Contacts of the helix formed by residues 78 - 100 (chain A) in PDB entry 3UX9
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 5.5 2.3 + - - +
23A ARG* 3.4 19.5 + - + +
77A TRP* 1.3 73.5 - - - +
79A GLU* 1.3 68.9 + - - +
80A ASP* 3.6 19.2 + - - +
81A LEU* 3.6 33.4 + - + +
82A LEU* 3.0 26.9 + - - +
43D PRO* 5.4 8.9 - - - +
44D GLY* 5.4 4.2 + - - -
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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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77A TRP 3.5 3.1 + - - -
78A ASP* 1.3 76.8 + - - +
80A ASP* 1.3 65.9 + - - +
82A LEU* 3.8 3.9 - - - +
83A ASP* 3.0 24.9 + - + +
43D PRO* 6.2 1.5 - - + +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 3.5 10.8 + - - +
79A GLU* 1.3 80.3 - - - +
81A LEU* 1.3 68.4 + - + +
83A ASP* 3.2 13.3 + - - +
84A LYS* 3.2 48.3 + - - +
43D PRO* 5.2 4.3 - - + +
44D GLY* 3.8 31.6 - - - +
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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
----------------------------------------------------------
17A LEU* 4.6 18.1 - - + +
20A GLN* 3.3 50.7 - - + +
21A MET* 3.8 19.7 - - + -
78A ASP* 3.6 27.4 + - + +
79A GLU 3.4 0.4 - - - -
80A ASP* 1.3 82.2 - - + +
82A LEU* 1.3 60.3 + - - +
83A ASP 3.2 0.2 + - - -
84A LYS* 3.2 14.3 + - + +
85A PHE* 2.8 30.3 + - - +
248D LEU* 6.3 0.7 - - + -
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Residues in contact with LEU 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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21A MET* 4.3 8.2 - - + +
68A PHE* 3.9 34.5 - - + +
73A SER* 3.8 22.2 - - - +
74A SER* 3.9 25.4 - - - -
77A TRP* 4.2 17.3 - - + +
78A ASP 3.0 18.8 + - - +
79A GLU* 3.8 4.0 - - - +
81A LEU* 1.3 79.5 - - - +
83A ASP* 1.3 56.5 + - - +
85A PHE* 3.4 7.4 - - + +
86A CYS* 2.8 45.9 + - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.0 13.2 + - + +
80A ASP* 3.2 11.2 + - - +
82A LEU* 1.3 74.9 - - - +
84A LYS* 1.3 65.2 + - - +
86A CYS* 3.2 4.6 + - - +
87A THR* 2.8 51.1 + - - +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 25.3 - - + +
80A ASP* 3.3 42.5 + - - +
81A LEU* 3.5 12.3 - - + +
83A ASP* 1.3 79.1 + - - +
85A PHE* 1.3 63.5 + - - +
87A THR* 3.3 8.5 + - - -
88A GLU* 3.0 24.4 + - - +
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Residues in contact with PHE 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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14A THR* 3.7 22.4 - - + -
17A LEU* 3.6 29.6 - - + +
18A LEU* 3.3 40.6 - - + -
21A MET* 4.0 15.9 - - - -
64A ILE* 4.3 10.1 - - + -
68A PHE* 3.9 25.4 - + + -
81A LEU 2.8 16.6 + - - +
82A LEU* 3.4 18.2 - - + +
83A ASP 3.2 0.2 - - - -
84A LYS* 1.3 79.6 - - - +
86A CYS* 1.3 63.3 + - - +
88A GLU* 3.3 3.6 + - - +
89A LEU* 3.1 48.5 + - + +
152A LEU* 5.3 0.7 - - + -
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Residues in contact with CYS 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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65A PHE* 3.9 8.1 - - + -
68A PHE* 3.9 20.4 - - - -
69A THR* 3.8 30.3 - - + -
82A LEU* 2.8 35.8 + - - +
83A ASP* 3.8 5.2 - - - +
85A PHE* 1.3 75.6 - - - +
87A THR* 1.3 64.1 + - + +
89A LEU* 3.3 12.5 + - - +
90A TYR* 2.8 26.2 + - - +
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Residues in contact with THR 87 (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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83A ASP* 2.8 40.8 + - - +
84A LYS* 3.3 12.1 + - - -
86A CYS* 1.3 78.1 - - + +
88A GLU* 1.3 60.0 + - - +
90A TYR* 3.0 28.2 - - + +
91A GLN* 3.0 24.6 + - - +
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Residues in contact with GLU 88 (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 ASP 5.3 3.5 - - - +
13A ARG* 3.6 32.7 + - + +
14A THR* 3.9 21.8 - - + -
17A LEU* 4.6 6.3 - - + -
84A LYS 3.0 14.0 + - - +
85A PHE 3.5 9.2 - - - +
87A THR* 1.3 74.0 + - - +
89A LEU* 1.3 67.6 + - - +
90A TYR 3.0 0.3 + - - -
91A GLN* 3.1 26.2 + - - +
92A GLN* 2.9 33.3 + - + +
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Residues in contact with LEU 89 (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 THR* 4.0 13.0 - - + -
61A ILE* 3.9 17.2 - - + +
64A ILE* 4.0 22.9 - - + +
65A PHE* 3.9 32.5 - - + -
68A PHE* 5.0 0.9 - - + -
85A PHE* 3.1 42.5 + - + +
86A CYS* 3.5 15.7 - - - +
88A GLU* 1.3 79.4 - - - +
90A TYR* 1.3 56.1 + - - +
