Contacts of the helix formed by residues 75 - 95 (chain T) in PDB entry 4GGF
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 SER 75 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T PHE* 3.8 2.0 - - - -
30T ASP 4.6 1.1 - - - -
31T THR* 4.2 16.6 - - - +
73T GLN* 4.0 1.4 - - - +
74T LEU* 1.3 76.1 - - - +
76T PHE* 1.3 60.6 + - - +
77T GLU* 3.5 17.8 + - - +
78T GLU* 3.0 36.6 + - - +
79T PHE* 2.8 27.4 + - - +
204T CA 4.5 0.6 - - - -
63U ASP* 5.3 0.2 - - - +
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Residues in contact with PHE 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S GLY* 3.4 28.3 - - - -
80S VAL* 3.9 8.1 - - + -
83S HIS* 3.4 45.0 - + + +
12T ILE* 5.8 0.4 - - + -
15T ILE* 3.9 26.5 - - + -
16T ILE* 3.7 31.6 - - + -
19T PHE* 3.5 39.1 - + + -
30T ASP 4.6 1.6 + - - -
75T SER* 1.3 75.7 - - - +
77T GLU* 1.3 61.2 + - - +
79T PHE* 3.1 5.6 + + - +
80T ILE* 2.8 48.6 + - + +
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Residues in contact with GLU 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S VAL* 3.8 26.1 - - + +
83S HIS* 4.9 10.6 + - - -
84S LYS* 6.0 1.7 - - - +
75T SER* 3.2 19.6 - - - +
76T PHE* 1.3 85.6 + - - +
78T GLU* 1.3 61.6 + - - +
80T ILE* 3.4 17.0 - - - +
81T MET* 4.0 0.3 - - - +
61U ASN* 2.8 44.8 + - - +
62U THR* 3.8 10.8 + - - +
63U ASP* 4.1 10.1 - - + -
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Residues in contact with GLU 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T LEU* 3.2 33.2 - - - +
67T ASP* 3.8 0.2 - - - +
68T THR* 3.1 32.3 + - + +
69T ASN* 3.0 17.0 + - - +
73T GLN 3.0 5.9 - - - +
74T LEU* 3.2 5.6 - - + +
75T SER* 3.0 33.0 + - - +
77T GLU* 1.3 77.1 - - - +
79T PHE* 1.3 63.1 + - - +
80T ILE 3.3 0.7 + - - -
81T MET* 3.3 18.9 + - - +
204T CA 2.5 30.7 - - - -
61U ASN* 4.1 4.9 - - - +
63U ASP* 4.2 7.1 - - + +
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Residues in contact with PHE 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S LEU* 5.2 2.5 - - + -
15T ILE* 4.2 11.9 - - + -
18T THR* 6.0 0.4 - - + -
19T PHE* 3.7 33.2 - + + -
32T LEU* 3.8 15.0 - - + -
37T PHE* 4.4 12.1 - + - -
40T LEU* 3.8 36.6 - - + -
66T LEU* 5.3 0.9 - - - -
74T LEU* 4.4 17.6 - - + +
75T SER 2.8 16.1 + - - +
76T PHE* 3.1 10.5 + + - +
78T GLU* 1.3 78.9 - - - +
80T ILE* 1.3 66.5 + - - +
82T LEU* 2.9 25.0 + - + +
83T MET* 3.5 45.8 + - + +
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Residues in contact with ILE 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S VAL* 4.3 6.1 - - + +
76S ILE* 3.8 33.7 - - + +
79S GLY* 3.6 30.7 - - - -
80S VAL* 4.1 17.3 - - + -
12T ILE* 6.3 0.9 - - + -
15T ILE* 4.9 7.6 - - + -
76T PHE* 2.8 35.6 + - + +
77T GLU 3.4 16.2 - - - +
79T PHE* 1.3 76.1 - - - +
81T MET* 1.3 62.1 + - - +
83T MET* 3.1 19.0 + - + -
84T ALA* 3.0 21.6 + - - +
61U ASN* 4.4 1.8 - - + -
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Residues in contact with MET 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ILE* 3.9 27.1 - - + -
66T LEU* 4.3 3.8 - - + -
68T THR* 6.1 1.3 - - + -
78T GLU* 3.7 9.9 - - - +
79T PHE 3.1 1.2 - - - -
80T ILE* 1.3 77.4 - - - +
82T LEU* 1.3 58.1 + - - +
84T ALA* 3.4 4.2 + - - +
85T ARG* 2.9 54.5 + - - +
