Contacts of the helix formed by residues 88 - 109 (chain F) in PDB entry 1PQ3
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 ASN 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35F GLN* 3.4 50.0 + - + +
37F GLN 4.9 3.4 + - - -
79F ASP* 3.0 35.3 + - - +
80F ASP 4.7 1.6 + - - -
87F VAL* 1.3 91.7 - - - +
89F PRO* 1.3 74.3 - - - +
91F SER* 3.9 7.6 - - - -
92F VAL* 3.0 18.5 + - - +
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Residues in contact with PRO 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ASP* 3.2 13.0 - - - +
80F ASP 3.3 13.5 - - - +
82F TYR* 3.8 15.0 - - + -
86F ILE* 3.4 30.3 - - + +
87F VAL 3.1 4.0 - - - +
88F ASN* 1.3 91.4 - - - +
90F ARG* 1.3 59.2 + - - +
92F VAL* 3.0 1.0 + - - +
93F GLY 2.8 23.0 + - - -
159F LEU* 4.1 9.4 - - + -
178F LEU* 4.5 4.3 - - + -
179F PRO* 3.5 28.5 - - + +
181F PHE* 3.3 9.0 - - + -
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.1 37.6 + - - +
62B GLY* 3.3 25.9 + - - -
63B CYS 3.3 16.2 + - - -
64B HIS* 3.7 27.4 + - + +
65B LEU 5.8 0.4 - - - +
76F VAL* 3.8 17.1 - - + +
78F LYS 4.0 1.7 + - - -
79F ASP* 2.7 61.2 + - - +
80F ASP 3.7 5.3 + - - +
82F TYR* 5.9 0.2 - - - +
89F PRO* 1.3 77.2 - - - +
91F SER* 1.3 56.9 + - - +
94F LEU* 2.9 31.2 + - - +
179F PRO* 3.2 35.9 + - - +
180F GLY* 4.1 7.6 - - - +
3077F SO4 5.9 0.2 - - - +
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 3.7 4.1 - - - -
35F GLN* 2.9 31.9 + - - -
74F THR 5.2 3.0 + - - +
75F PRO* 5.0 2.3 - - - +
76F VAL* 3.8 24.8 + - - +
79F ASP* 2.7 26.6 + - - -
88F ASN* 3.6 13.5 - - - -
90F ARG* 1.3 73.9 - - - +
92F VAL* 1.3 58.0 + - - +
94F LEU* 4.1 1.0 - - - +
95F ALA* 3.2 28.2 + - - +
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Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 3.6 19.5 - - + -
35F GLN 3.1 29.4 - - - +
36F GLY* 4.1 3.6 - - - -
88F ASN* 3.0 18.4 + - + +
89F PRO 3.5 3.1 - - - +
91F SER* 1.3 74.6 - - - +
93F GLY* 1.3 64.5 + - - +
95F ALA* 4.0 0.5 - - - +
96F ASN* 3.1 41.1 + - - +
121F SER* 3.8 16.2 - - - +
124F ILE* 4.8 1.6 - - + -
159F LEU* 3.5 25.1 - - + -
181F PHE* 4.1 7.6 - - + -
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Residues in contact with GLY 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F PRO 2.8 12.0 + - - -
90F ARG 3.4 1.3 + - - -
92F VAL* 1.3 79.4 - - - +
94F LEU* 1.3 59.6 + - - +
96F ASN* 4.7 2.0 - - - -
97F GLN* 3.1 17.7 + - - +
180F GLY 3.2 24.5 - - - -
181F PHE* 3.7 15.7 - - - -
183F TRP* 3.1 15.9 + - - -
184F ILE* 5.6 0.7 - - - -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 6.5 0.2 - - + -
74F THR* 3.5 34.5 - - - +
75F PRO 4.9 0.9 - - - +
76F VAL* 3.9 14.1 - - + -
90F ARG 2.9 18.8 + - - +
91F SER 4.1 2.9 - - - +
93F GLY* 1.3 74.9 - - - +
95F ALA* 1.3 66.1 + - - +
97F GLN* 3.2 27.8 + - + +
98F GLU* 3.2 36.2 + - + +
180F GLY* 4.2 1.0 + - - -
