Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 1JQI
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A HIS* 3.2 24.8 + - - -
58A MET* 5.0 1.7 - - - +
59A ASP* 3.9 12.1 - - - -
69A LEU* 1.3 81.5 - - - +
71A TYR* 1.3 60.4 + - - +
72A LEU* 4.0 1.9 - - - +
73A ALA* 2.9 21.5 + - - +
74A TYR* 3.0 22.7 + - - +
312A ASP* 3.3 25.0 - - + +
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Residues in contact with TYR 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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59A ASP* 3.4 33.8 + - + -
70A ASP* 1.3 71.0 - - - +
72A LEU* 1.3 59.2 + - - +
74A TYR* 3.5 30.7 - + + +
75A SER* 3.0 28.8 + - - -
96A ASN* 4.6 3.1 + - + -
97A SER* 2.8 35.2 + - - -
101A GLY* 5.8 0.3 - - - -
246A MET* 3.6 38.1 - - + +
249A ILE* 4.2 21.5 - - + -
308A ALA* 3.6 17.7 - - + +
311A LYS* 3.4 27.8 - - + -
312A ASP* 2.8 20.0 + - - +
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Residues in contact with LEU 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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10A LEU* 4.1 21.3 - - + -
11A PRO* 5.0 4.9 - - + -
14A HIS* 4.2 20.2 - - + +
70A ASP* 3.3 6.2 - - - +
71A TYR* 1.3 76.3 - - - +
73A ALA* 1.3 63.3 + - - +
75A SER* 3.5 0.9 + - - -
76A ILE* 3.3 29.4 + - + +
305A TRP* 4.1 40.4 - - + -
308A ALA* 3.9 7.4 - - + +
309A MET* 3.8 28.7 - - + -
312A ASP* 3.1 17.3 + - - +
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Residues in contact with ALA 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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14A HIS* 3.5 20.6 - - + +
17A LEU* 3.6 12.6 - - + +
58A MET* 3.9 3.4 - - + -
69A LEU* 3.9 29.8 - - + -
70A ASP* 2.9 23.0 + - - +
72A LEU* 1.3 77.9 - - - +
74A TYR* 1.3 55.9 + - - +
76A ILE* 3.4 2.6 + - - +
77A ALA* 3.0 31.2 + - - +
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Residues in contact with TYR 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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58A MET* 3.7 31.1 - - + +
59A ASP 5.8 1.1 - - - +
70A ASP 3.0 14.6 + - - +
71A TYR* 3.5 42.4 - + + +
72A LEU 3.3 0.2 - - - -
73A ALA* 1.3 76.5 - - - +
75A SER* 1.3 58.8 + - - +
77A ALA* 3.5 1.2 + - - +
78A LEU* 2.9 46.7 + - + +
92A MET* 4.4 5.4 - - + -
93A SER* 3.1 31.6 + - - -
96A ASN* 3.4 30.5 - - + -
97A SER* 2.7 28.9 + - - -
249A ILE* 5.3 2.2 - - + -
250A GLY* 4.0 14.4 - - - -
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Residues in contact with SER 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 TYR 3.0 16.7 + - - -
72A LEU 3.8 4.7 - - - -
73A ALA 3.3 0.2 - - - -
74A TYR* 1.3 80.9 - - - +
76A ILE* 1.3 61.9 + - - +
78A LEU* 3.3 1.0 + - - -
79A GLU* 3.0 23.9 + - - +
249A ILE* 4.8 4.0 - - - -
253A SER* 2.7 30.9 + - - -
256A LEU* 5.1 2.3 - - - +
304A THR* 3.3 18.9 - - - +
305A TRP* 4.0 13.8 + - - -
308A ALA* 4.4 10.3 - - - -
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Residues in contact with ILE 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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5A TYR* 5.1 1.1 - - - +
10A LEU* 3.9 28.0 - - + -
14A HIS* 4.1 19.3 - - + +
17A LEU* 4.3 5.2 - - + -
18A ARG* 3.6 42.6 - - + -
72A LEU* 3.3 26.9 + - + +
73A ALA 3.4 4.2 + - - +
75A SER* 1.3 75.9 - - - +
77A ALA* 1.3 62.9 + - - +
79A GLU* 3.5 8.3 + - - +
80A GLU* 3.4 23.3 + - + +
305A TRP* 3.8 29.4 - - + +
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Residues in contact with ALA 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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17A LEU* 3.6 17.0 - - + -
21A CYS* 3.6 22.2 - - - +
55A LEU* 4.3 1.6 - - + -
58A MET* 3.8 23.1 - - + -
73A ALA 3.0 17.5 + - - +
74A TYR 3.9 0.2 - - - +
76A ILE* 1.3 77.3 - - - +
78A LEU* 1.3 60.2 + - - +
80A GLU* 3.5 2.6 + - - +
81A ILE* 3.1 31.3 + - - +
92A MET* 4.3 4.7 - - + -
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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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74A TYR* 2.9 29.7 + - + +
