Contacts of the helix formed by residues 79 - 105 (chain A) in PDB entry 3P1Q
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 PRO 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY* 1.3 83.6 - - - +
80A GLU* 1.3 72.3 + - - +
81A VAL 3.4 0.9 - - - -
82A ARG* 3.3 29.9 + - + +
83A GLU* 2.9 51.0 + - - +
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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
----------------------------------------------------------
77A LYS 2.9 24.5 - - - +
78A GLY* 3.3 2.5 + - - -
79A PRO* 1.3 94.4 - - - +
81A VAL* 1.3 60.4 + - + +
83A GLU* 3.6 15.5 - - - +
84A TYR* 2.8 32.6 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.1 12.7 - - + +
65A ILE* 4.0 20.6 - - + -
66A GLU* 3.5 42.2 - - + +
69A SER* 5.1 10.5 - - - +
77A LYS* 5.8 9.9 - - + -
78A GLY 4.6 4.6 + - - +
79A PRO 3.4 0.6 - - - -
80A GLU* 1.3 76.4 - - + +
82A ARG* 1.3 64.0 + - - +
84A TYR* 3.3 2.9 + - - +
85A ARG* 2.9 24.4 + - - +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.6 28.9 - - + +
78A GLY 5.3 0.6 + - - +
79A PRO* 3.3 35.4 + - + +
81A VAL* 1.3 79.4 - - - +
83A GLU* 1.3 74.3 + - - +
85A ARG* 3.7 6.5 - - - +
86A GLU* 2.9 74.6 + - - +
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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
----------------------------------------------------------
79A PRO* 2.9 40.9 + - - +
80A GLU* 3.6 18.8 + - - +
82A ARG* 1.3 92.9 + - - +
84A TYR* 1.3 58.0 + - + +
86A GLU* 3.3 10.8 + - - +
87A LYS* 2.9 26.6 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 6.1 0.5 - - - +
62A LEU* 3.5 37.7 - - + -
80A GLU 2.8 17.4 + - - +
81A VAL* 4.1 3.1 - - - +
83A GLU* 1.3 75.2 - - - +
85A ARG* 1.3 64.2 + - - +
87A LYS* 3.1 34.1 + - + -
88A VAL* 3.0 37.6 + - + +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 3.4 33.7 - - + +
62A LEU* 3.9 21.1 - - + +
63A SER* 4.0 21.3 - - - +
66A GLU* 2.6 43.7 + - - +
81A VAL 2.9 17.3 + - - +
82A ARG* 3.7 16.4 - - - +
84A TYR* 1.3 75.0 - - - +
86A GLU* 1.3 84.3 + - - +
88A VAL* 3.3 3.0 + - - +
89A GLU* 2.8 54.6 + - - +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 2.9 63.0 + - - +
83A GLU* 3.5 7.8 - - - +
85A ARG* 1.3 97.7 + - - +
87A LYS* 1.3 56.2 + - - +
89A GLU* 3.6 8.0 - - - +
90A THR* 2.8 39.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 13.7 + - - +
84A TYR* 3.1 38.8 + - + +
86A GLU* 1.3 74.1 - - - +
88A VAL* 1.3 64.6 + - + +
90A THR* 3.3 5.7 + - - -
91A GLU* 3.1 51.1 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 3.7 32.0 - - + +
58A ALA* 4.3 10.1 - - + -
59A TRP* 4.0 16.6 - - + +
62A LEU* 3.5 21.5 - - + -
84A TYR* 3.0 39.4 + - + +
85A ARG 3.8 3.6 - - - +
87A LYS* 1.3 76.8 - - + +
89A GLU* 1.3 58.2 + - - +
91A GLU* 3.2 11.1 + - - +
92A LEU* 2.8 27.5 + - - +
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 2.9 36.2 + - + +
85A ARG* 2.8 44.5 + - - +
86A GLU* 3.6 6.6 - - - +
87A LYS 3.2 0.2 - - - -
88A VAL* 1.3 76.9 - - - +
90A THR* 1.3 58.1 + - - +
92A LEU* 3.2 5.4 + - - +
93A GLN* 2.7 48.8 + - - +
134A VAL* 3.9 33.5 - - + +
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Residues in contact with THR 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 GLU* 2.8 23.5 + - - +
87A LYS* 3.7 5.8 - - - -
89A GLU* 1.3 76.4 - - - +
91A GLU* 1.3 65.6 + - + +
93A GLN* 3.3 15.1 + - - +
94A GLY* 3.0 19.9 + - - -
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Residues in contact with GLU 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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55A GLN* 3.5 21.0 + - + +
87A LYS* 3.1 46.3 + - + +
88A VAL* 3.2 10.9 + - - +
90A THR* 1.3 77.9 - - + +
92A LEU* 1.3 62.0 + - - +
94A GLY* 3.2 3.1 + - - +
95A VAL* 3.0 20.6 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.4 7.1 - - + +
55A GLN* 3.4 26.1 - - + +
56A ARG* 3.9 33.7 - - + +
59A TRP* 4.1 19.1 - - + -
88A VAL 2.8 16.3 + - - +
89A GLU 3.4 4.9 - - - +
91A GLU* 1.3 77.0 - - - +
93A GLN* 1.3 67.9 + - + +
95A VAL* 3.1 4.0 + - - +
96A CYS* 2.9 39.2 + - - -
130A TYR* 4.2 17.7 - - + +
131A LEU* 5.0 0.7 - - + -
134A VAL* 4.2 21.8 - - + -
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 2.7 39.8 + - - +
90A THR* 3.6 18.5 + - - +
92A LEU* 1.3 74.9 - - + +
94A GLY* 1.3 57.2 + - - +
96A CYS* 3.3 1.7 + - - +
97A ASP* 2.8 39.2 + - - +
131A LEU* 3.7 26.0 + - + +
134A VAL* 3.9 26.3 + - + +
135A ALA* 5.6 2.6 - - - +
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Residues in contact with GLY 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 THR 3.0 14.3 + - - -
