Contacts of the helix formed by residues 80 - 100 (chain A) in PDB entry 1XTG
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 THR 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 1.3 88.5 - - - +
81A ASP* 1.3 65.2 + - - +
82A ASN* 3.8 9.3 + - - +
83A GLU* 3.1 34.0 + - - +
84A LYS* 3.0 26.9 + - - +
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Residues in contact with ASP 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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10A TYR* 3.4 34.9 - - + +
11A LYS* 6.0 3.7 - - + +
80A THR* 1.3 74.6 - - - +
82A ASN* 1.3 60.1 + - - +
84A LYS* 3.3 6.4 + - - +
85A ASP* 2.8 30.2 + - - +
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Residues in contact with ASN 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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80A THR* 3.2 8.1 + - - +
81A ASP* 1.3 80.0 - - - +
83A GLU* 1.3 58.7 + - + +
85A ASP* 3.3 7.5 + - - +
86A ASN* 2.9 28.1 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR 3.7 5.7 - - - +
77A TYR* 3.5 21.1 - - + -
78A LEU* 3.0 32.0 + - + +
79A SER 3.1 17.5 + - - -
80A THR* 3.1 30.0 + - - +
82A ASN* 1.3 76.0 - - + +
84A LYS* 1.3 55.8 + - - +
86A ASN* 3.1 6.6 + - - +
87A TYR* 2.7 36.0 + - - +
191A ASP* 5.1 1.9 - - - +
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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
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10A TYR* 3.5 41.7 + - + +
46A PRO* 3.3 23.6 - - + +
47A GLU* 2.7 34.2 + - - -
78A LEU* 3.4 33.7 - - + +
79A SER* 4.1 12.2 + - - +
80A THR 3.0 17.8 + - - +
81A ASP* 3.7 8.1 + - - +
83A GLU* 1.3 75.6 - - - +
85A ASP* 1.3 57.4 + - - +
87A TYR* 3.4 2.6 + - - +
88A LEU* 3.0 28.4 + - - +
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Residues in contact with ASP 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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8A PHE 4.3 0.5 - - - +
9A ASN* 3.5 5.6 - - - +
10A TYR* 2.9 36.0 + - + +
81A ASP 2.8 18.3 + - - +
82A ASN* 3.6 8.3 - - - +
84A LYS* 1.3 77.7 - - - +
86A ASN* 1.3 62.5 + - - +
88A LEU* 3.4 4.9 + - - +
89A LYS* 2.6 59.2 + - - +
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Residues in contact with ASN 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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82A ASN 2.9 17.2 + - - +
83A GLU* 3.6 7.0 - - - +
85A ASP* 1.3 75.1 + - - +
87A TYR* 1.3 60.8 + - - +
89A LYS* 3.5 5.1 + - - +
90A GLY* 2.9 25.5 + - - -
191A ASP* 3.3 23.3 - - - +
375A LYS* 5.7 1.4 + - - -
377A ASN* 3.9 16.4 + - - +
379A VAL* 3.1 33.9 - - - +
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Residues in contact with TYR 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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44A VAL* 4.0 13.2 - - + -
45A ILE 4.4 1.1 - - - -
46A PRO* 3.6 26.0 - - + -
77A TYR* 3.7 14.1 - - - -
78A LEU* 4.0 20.0 - - + -
83A GLU 2.7 20.4 + - - +
84A LYS* 3.6 4.3 - - - +
86A ASN* 1.3 70.3 - - - +
88A LEU* 1.3 70.9 + - - +
90A GLY* 3.1 0.7 + - - -
91A VAL* 2.9 39.8 + - + +
153A ILE* 3.6 12.1 - - - +
154A ILE* 3.1 18.4 + - - -
155A GLY* 4.0 14.1 - - - -
188A PHE 2.8 28.9 + - - -
189A SER* 4.0 2.2 - - - -
190A PRO* 3.6 25.9 - - + +
191A ASP* 4.3 6.2 + - - +
