Contacts of the helix formed by residues 79 - 102 (chain D) in PDB entry 1GQA
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 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D ALA* 2.9 15.8 + - + +
76D ILE 3.8 3.3 - - - +
78D GLN* 1.3 80.0 - - + +
80D ALA* 1.3 62.8 + - - +
81D ASP* 3.2 8.1 + - - +
82D GLY* 3.3 26.2 + - - -
83D PHE* 3.0 21.3 + - - +
126D PHE* 4.1 14.2 - - + -
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ILE 3.6 13.1 + - - +
77D TRP* 4.4 8.7 - - - +
78D GLN 3.6 4.0 + - - -
79D ASP* 1.3 75.1 - - - +
81D ASP* 1.3 62.9 + - - +
83D PHE* 3.4 3.0 + - - +
84D GLN* 3.1 23.9 + - - +
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Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASP* 3.2 5.9 - - - +
80D ALA* 1.3 79.6 - - - +
82D GLY* 1.3 61.0 + - - +
84D GLN* 3.4 14.7 + - - +
85D ALA* 3.1 21.5 + - - +
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ASP* 3.3 23.4 + - - -
81D ASP* 1.3 75.9 - - - +
83D PHE* 1.3 66.2 - - - +
85D ALA* 3.2 8.8 + - - +
86D LYS* 3.0 27.3 + - - +
126D PHE* 4.0 6.3 - - - -
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TYR* 3.5 48.5 - + - -
76D ILE* 3.8 37.5 - - + +
79D ASP 3.0 16.0 + - - +
80D ALA* 3.9 4.5 - - - +
82D GLY* 1.3 75.5 - - - +
84D GLN* 1.3 64.7 + - - +
86D LYS* 3.1 5.0 + - - +
87D GLY* 3.0 19.7 + - - -
122D CYS* 3.6 24.5 - - - -
126D PHE* 3.6 33.4 - + + -
131D HEC 3.6 17.3 - - + -
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Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA 3.1 17.6 + - - +
81D ASP* 3.6 14.2 - - - +
83D PHE* 1.3 77.7 - - - +
85D ALA* 1.3 63.0 + - - +
87D GLY* 3.1 3.4 + - - +
88D MET* 2.9 44.3 + - + +
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP 3.1 11.4 + - - +
82D GLY* 3.3 13.0 - - - +
83D PHE 3.1 0.2 - - - -
84D GLN* 1.3 81.8 - - - +
86D LYS* 1.3 64.3 + - + +
88D MET* 3.3 12.2 + - - +
89D ALA* 3.1 22.4 + - - +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLY 3.0 20.8 + - - +
83D PHE 3.5 5.2 - - - +
85D ALA* 1.3 75.9 - - + +
87D GLY* 1.3 62.6 + - - +
89D ALA* 3.3 10.5 + - + +
90D PHE* 3.1 21.7 + - - +
118D THR* 5.1 2.1 - - - +
121D SER* 2.6 44.2 + - - +
122D CYS* 4.0 21.8 - - + +
125D ASP* 3.1 29.2 + - - -
126D PHE* 3.7 18.2 - - + -
131D HEC 4.2 4.1 - - - +
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 3.0 12.5 + - - -
84D GLN* 3.1 5.1 + - - -
86D LYS* 1.3 76.4 - - - +
88D MET* 1.3 56.0 + - - +
90D PHE* 3.3 10.4 + - - +
91D PHE* 2.9 26.7 + - - +
131D HEC 3.8 15.8 - - - +
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Residues in contact with MET 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D GLN* 2.9 48.0 + - + +
85D ALA* 3.7 9.2 - - - +
87D GLY* 1.3 73.2 - - - +
89D ALA* 1.3 58.8 + - - +
91D PHE* 3.0 10.8 + - + +
92D GLU* 2.7 59.0 + - - +
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA 3.1 10.2 + - - +
86D LYS* 3.5 13.2 - - + +
88D MET* 1.3 78.3 - - - +
90D PHE* 1.3 60.7 + - - +
92D GLU* 3.6 9.2 + - - +
93D ALA* 3.1 25.1 + - - +
118D THR* 3.6 16.1 - - + +
121D SER* 6.5 0.4 - - - -
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TYR* 4.6 15.5 - + - -
14D PHE* 5.9 1.6 - + - -
17D VAL* 3.9 26.0 - - + -
46D LEU* 4.9 4.9 - - + -
49D LEU* 6.5 0.2 - - + -
50D THR* 3.9 19.7 - - + -
86D LYS 3.1 6.5 + - - +
87D GLY* 3.4 11.2 - - - +
89D ALA* 1.3 73.4 - - - +
91D PHE* 1.3 67.3 + - - +
93D ALA* 3.2 1.9 + - - +
94D VAL* 3.0 48.5 + - + +
115D VAL* 4.4 2.0 - - + -
118D THR* 3.4 23.9 - - - +
131D HEC 3.5 61.9 - + + -
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 3.3 57.2 + - - -
51D LYS* 3.3 35.2 - - + -
87D GLY 2.9 17.1 + - - +
88D MET* 3.0 15.2 + - + +
90D PHE* 1.3 73.0 - - + +
