Contacts of the helix formed by residues 125 - 146 (chain E) in PDB entry 3P05
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 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E MET* 4.5 8.7 - - + -
123E PRO* 3.8 15.9 - - + +
124E ILE* 1.4 81.6 - - + +
126E VAL* 1.3 64.9 + - - +
127E GLY 3.1 4.0 - - - +
128E GLU* 3.0 23.9 + - + -
129E ILE* 2.9 42.5 + - + +
132E ARG* 5.1 5.4 - - - +
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PRO* 3.9 19.2 - - + +
99E PRO* 4.4 10.1 - - + -
104E ILE* 3.8 30.4 - - + +
114E GLN* 3.9 13.5 - - + +
117E TRP* 4.1 24.7 - - + -
118E MET* 3.4 25.3 - - + +
124E ILE* 2.8 20.9 + - + +
125E PRO* 1.3 71.0 - - - +
127E GLY* 1.3 65.3 + - - +
129E ILE* 4.2 7.2 - - + -
130E TYR* 2.9 27.0 + - - +
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Residues in contact with GLY 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ALA 3.2 26.9 - - - -
49E PRO* 4.1 8.9 - - - +
52E LEU* 3.6 6.7 - - - +
118E MET* 4.1 8.2 - - - +
125E PRO 3.1 1.0 - - - -
126E VAL* 1.3 84.9 - - - +
128E GLU* 1.3 58.1 + - - +
130E TYR* 3.6 2.4 - - - +
131E LYS* 2.9 30.4 + - - +
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E SER 5.1 0.2 - - - +
45E GLU* 5.3 2.2 - - - +
46E GLY* 4.5 14.0 + - - -
47E ALA 5.2 2.1 + - - +
125E PRO* 3.0 24.7 + - + +
127E GLY* 1.3 75.4 - - - +
129E ILE* 1.3 61.5 + - - +
131E LYS* 3.3 34.6 + - - +
132E ARG* 3.1 44.3 + - - +
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E TRP* 4.2 29.2 - - + -
104E ILE* 3.8 14.1 - - + -
124E ILE* 4.6 6.5 - - + -
125E PRO* 2.9 47.3 + - + +
126E VAL* 3.9 6.5 - - + +
128E GLU* 1.3 74.5 - - - +
130E TYR* 1.3 67.9 + - - +
132E ARG* 3.2 32.8 + - - +
133E TRP* 3.3 44.0 + - + +
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Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PRO* 3.8 16.2 - - + -
52E LEU* 3.7 20.6 - - + -
53E ASN* 2.7 28.5 + - - -
56E LEU* 4.0 4.3 - - - +
73E ILE* 3.9 25.9 - - + +
104E ILE* 3.3 25.1 - - - +
105E ALA* 3.4 38.3 + - + +
107E THR* 5.8 0.3 - - - +
126E VAL 2.9 18.4 + - - +
127E GLY 3.6 2.9 - - - +
129E ILE* 1.3 74.4 - - - +
131E LYS* 1.3 57.5 + - - +
133E TRP* 3.0 15.0 + + + +
134E ILE* 2.9 49.4 + - + +
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Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE* 3.9 13.2 - - + -
41E SER* 3.5 28.4 + - - +
44E SER* 2.9 46.9 + - - +
45E GLU* 3.7 17.2 + - - +
47E ALA* 5.5 1.6 - - + +
52E LEU* 4.1 12.5 - - + +
127E GLY 2.9 17.2 + - - +
128E GLU* 3.3 37.8 + - - +
129E ILE 3.2 0.2 - - - -
130E TYR* 1.3 71.6 - - - +
132E ARG* 1.3 58.6 + - + +
134E ILE* 3.1 7.1 + - - +
135E ILE* 2.8 40.2 + - + +
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Residues in contact with ARG 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PRO* 5.1 5.7 - - - +
128E GLU* 3.1 35.1 + - - +
129E ILE* 3.2 36.5 + - - +
131E LYS* 1.3 73.5 - - + +
133E TRP* 1.3 67.4 + - + +
135E ILE* 3.5 9.4 + - + +
