Contacts of the helix formed by residues 76 - 98 (chain k) in PDB entry 5GJQ
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 LEU 76 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j PHE* 3.0 39.5 - - + -
16j GLY 5.0 4.5 - - - +
17j ARG* 6.1 1.8 - - - -
18j LEU* 4.6 11.2 - - + -
25k ALA* 4.3 13.9 - - + +
75k GLY* 1.3 73.7 - - - +
77k THR* 1.3 67.4 + - - +
78k ALA* 2.9 4.3 + - + +
79k ASP* 3.0 35.6 + - - +
80k ALA 3.0 8.8 + - - -
125k ARG* 4.0 6.5 - - - +
128k GLY* 3.0 15.2 + - - +
129k ILE* 3.1 6.5 - - - +
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Residues in contact with THR 77 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155j ASN* 2.3 46.1 + - - +
73k PHE* 3.9 30.3 - - + -
75k GLY 4.2 10.8 - - - +
76k LEU* 1.3 72.1 - - - +
78k ALA* 1.3 55.8 + - - +
80k ALA* 3.1 4.4 - - - +
81k ARG* 2.9 27.5 + - - +
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Residues in contact with ALA 78 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119j GLN* 3.6 17.5 - - + -
153j SER* 3.4 26.7 - - - +
154j GLY 4.0 4.0 - - - +
155j ASN* 4.6 2.9 - - + -
76k LEU* 3.0 2.1 - - + -
77k THR* 1.3 78.6 + - - +
79k ASP* 1.3 64.6 + - - +
81k ARG* 2.9 41.8 + - - +
82k ILE* 3.0 16.5 + - - +
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Residues in contact with ASP 79 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119j GLN* 3.5 24.4 + - - +
122j THR* 4.7 1.0 + - - -
76k LEU* 3.0 20.0 + - - +
78k ALA* 1.3 76.1 - - - +
80k ALA* 1.3 58.3 + - - +
82k ILE* 3.2 4.6 + - - +
83k VAL* 2.9 32.4 + - - +
125k ARG* 2.4 33.7 + - - -
127k PHE* 3.6 20.7 - - + -
128k GLY 3.4 17.2 + - - -
129k ILE* 3.8 13.5 - - + -
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Residues in contact with ALA 80 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71k MET* 4.7 3.1 - - + +
73k PHE* 3.2 43.9 - - + -
76k LEU 3.0 8.1 + - - +
77k THR 3.1 12.8 - - - +
79k ASP* 1.3 76.9 - - - +
81k ARG* 1.3 56.7 + - - +
83k VAL* 4.1 0.3 - - - +
84k ILE* 2.8 32.7 + - - +
129k ILE* 3.5 20.9 - - + +
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Residues in contact with ARG 81 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112j THR* 4.7 10.3 + - - -
115j CYS* 4.0 8.7 + - - +
116j ASP* 3.4 24.3 + - - +
119j GLN* 5.1 0.2 - - - +
154j GLY 2.7 28.5 + - - -
155j ASN* 2.5 34.4 + - - +
156j TYR* 3.9 28.1 - - - +
73k PHE* 5.3 2.7 - - + -
77k THR 2.9 8.5 + - - +
78k ALA* 2.9 26.8 + - - +
80k ALA* 1.3 76.8 - - - +
82k ILE* 1.3 67.5 + - + +
84k ILE* 3.7 5.3 - - - +
85k ASN* 3.0 34.7 + - - +
88k ARG* 6.2 1.3 - - - +
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Residues in contact with ILE 82 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116j ASP* 3.4 38.8 - - + +
119j GLN* 3.4 34.3 - - + +
123j GLN* 4.9 2.0 - - - +
78k ALA 3.0 14.6 + - - +
79k ASP* 3.4 7.6 - - - +
81k ARG* 1.3 78.5 - - - +
83k VAL* 1.3 65.0 + - - +
85k ASN* 3.2 8.1 + - + +
86k ARG* 3.0 36.1 + - + +
127k PHE* 4.2 20.6 - - + -
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Residues in contact with VAL 83 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71k MET* 5.0 4.3 - - + -
79k ASP 2.9 22.3 + - - +
80k ALA 4.1 0.4 - - - +
82k ILE* 1.3 72.1 - - - +
84k ILE* 1.3 58.4 + - - +
86k ARG* 3.4 5.2 + - - +