75A SER 3.8 3.6 - - - +
77A ALA* 1.3 74.8 - - - +
79A GLU* 1.3 59.0 + - - +
81A ILE* 4.5 1.1 - - + -
82A SER* 2.6 42.4 + - - +
89A GLY* 3.1 31.4 - - - +
92A MET* 3.7 28.7 - - + +
93A SER* 3.8 14.1 - - - +
250A GLY* 3.1 42.8 - - - +
253A SER* 3.9 6.5 - - - -
254A GLN* 4.4 1.3 - - + +
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Residues in contact with GLU 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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5A TYR* 4.1 10.3 + - - -
75A SER 3.0 16.2 + - - +
76A ILE* 3.7 7.8 - - - +
77A ALA 3.3 0.2 - - - -
78A LEU* 1.3 77.4 - - - +
80A GLU* 1.3 68.6 + - - +
82A SER 3.3 0.9 + - - -
83A ARG* 2.9 27.5 + - + +
253A SER* 3.5 16.8 + - - +
256A LEU* 4.0 15.3 - - + +
257A GLY* 3.4 23.3 - - - +
260A GLN* 4.3 11.8 - - + +
301A ARG* 3.0 47.2 + - - +
305A TRP* 4.9 4.0 + - - -
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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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5A TYR* 4.8 1.9 + - - -
18A ARG* 3.5 30.1 - - + +
21A CYS* 3.8 20.9 - - + -
22A ARG* 3.0 52.7 + - - +
25A ALA* 3.4 17.4 - - - +
76A ILE* 3.4 15.3 + - - +
77A ALA 3.9 1.8 - - - +
78A LEU 3.4 0.2 - - - -
79A GLU* 1.3 90.0 - - - +
81A ILE* 1.3 62.0 + - - +
83A ARG* 3.4 32.3 + - - +
84A GLY 3.5 0.2 + - - -
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Residues in contact with ILE 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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21A CYS* 4.3 16.4 - - + +
24A PHE* 3.8 29.6 - - + -
25A ALA* 4.4 0.2 - - - -
29A LEU* 3.7 19.1 - - + +
50A MET* 4.0 17.3 - - + -
55A LEU* 4.0 16.8 - - + -
77A ALA 3.1 18.7 + - - +
78A LEU 3.9 4.0 - - - +
80A GLU* 1.3 75.2 - - - +
82A SER* 1.3 60.0 + - - +
84A GLY* 2.9 17.2 + - - -
85A CYS 3.0 11.4 + - - +
88A THR* 4.0 11.0 - - + -
89A GLY* 4.1 13.5 - - - -
92A MET* 4.1 15.9 - - - -
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Residues in contact with SER 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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78A LEU* 2.6 24.8 + - - +
79A GLU 3.8 3.6 - - - -
81A ILE* 1.3 76.7 - - - +
83A ARG* 1.3 61.8 + - - +
84A GLY 3.3 0.3 + - - -
85A CYS* 3.4 17.0 + - - -
86A ALA* 3.4 14.3 + - - +
89A GLY* 3.6 13.7 - - - -
254A GLN* 3.2 47.9 - - - +
257A GLY* 4.2 5.7 - - - -
258A ILE* 4.4 3.8 + - - +
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Residues in contact with ARG 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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22A ARG* 4.2 21.1 + - - +
25A ALA* 5.7 2.8 - - - +
26A GLU* 3.2 30.1 + - - +
30A VAL* 5.2 8.5 - - - +
79A GLU* 2.9 14.8 + - + +
80A GLU* 3.4 29.3 + - - +
81A ILE 3.1 0.2 - - - -
82A SER* 1.3 76.8 - - - +
84A GLY* 1.3 61.6 + - - +
257A GLY* 3.3 24.0 - - - +
260A GLN* 3.7 24.2 - - - -
261A ALA* 3.7 24.9 - - + +
264A ASP* 2.9 24.4 + - - +
268A LYS* 5.4 4.9 - - - +
357A TYR* 4.9 6.2 + - - -
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Residues in contact with GLY 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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25A ALA* 4.3 7.1 - - - +
29A LEU* 4.0 20.0 - - - +
30A VAL* 4.2 19.1 + - - -
33A ALA* 3.4 18.9 - - - +
80A GLU 3.5 3.6 + - - -
81A ILE 2.9 7.5 + - - -
83A ARG* 1.3 83.5 - - - +
85A CYS* 1.3 61.7 + - - +
356A ARG* 4.2 5.1 + - - -
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Residues in contact with CYS 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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29A LEU* 4.3 11.6 - - + +
33A ALA* 4.3 16.6 - - + -
36A LEU* 4.3 19.1 - - + -
81A ILE 3.0 11.8 + - - +
82A SER* 3.4 4.7 + - - -
84A GLY* 1.3 80.5 - - - +
86A ALA* 1.3 65.3 + - - +
87A SER* 3.2 15.2 + - - -
88A THR* 3.3 34.3 + - - +
89A GLY 3.1 17.0 + - - -
211A ALA* 5.1 1.3 - - - -
356A ARG* 4.9 4.3 - - - +
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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