91A GLU* 3.2 4.5 + - - -
92A LEU 3.2 0.2 - - - -
93A GLN* 1.3 77.1 - - - +
95A VAL* 1.3 57.8 + - - +
97A ASP* 3.4 8.7 + - - +
98A THR* 3.0 31.9 + - - -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.8 28.5 - - + -
51A VAL* 4.1 15.7 - - + -
52A VAL* 4.3 14.4 - - + -
55A GLN* 3.5 34.8 - - - +
91A GLU 3.0 5.9 + - - +
92A LEU 3.1 6.9 + - - +
94A GLY* 1.3 71.1 - - - +
96A CYS* 1.3 68.6 + - - +
98A THR* 3.1 8.5 + - - -
99A VAL* 3.0 23.5 + - + +
127A TYR* 4.9 0.2 - - + -
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Residues in contact with CYS 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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52A VAL* 4.0 5.6 - - - -
92A LEU* 2.9 30.1 + - - -
93A GLN 3.7 1.1 - - - +
95A VAL* 1.3 76.7 - - - +
97A ASP* 1.3 58.2 + - - +
99A VAL* 3.2 2.1 + - - +
100A LEU* 2.9 35.0 + - - +
127A TYR* 3.7 37.9 - - + +
130A TYR* 3.8 21.1 - - - -
131A LEU* 3.6 27.8 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN* 2.8 25.5 + - - +
94A GLY* 3.8 7.4 - - - +
95A VAL 3.2 0.4 - - - -
96A CYS* 1.3 76.4 - - - +
98A THR* 1.3 58.0 + - - +
100A LEU* 3.8 6.6 - - - +
101A GLY* 2.8 26.2 + - - -
131A LEU* 3.8 21.2 - - - +
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Residues in contact with THR 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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27A LYS* 3.6 31.2 - - + -
48A TYR* 3.6 23.8 - - + +
94A GLY 3.0 14.9 + - - -
95A VAL* 3.1 12.0 + - - -
97A ASP* 1.3 74.3 - - - +
99A VAL* 1.3 65.9 + - - +
101A GLY* 3.2 2.3 + - - -
102A LEU* 3.0 23.8 + - + +
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Residues in contact with VAL 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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44A LEU* 6.2 0.4 - - + -
48A TYR* 3.3 48.7 - - + -
95A VAL 3.0 17.8 + - - +
96A CYS 3.8 2.9 - - - +
98A THR* 1.3 75.7 - - - +
100A LEU* 1.3 64.2 + - - +
102A LEU* 3.0 11.9 + - + +
103A LEU* 2.9 30.4 + - + +
123A MET* 3.8 22.4 - - + -
127A TYR* 3.6 35.7 - - + -
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Residues in contact with LEU 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 CYS 2.9 21.5 + - - +
97A ASP* 3.9 8.1 - - - +
99A VAL* 1.3 75.9 - - - +
101A GLY* 1.3 57.7 + - - +
103A LEU* 3.3 8.0 + - + +
104A ASP* 2.8 29.7 + - - +
124A LYS* 3.7 33.7 - - + +
127A TYR* 4.0 13.9 - - + -
128A TYR* 3.7 42.8 - - + +
131A LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 101 (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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97A ASP 2.8 17.0 + - - -
98A THR* 3.7 3.6 - - - -
99A VAL 3.2 0.2 - - - -
100A LEU* 1.3 74.7 - - - +
102A LEU* 1.3 60.8 + - - +
104A ASP* 4.3 4.5 - - - -
105A SER* 2.8 36.6 + - - -
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Residues in contact with LEU 102 (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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27A LYS* 4.1 20.6 - - + -
30A VAL* 3.8 20.1 - - + +
31A GLU* 4.0 28.9 - - + +
44A LEU* 4.3 11.0 - - + -
48A TYR* 4.1 31.4 - - + +
98A THR* 3.0 20.1 + - + +
99A VAL* 3.0 9.8 + - + +
101A GLY* 1.3 76.9 - - - +
103A LEU* 1.3 64.3 + - + +
105A SER 3.3 17.7 + - - +
107A LEU* 3.3 31.1 + - + +
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Residues in contact with LEU 103 (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 LEU* 5.3 0.2 - - + -
99A VAL* 2.9 27.5 + - + +
100A LEU* 3.6 13.9 - - + +
102A LEU* 1.3 77.1 - - + +
104A ASP* 1.3 61.1 + - - +
107A LEU* 3.4 13.0 + - + -
108A ILE* 3.0 44.7 + - + +
109A LYS 4.6 0.2 + - - -
120A TYR* 3.7 45.3 - - + +
123A MET* 3.8 20.0 - - + +
124A LYS* 3.5 38.6 - - + +
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU 2.8 17.8 + - - +
101A GLY* 3.9 6.5 - - - +
103A LEU* 1.3 78.9 - - - +
105A SER* 1.3 64.0 + - - +
106A HIS* 3.7 2.3 + - - -
108A ILE* 5.5 2.6 - - - +
109A LYS* 2.9 26.2 + - - -
124A LYS* 5.0 9.6 + - - +
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.9 6.4 - - - +
31A GLU* 5.9 2.1 - - - +
101A GLY* 2.8 19.3 + - - +
102A LEU* 3.3 16.4 + - - +
104A ASP* 1.3 85.0 + - - +
106A HIS* 1.3 76.1 + - - +
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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) + - + + + + + -
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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