92A GLN* 3.3 22.6 + - - +
93A LEU* 2.8 35.8 + - - +
152A LEU* 5.8 1.8 - - + -
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Residues in contact with TYR 90 (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 PHE* 4.6 18.8 - + + -
86A CYS 2.8 14.6 + - - +
87A THR* 3.0 20.4 - - - +
88A GLU 3.0 0.2 - - - -
89A LEU* 1.3 77.2 - - - +
91A GLN* 1.3 66.5 + - + +
93A LEU* 3.5 6.9 + - + +
94A ASN* 3.1 50.6 + - - +
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Residues in contact with GLN 91 (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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87A THR* 3.0 23.0 + - - +
88A GLU* 3.8 25.4 + - - +
90A TYR* 1.3 76.5 - - + +
92A GLN* 1.3 68.9 + - - +
93A LEU 3.0 1.6 - - - -
94A ASN* 3.0 11.7 + - - +
95A ASP* 2.8 37.7 + - - +
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Residues in contact with GLN 92 (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 4.2 11.7 - - - +
10A ASP 3.9 13.6 + - - +
11A ASN* 3.6 26.1 - - - +
14A THR* 3.7 20.5 + - - +
61A ILE* 3.6 19.9 - - + +
88A GLU* 2.9 24.0 + - - +
89A LEU* 3.4 34.9 - - - +
91A GLN* 1.3 75.0 - - - +
93A LEU* 1.3 64.9 + - - +
95A ASP* 3.3 7.6 + - - +
96A LEU* 2.8 32.6 + - + +
152A LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 93 (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 HIS* 3.7 32.5 - - + +
61A ILE* 3.9 11.9 - - + -
62A GLN* 3.9 41.3 - - + +
65A PHE* 4.2 29.6 - - + -
89A LEU 2.8 18.7 + - - +
90A TYR* 3.6 8.5 - - + +
91A GLN 3.0 0.2 - - - -
92A GLN* 1.3 75.2 - - - +
94A ASN* 1.3 56.1 + - - +
96A LEU* 3.0 5.6 + - + +
97A GLU* 2.7 45.3 + - - +
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Residues in contact with ASN 94 (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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90A TYR* 3.1 49.3 + - - +
91A GLN* 3.0 9.5 + - - +
93A LEU* 1.3 77.9 - - - +
95A ASP* 1.3 69.9 + - - +
97A GLU* 3.0 19.5 + - - +
98A ALA* 3.2 12.3 + - - +
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Residues in contact with ASP 95 (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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91A GLN* 2.8 32.9 + - - +
92A GLN* 3.6 6.9 + - - +
94A ASN* 1.3 76.4 - - - +
96A LEU* 1.3 66.8 + - + +
97A GLU 3.1 0.9 + - - -
98A ALA* 3.3 17.8 + - - +
99A CYS* 3.7 11.1 - - - -
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Residues in contact with LEU 96 (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* 4.9 22.2 - - + +
54A ILE* 3.4 22.9 - - + +
57A LEU* 4.4 6.7 - - + -
58A HIS* 3.9 33.2 - - + +
61A ILE* 3.6 33.2 - - + -
92A GLN* 2.8 26.4 + - + +
93A LEU* 3.2 10.1 - - - +
95A ASP* 1.3 76.2 - - + +
97A GLU* 1.3 59.1 + - - +
99A CYS* 3.3 4.3 + - - -
100A VAL* 2.9 26.9 + - - +
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Residues in contact with GLU 97 (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 HIS* 3.1 30.6 + - - +
62A GLN* 4.8 5.0 + - - -
93A LEU* 2.7 38.9 + - - +
94A ASN* 3.4 11.3 + - - +
95A ASP 3.0 0.6 - - - -
96A LEU* 1.3 75.1 - - - +
98A ALA* 1.3 67.4 + - - +
100A VAL* 3.5 19.8 + - - +
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Residues in contact with ALA 98 (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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94A ASN 3.2 10.0 + - - +
95A ASP* 3.5 11.7 - - - +
97A GLU* 1.3 78.6 - - - +
99A CYS* 1.3 63.8 + - - +
100A VAL 3.0 6.2 + - - -
101A MET* 3.3 21.2 + - - +
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Residues in contact with CYS 99 (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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54A ILE* 3.6 27.7 - - + +
95A ASP 3.7 15.3 - - - -
96A LEU* 3.3 2.1 + - - -
98A ALA* 1.3 82.4 - - - +
100A VAL* 1.3 55.3 + - - +
101A MET* 3.0 31.3 + - + +
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Residues in contact with VAL 100 (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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54A ILE* 3.8 22.4 - - + +
55A SER* 4.8 17.3 - - - +
58A HIS* 4.5 20.2 - - + +
96A LEU 2.9 22.7 - - - +
97A GLU* 4.0 13.6 - - - +
98A ALA 3.0 4.3 + - - -
99A CYS* 1.3 76.4 - - - +
101A MET* 1.3 56.7 + - - +
102A GLN* 4.3 5.9 + - + -
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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