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 3.6 32.3 - - + -
73F PHE* 3.2 42.8 - - + -
74F THR 5.4 0.6 + - - +
91F SER 3.2 17.9 + - - +
92F VAL 4.0 1.6 - - - +
94F LEU* 1.3 79.0 - - - +
96F ASN* 1.3 63.9 + - - +
98F GLU* 3.4 1.5 + - - -
99F LEU* 3.1 18.1 + - - +
122F LEU* 5.4 2.9 - - + -
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Residues in contact with ASN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 5.4 1.0 - - - -
92F VAL* 3.1 40.7 + - - +
93F GLY* 3.9 1.8 - - - +
95F ALA* 1.3 76.4 - - - +
97F GLN* 1.3 58.8 + - - +
99F LEU* 3.3 4.4 + - - +
100F ALA* 2.8 31.4 + - - +
121F SER* 3.1 22.7 + - - +
122F LEU* 3.2 18.8 - - - +
124F ILE* 3.7 10.3 - - + +
125F GLY* 2.6 34.2 + - - +
183F TRP* 3.5 16.6 - - + -
184F ILE* 5.6 0.2 - - + -
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLY 3.1 11.5 + - - +
94F LEU* 3.2 21.3 + - + +
96F ASN* 1.3 75.2 - - - +
98F GLU* 1.3 63.2 + - - +
100F ALA* 3.3 14.8 - - + +
101F GLU* 3.3 23.9 + - + +
132F ARG* 5.8 1.1 - - - +
183F TRP* 3.2 55.2 - - + +
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Residues in contact with GLU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 5.1 1.3 - - + -
72F SER 4.0 5.4 - - - +
73F PHE* 3.9 18.4 - - + -
74F THR* 2.5 40.8 + - - -
94F LEU* 3.2 33.5 - - + +
95F ALA* 3.6 5.5 - - - +
97F GLN* 1.3 76.0 - - + +
99F LEU* 1.3 65.8 + - - +
101F GLU* 3.1 21.8 + - - +
102F VAL* 3.3 17.4 + - + +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ILE* 4.1 13.0 - - + -
31F ALA* 4.4 6.1 - - + -
71F LEU* 3.8 26.5 - - + -
73F PHE* 3.9 6.0 - - + -
95F ALA 3.1 13.4 + - - +
96F ASN* 3.7 6.5 - - - +
98F GLU* 1.3 79.8 - - - +
100F ALA* 1.3 57.1 + - - +
102F VAL* 3.1 2.3 + - - +
103F VAL* 2.9 45.4 + - + +
115F THR* 4.4 13.7 - - + +
122F LEU* 3.6 37.2 - - + +
126F THR* 3.5 29.6 - - + +
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Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ASN 2.8 17.5 + - - +
97F GLN 3.3 7.9 - - - +
99F LEU* 1.3 79.2 - - - +
101F GLU* 1.3 56.4 + - - +
103F VAL* 4.6 0.4 - - - -
104F SER* 3.1 23.6 + - - -
125F GLY 3.6 23.3 + - - +
129F GLY* 3.2 14.3 - - - +
132F ARG* 3.8 13.8 + - - +
183F TRP* 3.8 22.4 - - + -
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Residues in contact with GLU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F GLN* 3.6 24.4 + - + +
98F GLU* 3.1 13.8 + - - +
100F ALA* 1.3 78.0 - - - +
102F VAL* 1.3 66.3 + - + +
104F SER* 3.1 8.6 + - - -
105F ARG* 3.0 25.8 + - - +
132F ARG* 3.9 14.5 + - - +
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ILE* 3.7 21.8 - - + -
68F PHE* 3.4 32.5 - - + -
71F LEU* 3.8 28.5 - - + -
98F GLU* 3.5 14.1 - - + +
99F LEU 3.1 5.3 + - - +
101F GLU* 1.3 77.0 - - + +
103F VAL* 1.3 62.5 + - - +
105F ARG* 3.2 8.1 - - - +
106F ALA* 3.1 21.0 + - - +