136E LEU* 2.9 28.8 + - - +
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Residues in contact with TRP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LEU* 4.7 1.4 - - - +
72E THR* 4.2 6.6 - - - +
73E ILE* 4.3 21.6 - - + +
76E GLU* 3.6 50.1 + - + +
77E ALA* 3.7 27.8 - - + -
80E TRP* 3.8 20.8 - + + -
101E GLY 3.7 12.1 - - - -
104E ILE* 3.7 27.4 - - + -
105E ALA* 4.5 4.7 - - + -
129E ILE* 3.4 33.7 + - + +
130E TYR* 3.0 21.0 + + + +
132E ARG* 1.3 81.5 - - + +
134E ILE* 1.3 63.1 + - - +
136E LEU* 3.2 9.1 + - + +
137E GLY* 3.1 18.0 + - - -
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Residues in contact with ILE 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE* 3.6 30.3 - - + -
52E LEU* 4.0 19.5 - - + -
56E LEU* 4.0 22.7 - - + -
69E LEU* 3.7 9.8 - - + +
73E ILE* 4.1 13.0 - - + -
130E TYR* 2.9 56.7 + - + +
131E LYS 3.1 6.0 + - - +
133E TRP* 1.3 77.4 - - - +
135E ILE* 1.3 56.7 + - - +
137E GLY* 3.1 3.5 + - - -
138E LEU* 2.8 39.6 + - + +
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Residues in contact with ILE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.1 22.7 - - + -
40E PHE* 4.0 21.5 - - + -
41E SER* 3.5 24.0 - - - +
131E LYS* 2.8 33.1 + - + +
132E ARG* 3.9 8.3 - - + +
134E ILE* 1.3 69.9 - - - +
136E LEU* 1.3 64.3 + - - +
138E LEU* 3.7 6.0 - - + +
139E ASN* 2.9 43.8 + - - +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E THR* 4.0 9.0 - - + -
76E GLU* 3.4 43.1 - - + +
132E ARG 2.9 14.7 + - - +
133E TRP* 3.2 9.6 + - + +
135E ILE* 1.3 77.2 - - - +
137E GLY* 1.3 62.5 + - - +
139E ASN* 3.5 10.8 + - + +
140E LYS* 3.3 31.1 + - + +
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LEU* 3.8 20.4 - - - -
72E THR* 3.8 20.8 - - - +
133E TRP 3.1 10.5 + - - -
134E ILE 3.5 2.7 - - - -
136E LEU* 1.3 76.0 - - - +
138E LEU* 1.3 64.2 + - - +
140E LYS* 3.3 5.8 + - - +
141E ILE* 3.1 28.3 + - - +
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Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TRP* 5.3 5.2 - - + -
32E PHE* 3.9 29.8 - - + -
36E VAL* 5.1 7.2 - - + -
37E ILE* 4.0 23.1 - - + -
40E PHE* 4.1 30.7 - - + -
56E LEU* 6.0 1.6 - - + -
69E LEU* 4.2 19.5 - - + +
134E ILE* 2.8 38.4 + - + +
135E ILE* 3.3 8.5 + - + +
137E GLY* 1.3 71.4 - - - +
139E ASN* 1.3 58.3 + - - +
141E ILE* 3.2 7.3 + - + +
142E VAL* 2.9 32.8 + - + +
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Residues in contact with ASN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 2.8 27.9 - - - +
135E ILE* 2.9 36.9 + - - +
136E LEU* 3.7 11.8 - - + +
138E LEU* 1.3 76.8 - - - +
140E LYS* 1.3 63.0 + - + +
142E VAL* 3.4 1.0 + - - -
143E ARG* 3.0 27.4 + - - +
176E GLN* 3.4 39.6 + - - +
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Residues in contact with LYS 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D GLU* 3.4 35.2 + - - +
68E MET* 6.1 3.4 - - - -
72E THR* 2.9 35.7 + - + +
75E GLU* 3.9 18.2 + - - -