60U ILE* 4.8 1.8 - - + -
61U ASN* 3.3 41.5 - - + +
63U ASP* 5.1 1.3 - - - +
67U ASN* 3.5 24.9 - - - +
69U GLN* 4.3 9.4 + - + +
70U GLU* 3.6 27.6 - - + +
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Residues in contact with LEU 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37T PHE* 3.8 34.3 - - + -
45T LEU* 4.2 14.6 - - + -
49T LEU* 4.7 8.3 - - + -
62T ILE* 4.3 18.2 - - + -
66T LEU* 3.8 19.8 - - + +
79T PHE* 2.9 16.6 + - + +
81T MET* 1.3 77.5 - - - +
83T MET* 1.3 76.4 + - + +
85T ARG* 3.3 11.7 + - + +
86T LEU* 2.9 49.1 + - + +
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Residues in contact with MET 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S LEU* 4.0 28.0 - - + -
9S LEU* 4.1 20.8 - - + +
15T ILE* 3.7 24.9 - - + -
45T LEU* 4.1 16.2 - - + -
79T PHE* 3.6 40.6 - - + +
80T ILE* 3.4 15.7 - - + +
82T LEU* 1.3 98.2 - - + +
84T ALA* 1.3 56.5 + - - +
86T LEU* 3.3 7.7 + - + +
87T THR* 2.8 35.7 + - - -
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Residues in contact with ALA 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S LEU* 3.6 22.8 - - + +
75S VAL* 6.2 2.2 - - + -
76S ILE* 3.8 33.4 - - + -
80T ILE* 3.0 12.6 + - + +
81T MET* 3.8 4.9 - - - +
83T MET* 1.3 76.7 - - - +
85T ARG* 1.3 57.8 + - + +
87T THR* 3.3 5.1 + - - -
88T TRP* 2.9 30.9 + - - +
69U GLN* 6.2 0.7 - - - +
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Residues in contact with ARG 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62T ILE* 6.2 1.0 - - - +
65T ASP* 3.0 32.3 + - - -
66T LEU* 3.9 22.9 - - - +
81T MET* 2.9 26.9 + - - +
82T LEU* 3.3 13.9 + - + +
84T ALA* 1.3 77.1 - - + +
86T LEU* 1.3 59.1 + - + +
88T TRP* 3.5 9.7 + - - +
89T ALA* 2.9 29.3 + - - +
27U HIS* 6.3 0.6 - - - +
67U ASN* 3.6 14.3 - - - +
69U GLN* 2.8 41.1 + - - +
88V TRP* 4.4 22.2 - - + -
92V GLU* 6.0 0.7 - - - -
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Residues in contact with LEU 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S LEU* 3.9 10.5 - - + -
45T LEU* 3.8 40.2 - - + -
48T PHE* 4.2 10.2 - - + -
49T LEU* 4.0 26.9 - - + -
82T LEU* 2.9 37.5 + - + +
83T MET* 3.8 7.4 - - + +
85T ARG* 1.3 76.5 - - + +
87T THR* 1.3 61.7 + - - +
89T ALA* 3.8 6.3 - - + +
90T SER* 2.9 30.8 + - - -
109T LEU* 3.9 19.0 - - + +
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Residues in contact with THR 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S LEU* 3.5 44.7 - - - +
12S ILE* 4.1 11.3 - - + +
13S ILE* 3.6 10.9 - - + +
68S PHE* 3.7 25.4 - - + -
72S LEU* 4.0 12.1 - - + -
83T MET 2.8 21.5 + - - -
84T ALA* 3.6 5.3 - - - -
86T LEU* 1.3 75.5 - - - +
88T TRP* 1.3 65.4 + - - +
90T SER* 3.3 4.2 + - - -
91T HIS* 3.1 20.4 + - - +
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Residues in contact with TRP 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S PHE* 3.8 21.5 - + - -
69S GLN* 2.9 59.2 - - + -
72S LEU* 4.0 8.0 - - + +
84T ALA 2.9 17.7 + - - +
85T ARG* 3.5 9.0 - - - +
87T THR* 1.3 77.7 - - - +
89T ALA* 1.3 61.8 + - + +
91T HIS* 3.2 4.0 + - - +
92T GLU* 2.8 65.8 + - + +
205T GOL 3.3 20.4 - - - -
85V ARG* 4.5 17.7 - - + -
88V TRP* 4.0 34.2 - + - +