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Residues in contact with VAL 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ILE* 3.8 15.7 - - + -
99F LEU* 2.9 42.4 + - + +
100F ALA 4.0 3.6 - - - +
102F VAL* 1.3 72.2 - - - +
104F SER* 1.3 57.5 + - - +
105F ARG 2.9 4.6 + - - -
106F ALA* 3.0 3.1 + - - +
107F VAL* 2.9 36.3 + - + +
113F CYS* 4.0 17.9 - - + -
115F THR* 4.2 0.7 - - - +
126F THR* 3.7 37.2 - - + +
129F GLY* 4.5 2.2 - - - -
130F HIS* 3.9 10.3 - - + +
291F ALA* 5.4 2.9 - - + -
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Residues in contact with SER 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ALA 3.1 13.2 + - - -
101F GLU* 3.1 15.6 + - - -
103F VAL* 1.3 79.8 - - - +
105F ARG* 1.3 56.1 + - - +
107F VAL* 4.3 5.3 - - - +
108F SER* 3.0 28.3 + - - -
129F GLY* 3.1 26.9 + - - -
132F ARG* 4.0 21.7 + - - -
133F HIS* 5.2 5.0 - - - +
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Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 4.9 9.9 - - + -
101F GLU 3.0 15.3 + - - +
102F VAL* 3.2 14.4 - - - +
103F VAL 2.9 0.2 - - - -
104F SER* 1.3 78.2 - - - +
106F ALA* 1.3 63.7 + - - +
108F SER* 3.1 20.4 - - - -
109F ASP* 3.1 23.1 + - - +
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA* 4.0 20.9 - - + -
29F ILE* 5.0 0.9 - - + -
68F PHE* 3.6 28.7 - - + -
102F VAL 3.1 5.3 + - - +
103F VAL 3.0 7.4 + - - +
105F ARG* 1.3 76.1 - - - +
107F VAL* 1.3 66.1 + - - +
108F SER 3.0 1.3 - - - -
109F ASP* 3.1 9.4 + - - -
111F TYR* 3.0 30.3 + - + +
113F CYS* 4.3 12.3 - - + -
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Residues in contact with VAL 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL* 2.9 30.9 + - + +
104F SER* 4.3 6.3 - - - +
106F ALA* 1.3 72.8 - - - +
108F SER* 1.3 63.1 + - - +
110F GLY* 3.2 13.0 + - - -
111F TYR 3.6 13.2 - - - +
113F CYS* 4.2 20.2 - - + -
130F HIS* 4.0 35.7 - - + +
133F HIS* 4.0 25.8 + - + -
134F CYS* 4.0 10.5 - - - -
290F SER* 4.8 5.2 - - - +
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Residues in contact with SER 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F SER 3.0 23.1 + - - -
105F ARG* 3.1 11.2 - - - -
106F ALA 3.0 0.2 - - - -
107F VAL* 1.3 74.4 - - - +
109F ASP* 1.3 61.2 + - - +
110F GLY* 2.9 10.8 + - - -
133F HIS* 4.0 27.1 + - - -
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Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F SER* 5.3 1.0 + - - -
66F LYS* 5.3 4.9 + - - -
68F PHE* 5.1 4.2 - - - -
105F ARG* 3.3 23.3 - - - +
106F ALA* 3.1 4.0 + - - +
108F SER* 1.3 75.3 - - - +
110F GLY* 1.3 59.6 + - - +
111F TYR* 3.3 32.8 + - + -
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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
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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