136E LEU* 3.3 28.3 + - + +
137E GLY* 3.3 6.4 + - - +
138E LEU 3.3 0.6 - - - -
139E ASN* 1.3 75.5 - - + +
141E ILE* 1.3 59.9 + - + +
143E ARG* 3.3 19.6 + - - +
144E MET* 3.0 32.0 + - - +
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Residues in contact with ILE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PHE* 3.6 32.1 - - + -
65E ALA* 3.4 46.7 - - + +
66E MET* 5.7 0.4 - - - -
68E MET* 4.8 17.9 - - + -
69E LEU* 4.0 16.6 - - + +
137E GLY 3.1 17.8 + - - +
138E LEU* 3.2 18.1 + - + +
140E LYS* 1.3 75.4 - - + +
142E VAL* 1.3 59.2 + - - +
144E MET* 3.2 6.1 + - - +
145E TYR* 2.9 37.5 + - + +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PHE* 3.3 37.6 - - + +
33E SER 4.2 7.2 - - - +
34E PRO* 3.9 19.7 - - + -
36E VAL* 5.6 2.0 - - + -
37E ILE* 4.2 18.4 - - + -
138E LEU* 2.9 21.0 + - + +
139E ASN 3.7 4.5 - - - +
141E ILE* 1.3 75.9 - - - +
143E ARG* 1.3 62.0 - - - +
145E TYR* 3.5 1.3 + - - +
146E SER* 3.2 24.7 + - - -
174E ALA* 3.7 23.7 - - + +
176E GLN* 4.0 9.6 - - - +
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASN* 3.0 27.4 + - - +
140E LYS* 3.6 16.7 - - - +
141E ILE 3.2 0.2 - - - -
142E VAL* 1.3 78.9 - - - +
144E MET* 1.3 60.5 + - + +
146E SER 3.3 18.4 - - - +
147E PRO* 3.9 5.2 - - - +
174E ALA 3.7 14.1 - - - +
175E GLU* 3.2 33.6 + - + +
176E GLN* 2.5 34.2 + - - +
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Residues in contact with MET 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ARG* 4.2 10.6 + - - +
212D GLU* 3.9 19.1 - - - +
215D MET* 4.3 23.8 - - + -
216D THR* 3.9 22.9 - - - +
219D GLN* 4.0 29.6 - - - +
68E MET* 3.8 33.4 - - + +
140E LYS 3.0 20.6 + - - +
141E ILE* 3.2 6.4 + - - +
143E ARG* 1.3 77.3 - - + +
145E TYR* 1.3 67.0 + - + +
146E SER 3.2 0.7 + - - -
147E PRO* 3.7 17.9 - - - +
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Residues in contact with TYR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ARG* 3.6 54.3 + - + +
166D ASP* 4.6 4.0 + - - -
215D MET* 6.1 0.9 - - + -
31E ALA* 4.3 11.7 - - + -
32E PHE* 3.9 40.8 - + + +
62E HIS* 2.9 37.8 + + - +
64E ALA* 6.0 0.6 - - + +
65E ALA* 4.3 10.8 + - + +
68E MET* 5.6 5.6 - - + -
141E ILE* 2.9 31.5 + - + +
142E VAL 4.1 2.7 - - - +
144E MET* 1.3 80.5 - - + +
146E SER* 1.3 57.0 + - - +
147E PRO* 3.6 7.5 - - - +
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Residues in contact with SER 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PHE 5.9 1.1 - - - -
34E PRO* 5.9 1.8 - - - -
142E VAL* 3.2 10.6 + - - -
143E ARG* 3.3 10.3 - - - +
145E TYR* 1.3 75.6 - - - +
147E PRO* 1.3 64.8 - - - +
148E THR* 3.6 7.9 + - - +
170E LYS* 6.0 5.8 - - - +
171E THR* 4.7 8.8 + - - +
174E ALA* 3.0 35.9 - - - +
175E GLU* 4.8 7.1 - - - +
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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
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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