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Residues in contact with LEU 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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8A PHE* 3.6 39.9 - - + +
10A TYR* 4.5 8.3 - - + +
36A PHE* 3.8 39.9 - - + -
38A ILE* 4.7 6.5 - - + -
44A VAL* 3.9 29.2 - - + -
46A PRO* 5.0 4.7 - - + -
84A LYS 3.0 17.0 + - - +
85A ASP* 3.7 6.1 - - - +
87A TYR* 1.3 81.6 - - - +
89A LYS* 1.3 58.7 + - + +
91A VAL* 4.0 2.6 - - + +
92A THR* 2.8 40.4 + - - +
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Residues in contact with LYS 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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8A PHE 3.8 13.2 + - - +
9A ASN* 3.4 19.4 + - - -
85A ASP* 2.6 54.7 + - - +
86A ASN* 3.9 5.6 - - - +
87A TYR 3.2 0.2 - - - -
88A LEU* 1.3 75.7 - - + +
90A GLY* 1.3 60.4 + - - +
92A THR* 3.7 6.7 - - - -
93A LYS* 3.0 28.8 + - - +
379A VAL* 3.9 28.1 - - + +
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Residues in contact with GLY 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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86A ASN 2.9 16.6 + - - -
87A TYR 3.1 2.4 + - - -
89A LYS* 1.3 74.7 - - - +
91A VAL* 1.3 65.0 + - - +
93A LYS* 3.3 3.6 + - - +
94A LEU* 3.1 27.2 + - - +
190A PRO* 3.9 17.7 - - - -
191A ASP* 5.8 0.2 - - - -
378A ILE* 3.8 10.4 - - - +
379A VAL* 4.0 10.7 - - - +
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Residues in contact with VAL 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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38A ILE* 5.2 0.4 - - + -
44A VAL* 4.2 16.2 - - + -
87A TYR* 2.9 49.8 + - + +
88A LEU 4.0 3.6 - - - +
90A GLY* 1.3 75.5 - - - +
92A THR* 1.3 63.2 + - - +
94A LEU* 3.3 7.5 + - - +
95A PHE* 3.1 46.6 + - + -
153A ILE* 4.1 14.4 - - + -
188A PHE* 4.3 11.4 - - + -
190A PRO* 3.9 14.5 - - + +
221A LEU* 5.3 3.1 - - + -
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Residues in contact with THR 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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4A VAL* 3.8 32.4 - - + +
6A LYS 5.6 1.3 - - - +
8A PHE* 5.8 2.1 - - - +
38A ILE* 4.6 11.5 - - - +
88A LEU* 2.8 32.3 + - - +
89A LYS* 3.7 8.0 - - - -
91A VAL* 1.3 79.4 - - - +
93A LYS* 1.3 62.4 + - - +
95A PHE* 3.2 8.8 + - - +
96A GLU* 3.0 28.5 + - + +
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Residues in contact with LYS 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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89A LYS 3.0 17.7 + - - +
90A GLY* 3.3 6.3 + - - +
92A THR* 1.3 77.7 - - - +
94A LEU* 1.3 57.9 - - - +
96A GLU* 3.2 9.4 + - - +
97A ARG* 2.9 26.3 + - - +
378A ILE* 2.7 30.7 + - + +
379A VAL* 2.8 25.2 + - - +
380A PRO 3.7 3.4 + - - -
381A LYS* 4.1 4.0 - - - +
384A TYR* 2.6 43.6 + - + -
385A THR* 4.1 2.9 - - - +
386A ILE* 4.1 14.1 - - + +
427A CL 3.7 21.7 - - - +
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Residues in contact with LEU 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 GLY 3.1 16.8 + - - +
91A VAL* 3.8 4.5 - - - +
92A THR 3.2 0.2 - - - -
93A LYS* 1.3 73.4 - - - +
95A PHE* 1.3 61.1 + - - +
97A ARG* 3.2 3.8 + - + +
98A ILE* 2.9 34.0 + - - +
188A PHE* 3.6 37.9 - - + -
190A PRO* 3.8 16.6 - - + -
217A PRO* 3.8 15.5 - - + +