92D GLU* 1.3 74.9 + - + +
94D VAL* 3.2 4.7 + - - +
95D ALA* 3.0 28.3 + - + +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D MET* 2.7 44.5 + - - +
89D ALA* 4.0 6.4 - - - +
91D PHE* 1.3 82.7 - - + +
93D ALA* 1.3 63.0 + - - +
95D ALA* 3.2 17.4 + - + +
96D ALA* 3.2 14.0 + - - +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA 3.1 18.1 + - - +
90D PHE 3.2 3.6 + - - +
92D GLU* 1.3 77.5 - - - +
94D VAL* 1.3 62.6 + - + +
96D ALA* 3.4 14.4 + - - +
97D LEU* 3.4 8.8 + - - +
111D ALA* 5.1 1.2 - - - +
114D LYS* 4.4 9.3 - - + +
115D VAL* 3.6 30.4 - - + +
118D THR* 3.9 19.1 - - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA 4.9 0.4 - - - +
46D LEU* 3.9 16.2 - - + -
47D VAL* 3.8 33.6 - - + +
50D THR* 3.7 25.1 - - + +
90D PHE* 3.0 44.8 + - + +
91D PHE 3.5 4.7 - - - +
93D ALA* 1.3 79.7 - - - +
95D ALA* 1.3 61.8 + - - +
97D LEU* 3.1 23.3 + - + +
98D GLU 3.6 4.2 + - - -
115D VAL* 4.4 11.9 - - + -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 4.7 9.0 - - + -
51D LYS* 6.3 0.7 - - - +
91D PHE* 3.0 23.2 + - + +
92D GLU* 3.2 12.5 + - + +
94D VAL* 1.3 79.9 - - - +
96D ALA* 1.3 58.8 + - - +
97D LEU 3.6 0.3 + - - -
98D GLU* 3.8 6.8 + - - +
99D PRO* 3.6 15.8 - - - +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLU 3.2 14.6 + - - +
93D ALA* 3.8 7.6 - - - +
94D VAL 3.1 0.8 - - - -
95D ALA* 1.3 74.8 - - - +
97D LEU* 1.3 62.3 + - - +
98D GLU 3.3 1.1 - - - -
99D PRO* 3.7 15.1 - - - +
100D ALA* 3.8 11.3 - - - +
111D ALA* 4.6 4.9 - - + +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 6.0 1.1 - - + -
24D LEU* 3.6 26.0 - - + -
43D ALA* 3.9 19.5 - - + +
46D LEU* 4.2 12.8 - - + -
93D ALA 3.4 10.7 + - - +
94D VAL* 3.1 14.8 + - - +
96D ALA* 1.3 78.3 - - - +
98D GLU* 1.3 66.4 + - - +
100D ALA* 3.2 1.6 + - - +
101D ALA* 2.8 27.5 + - + +
108D LEU* 4.1 9.6 - - + -
111D ALA* 3.9 14.6 - - + -
112D VAL* 3.8 42.6 - - + +
115D VAL* 4.2 12.1 - - + -
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS* 5.1 13.7 - - + +
43D ALA* 4.2 8.9 - - + +
44D SER* 3.6 31.4 - - - +
47D VAL* 3.5 35.4 - - + +
94D VAL 3.6 3.6 + - - -
95D ALA* 4.0 7.4 - - - +
97D LEU* 1.3 84.2 - - - +
99D PRO* 1.3 70.5 - - + +
101D ALA* 3.2 14.0 + - - +
102D GLY 4.2 1.9 + - - -
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Residues in contact with PRO 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ALA 3.6 11.9 - - - +
96D ALA* 3.7 11.7 - - - +
97D LEU 3.7 0.4 - - - -
98D GLU* 1.3 96.7 - - + +
100D ALA* 1.3 60.7 + - - +
101D ALA 3.5 0.3 + - - -
102D GLY* 3.9 5.7 + - - -
103D ALA* 3.9 12.5 + - - +
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA 3.8 11.9 - - - +
97D LEU 3.2 7.7 + - - +
99D PRO* 1.3 80.2 - - + +
101D ALA* 1.3 66.2 + - - +
102D GLY 3.2 1.1 - - - -
103D ALA* 3.1 20.1 + - - +
104D GLY 4.1 0.7 - - - +
107D GLU* 4.2 13.2 - - + +
108D LEU* 3.8 15.6 + - - -
111D ALA* 4.0 21.1 - - + -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 2.8 18.7 + - - -
36D ALA 4.7 0.2 - - - -
39D ALA* 3.4 45.4 - - + +
40D LYS* 4.2 2.9 - - - -
43D ALA* 3.9 10.3 - - + -
97D LEU* 2.8 17.9 + - + +
98D GLU 3.2 10.0 + - - +
100D ALA* 1.3 77.9 - - - +
102D GLY* 1.3 57.6 + - - +
108D LEU* 3.9 18.0 - - + +
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.4 11.2 + - - -
36D ALA* 4.1 23.7 + - - +
40D LYS* 4.3 15.1 - - - +
98D GLU 4.2 2.2 + - - -
99D PRO 3.9 5.0 + - - -
100D ALA 3.2 0.4 - - - -
101D ALA* 1.3 79.8 - - - +
103D ALA* 1.3 55.3 + - - +
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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
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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