87k ALA* 2.9 27.7 + - - +
110k TYR* 6.4 0.2 - - + -
111k ILE* 3.6 36.6 - - + +
114k LEU* 4.2 13.6 - - + +
115k LYS* 4.8 3.1 - - + -
127k PHE* 3.8 41.1 - - + -
129k ILE* 4.1 19.5 - - + -
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Residues in contact with ILE 84 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63k CYS* 5.9 5.6 - - + -
65k LEU* 4.1 11.8 - - + +
71k MET* 4.4 18.3 - - + +
73k PHE* 6.2 2.7 - - + -
80k ALA 2.8 23.3 + - - +
81k ARG* 3.7 6.3 - - - +
83k VAL* 1.3 71.6 - - - +
85k ASN* 1.3 57.0 + - - +
87k ALA* 3.2 8.9 + - - +
88k ARG* 2.9 44.3 + - - +
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Residues in contact with ASN 85 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112j THR* 6.2 1.4 - - - -
116j ASP* 4.3 14.3 + - - -
81k ARG* 3.0 29.5 + - - +
82k ILE* 3.7 5.9 - - - +
84k ILE* 1.3 71.6 - - - +
86k ARG* 1.3 67.7 + - + +
88k ARG* 3.0 36.7 + - - +
89k VAL* 3.0 27.2 + - - +
70r ARG* 3.4 40.1 + - - +
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Residues in contact with ARG 86 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82k ILE* 3.0 26.8 + - + +
83k VAL 3.8 3.1 - - - +
85k ASN* 1.3 77.8 - - + +
87k ALA* 1.3 64.6 + - - +
89k VAL* 3.2 9.0 + - - +
90k GLU* 3.0 22.7 + - - +
110k TYR* 3.5 25.5 + - - +
114k LEU* 3.6 42.4 - - + +
117k ARG* 4.2 11.7 - - - +
118k TYR* 4.2 15.2 + - - -
124k ARG* 6.0 0.8 - - - +
127k PHE* 5.8 0.6 - - - -
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Residues in contact with ALA 87 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65k LEU* 4.4 9.6 - - + -
83k VAL 2.9 18.2 + - - +
84k ILE* 3.4 6.5 - - - +
86k ARG* 1.3 76.8 - - - +
88k ARG* 1.3 57.2 + - - +
90k GLU 3.4 0.3 + - - -
91k CYS* 2.9 25.9 + - - -
107k ILE* 3.3 28.9 - - + +
110k TYR* 4.1 8.2 - - - -
111k ILE* 4.0 24.7 - - + -
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Residues in contact with ARG 88 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63k CYS* 3.5 29.4 - - - +
64k ALA 3.1 24.2 + - - +
65k LEU* 3.6 30.9 - - + +
81k ARG* 6.2 1.6 - - - +
84k ILE* 2.9 23.8 + - - +
85k ASN* 3.0 35.6 + - - +
87k ALA* 1.3 75.2 - - - +
89k VAL* 1.3 66.8 + - - +
91k CYS* 3.1 6.2 + - - +
92k GLN* 3.1 24.3 + - - +
66r LEU* 4.5 12.1 - - + -
69r MET* 3.4 31.0 + - + -
70r ARG* 4.1 18.2 + - + +
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Residues in contact with VAL 89 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85k ASN 3.0 12.5 + - - +
86k ARG* 3.2 10.1 + - - +
88k ARG* 1.3 76.4 - - - +
90k GLU* 1.3 59.4 + - - +
92k GLN* 3.1 6.4 + - - +
93k SER* 2.9 38.8 + - - +
66r LEU* 3.4 37.9 - - + -
70r ARG* 3.8 11.0 - - - +
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Residues in contact with GLU 90 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86k ARG 3.0 15.2 + - - +
87k ALA 3.7 5.2 - - - +
89k VAL* 1.3 76.3 - - - +
91k CYS* 1.3 64.5 + - - +
93k SER* 4.4 12.0 - - - -
94k HIS* 3.0 25.8 + - - +
106k TYR* 3.2 30.3 + - + -
107k ILE* 4.5 2.2 - - + -
110k TYR* 3.5 51.0 + - + +
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Residues in contact with CYS 91 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65k LEU* 4.1 27.4 - - - +
66k ASP* 3.9 20.1 - - - +
69k VAL* 5.9 0.4 - - - -