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Residues in contact with ALA 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ARG 2.9 18.0 + - - +
86T LEU* 3.8 8.7 - - + +
87T THR 3.3 0.4 - - - -
88T TRP* 1.3 82.9 - - + +
90T SER* 1.3 63.4 + - - +
92T GLU* 3.4 6.8 + - - +
93T LYS* 3.0 22.2 + - - +
109T LEU* 4.0 19.3 - - + +
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Residues in contact with SER 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S LEU* 6.3 0.2 - - - -
10S ASN* 2.8 28.0 + - - -
13S ILE* 4.1 2.5 - - - -
48T PHE* 4.0 5.7 - - - -
86T LEU 2.9 17.8 + - - -
87T THR* 3.8 4.0 - - - -
89T ALA* 1.3 77.6 - - - +
91T HIS* 1.3 62.5 + - - +
93T LYS* 3.1 5.4 + - - +
94T MET* 3.1 26.6 + - - +
108T GLY* 3.6 4.5 - - - -
109T LEU* 3.1 37.3 + - - +
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Residues in contact with HIS 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S ILE* 3.6 16.2 - - + +
17S HIS* 3.2 14.9 - + - -
27S HIS* 3.2 17.7 - + - -
68S PHE* 3.6 27.2 - + + -
87T THR 3.1 12.7 + - - +
88T TRP* 3.6 7.4 - - - +
90T SER* 1.3 75.0 - - - +
92T GLU* 1.3 65.4 + - - +
94T MET* 3.0 19.9 + - - +
95T HIS* 3.2 12.3 + + - -
105T HIS* 3.4 13.5 - + - -
201T MN 2.3 30.3 + - - -
205T GOL 3.2 36.1 - - - -
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Residues in contact with GLU 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T TRP* 2.8 61.6 + - + +
89T ALA* 3.6 8.7 - - - +
91T HIS* 1.3 72.7 + - - +
93T LYS* 1.3 61.0 + - - +
95T HIS* 3.1 12.8 + - - +
96T GLU* 3.2 12.9 + - - +
205T GOL 3.3 37.7 + - - -
85V ARG* 5.7 2.1 - - - -
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Residues in contact with LYS 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T ALA 3.0 14.4 + - - +
90T SER 3.1 8.0 + - - +
92T GLU* 1.3 74.4 - - - +
94T MET* 1.3 63.3 + - - +
95T HIS 3.1 1.2 + - - -
96T GLU* 3.2 22.8 + - + +
106T LYS* 4.3 7.4 - - - +
107T PRO* 3.7 13.2 + - - +
108T GLY 3.0 24.7 + - - +
109T LEU* 3.6 14.6 - - + +
110T GLY 5.0 2.7 - - - +
111T GLU 2.4 31.7 + - - -
112T GLY* 4.3 7.5 + - - -
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Residues in contact with MET 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S ASN* 3.7 31.4 - - + +
13S ILE* 3.8 18.6 - - + -
14S ASP* 5.9 1.6 - - - +
90T SER* 3.1 15.9 + - - +
91T HIS* 3.0 17.8 + - - +
93T LYS* 1.3 77.0 - - - +
95T HIS* 1.3 56.6 - - - +
96T GLU 3.6 0.2 - - - -
98T ASP* 5.2 0.5 - - - +
104T HIS 4.0 2.9 - - - +
105T HIS* 3.5 44.6 - - + -
106T LYS* 2.8 52.1 + - - +
107T PRO 3.9 0.9 - - - -
108T GLY* 3.7 14.8 - - - +
111T GLU* 5.4 0.9 - - - +
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Residues in contact with HIS 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S HIS* 3.1 13.0 + + - -
91T HIS* 3.3 27.3 + + - -
92T GLU 3.1 6.9 + - - +
93T LYS 3.0 0.6 - - - -
94T MET* 1.3 77.6 - - - +
96T GLU* 1.3 63.3 + - - +
97T GLY 3.2 0.9 + - - -
98T ASP* 2.8 45.6 + - + +
103T HIS* 3.4 19.7 - + - -
104T HIS 3.7 7.2 + - - -
105T HIS* 3.2 11.7 + + - -
106T LYS* 5.1 0.4 - - - -
201T MN 2.3 36.0 + - - -
205T GOL 3.4 22.4 - - - +
61V HIS* 4.0 11.8 + + - +
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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