218A ALA* 3.9 15.9 - - + +
221A LEU* 3.8 13.9 - - + -
378A ILE* 3.5 17.9 - - + -
384A TYR* 3.5 29.2 - - + +
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Residues in contact with PHE 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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2A PRO 3.9 25.4 - - - +
4A VAL* 4.8 2.7 - - + -
38A ILE* 3.8 21.5 - - + -
42A ILE* 4.4 10.1 - - + -
91A VAL* 3.1 44.7 + - + -
92A THR* 3.2 8.9 + - - +
94A LEU* 1.3 76.2 - - - +
96A GLU* 1.3 60.0 + - - +
98A ILE* 3.3 7.9 + - + +
99A TYR* 2.8 28.5 + - - +
108A LEU* 3.7 35.8 - - + +
151A LEU* 4.3 8.3 - - + -
153A ILE* 3.8 30.3 - - + -
221A LEU* 4.3 9.9 - - + -
225A LEU* 4.4 15.3 - - + -
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Residues in contact with GLU 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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2A PRO 4.5 1.1 - - - -
3A PHE* 3.1 35.8 - - - -
4A VAL* 2.6 39.6 + - - +
92A THR* 3.0 26.3 + - + +
93A LYS* 3.5 8.3 - - - +
94A LEU 3.2 0.2 - - - -
95A PHE* 1.3 77.5 - - - +
97A ARG* 1.3 61.7 + - - +
99A TYR* 3.1 12.5 + - - +
100A SER* 2.9 22.3 + - - -
386A ILE* 3.7 28.5 - - + +
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Residues in contact with ARG 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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93A LYS 2.9 13.8 + - - +
94A LEU* 3.2 11.4 + - - +
96A GLU* 1.3 76.0 - - - +
98A ILE* 1.3 62.4 + - - +
100A SER* 2.5 24.6 + - - -
216A ASP* 3.0 20.0 + - - -
218A ALA* 3.7 14.7 - - + +
358A PHE* 3.4 36.3 + - + +
360A VAL* 3.8 17.4 - - - +
384A TYR* 3.0 39.6 + - + -
385A THR 3.8 1.8 - - - -
386A ILE* 3.0 42.9 + - - +
387A TYR* 3.3 21.2 + - - +
388A ASP 3.8 4.6 + - - -
389A GLY* 3.5 13.9 - - - +
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Residues in contact with ILE 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 LEU 2.9 12.0 + - - +
95A PHE* 3.6 9.2 - - - +
97A ARG* 1.3 77.1 - - - +
99A TYR* 1.3 59.6 + - - +
100A SER 3.1 4.3 + - - -
101A THR* 3.5 8.7 + - - -
104A GLY* 3.1 39.7 + - - +
107A LEU* 5.2 0.9 - - + -
108A LEU* 3.8 19.5 - - + -
218A ALA* 3.9 14.8 - - + +
221A LEU* 3.8 26.2 - - + -
222A ALA* 3.9 16.2 - - + +
225A LEU* 3.5 28.5 - - + -
354A PHE* 4.3 9.0 - - + -
358A PHE* 3.9 14.3 - - + -
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Residues in contact with TYR 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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2A PRO* 4.0 13.9 - - + -
3A PHE* 3.5 55.1 - + + +
95A PHE 2.8 17.2 + - - +
96A GLU* 3.1 18.1 + - - +
98A ILE* 1.3 76.3 - - - +
100A SER* 1.3 55.5 + - - +
101A THR 3.2 2.0 - - - -
105A ARG* 3.0 66.2 + - + +
108A LEU* 4.1 12.3 - - + -
109A THR* 6.0 1.3 - - - -
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Residues in contact with SER 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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96A GLU 2.9 10.1 + - - -
97A ARG* 2.5 21.9 + - - -
98A ILE 3.1 0.4 - - - -
99A TYR* 1.3 77.2 - - - +
101A THR* 1.3 67.0 + - - +
105A ARG* 3.6 10.1 + - - +
358A PHE* 4.3 2.6 - - - -
386A ILE* 3.9 14.4 + - - -
387A TYR* 3.7 44.0 + - - -
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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