1.3 72.7 - - - +
83A GLN* 1.3 61.4 + - - +
85A ALA* 3.2 3.7 + - + -
86A LYS 2.9 22.3 + - - -
87A ILE* 3.0 33.2 + - + +
89A PHE* 3.3 27.6 - + + -
92A PHE* 3.5 26.7 - + + -
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Residues in contact with GLN 83 (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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79A LYS* 2.7 47.5 + - - +
80A ILE* 3.0 30.7 + - + +
82A PHE* 1.3 75.2 - - - +
84A ARG* 1.3 59.7 + - + +
86A LYS* 2.9 31.0 + - - +
87A ILE 5.0 3.1 - - - +
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Residues in contact with ARG 84 (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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80A ILE* 2.8 34.8 + - + +
81A THR* 3.1 12.4 - - + +
83A GLN* 1.3 78.7 - - + +
85A ALA* 1.3 57.9 + - - +
86A LYS* 3.3 6.6 + - - +
356A HIS* 2.6 43.9 + - - +
359A LEU* 3.1 47.1 + - + +
360A ASP* 2.7 15.9 + - - +
364A ALA* 3.6 19.2 - - - +
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Residues in contact with ALA 85 (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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22A LEU* 4.3 22.2 - - + -
81A THR* 2.7 18.5 + - + +
82A PHE* 3.2 8.5 + - + +
84A ARG* 1.3 71.3 - - - +
86A LYS* 1.3 67.5 + - - +
87A ILE* 3.7 17.9 - - + -
355A VAL* 4.4 8.3 - - + -
359A LEU* 3.8 8.0 - - + +
364A ALA* 4.7 2.5 - - - -
367A LEU* 6.2 0.4 - - + -
368A ARG* 2.9 28.0 + - - +
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Residues in contact with LYS 86 (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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30A ASP* 2.9 0.9 - - - +
34A ARG* 2.7 33.1 + - - +
82A PHE 2.9 3.6 + - - -
83A GLN* 2.9 18.5 + - - +
84A ARG* 3.1 9.9 + - - +
85A ALA* 1.3 82.0 - - - +
87A ILE* 1.3 58.5 + - - +
364A ALA* 4.3 7.6 - - + +
368A ARG* 2.8 20.1 + - - +
509A PRO* 4.3 17.9 - - + -
510A ASP* 2.7 45.0 + - - +
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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