87k ALA 2.9 20.4 + - - -
88k ARG 3.1 11.0 + - - +
90k GLU* 1.3 76.1 - - - +
92k GLN* 1.3 64.5 + - - +
95k ARG* 3.5 16.1 + - - +
102k VAL* 3.5 34.1 - - + +
106k TYR* 5.8 0.2 - - - -
107k ILE* 3.5 26.4 - - - +
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Residues in contact with GLN 92 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66k ASP* 3.8 26.1 + - - -
67k ASP* 5.8 0.2 + - - -
88k ARG 3.1 9.6 + - - +
89k VAL* 3.1 9.9 + - - +
91k CYS* 1.3 78.4 - - - +
93k SER* 1.3 59.2 + - - +
94k HIS 3.1 2.0 - - - -
95k ARG* 2.9 35.6 + - - +
96k LEU* 3.0 13.0 + - - +
62r LYS* 4.0 23.6 + - + +
65r GLN* 3.3 37.6 + - + +
66r LEU* 4.5 18.2 - - + +
69r MET* 3.9 22.4 - - + +
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Residues in contact with SER 93 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89k VAL* 2.9 25.9 + - - +
90k GLU* 3.9 17.6 + - - -
92k GLN* 1.3 77.0 - - - +
94k HIS* 1.3 56.9 + - - +
96k LEU* 3.5 13.3 - - - +
97k THR* 2.8 37.3 + - - +
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Residues in contact with HIS 94 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90k GLU* 3.0 18.4 + - - +
91k CYS 3.5 7.6 - - - +
93k SER* 1.3 78.9 - - - +
95k ARG* 1.3 57.0 + - - +
97k THR* 3.4 6.2 + - - -
98k VAL* 2.8 53.2 + - + +
100k ASP* 3.9 4.7 + - + -
101k PRO 2.5 31.3 + - - -
102k VAL* 3.3 15.6 - - + +
103k THR* 5.1 7.6 - - + -
106k TYR* 3.4 44.8 - + + +
66s TYR* 4.9 14.2 + + - -
70s ASN* 5.4 1.4 + - - -
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Residues in contact with ARG 95 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66k ASP* 3.1 36.5 + - - -
67k ASP* 5.0 10.4 + - - +
68k ASN* 5.4 4.9 - - - +
91k CYS 3.5 8.9 + - - +
92k GLN* 2.9 27.6 + - - +
94k HIS* 1.3 75.3 - - - +
96k LEU* 1.3 64.4 + - - +
98k VAL 2.8 19.7 - - - +
99k GLU* 3.9 17.7 + - - +
100k ASP 4.0 1.1 - - - +
101k PRO* 3.4 44.8 - - + +
102k VAL 4.5 0.6 - - - +
62r LYS* 4.0 18.9 + - - +
65r GLN* 5.9 1.6 - - - -
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Residues in contact with LEU 96 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92k GLN 3.0 8.4 + - - +
93k SER* 3.5 17.0 - - - +
95k ARG* 1.3 79.3 - - - +
97k THR* 1.3 64.5 + - + +
98k VAL 3.3 0.5 + - - -
99k GLU* 4.2 2.4 - - - +
58r GLU* 3.5 36.1 - - + +
59r TYR* 4.7 9.9 - - + +
62r LYS* 3.0 49.7 - - + +
81s LYS* 2.8 30.6 + - - +
85s ASN* 5.1 3.4 - - - +
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Residues in contact with THR 97 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93k SER* 2.8 23.2 + - - +
94k HIS* 3.4 9.9 + - - -
96k LEU* 1.3 81.3 - - + +
98k VAL* 1.3 70.5 + - - +
78s ALA 4.1 9.5 - - - +
81s LYS* 4.0 13.1 - - - +
82s LEU* 4.6 14.1 + - + +
85s ASN* 4.7 15.0 - - - +
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Residues in contact with VAL 98 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94k HIS* 2.8 30.8 + - + +
95k ARG 2.8 16.1 - - - +
96k LEU 3.2 0.6 - - - -
97k THR* 1.3 91.2 - - - +
99k GLU* 1.3 60.2 + - - +
100k ASP* 2.8 53.8 - - + +
66s TYR* 4.5 26.9 - - + +
74s ILE* 5.6 1.3 - - + -
78s ALA* 3.7 23.1 - - + +
81s LYS* 5.4 0.2 - - - -
82s LEU* 5.9 3.4 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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