Contacts of the helix formed by residues 129 - 154 (chain T) in PDB entry 4N3E
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 129 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93T ARG* 6.3 1.3 - - + -
95T ASN* 2.8 28.8 + - - +
127T THR* 3.3 3.2 + - - +
128T VAL* 1.3 68.6 - - - +
130T GLU* 1.3 52.7 + - - +
131T GLU* 2.9 44.7 + - - +
132T GLU* 2.4 41.8 + - + +
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Residues in contact with GLU 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET 5.1 4.9 + - - -
2S ALA* 4.0 16.5 + - + +
4S TYR* 5.9 0.2 - - - +
4T TYR* 3.7 31.4 - - + -
128T VAL* 2.6 21.8 + - + +
129T ASN* 1.3 67.4 - - - +
131T GLU* 1.3 63.8 + - - +
132T GLU 3.1 0.2 - - - -
133T VAL* 3.4 26.1 + - + +
134T LYS* 3.2 24.2 + - - +
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Residues in contact with GLU 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129T ASN* 3.2 21.8 + - - +
130T GLU* 1.3 77.9 - - - +
132T GLU* 1.3 61.1 + - - +
134T LYS* 3.0 33.6 + - - +
135T ILE* 2.9 36.1 + - + +
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Residues in contact with GLU 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T LEU 5.7 4.0 - - - +
93T ARG* 5.1 15.9 - - + -
95T ASN* 4.8 6.3 - - - +
96T ILE* 5.8 2.9 - - + -
120T TYR* 5.1 9.0 - - + -
128T VAL* 5.4 1.1 - - + -
129T ASN* 2.4 42.2 + - + +
131T GLU* 1.3 67.8 - - - +
133T VAL* 1.3 50.0 + - + +
135T ILE* 2.7 18.3 + - - +
136T GLY* 2.5 35.8 + - - -
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Residues in contact with VAL 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ALA* 5.5 0.9 - - + -
4T TYR* 4.7 7.2 - - + -
6T ILE* 3.1 37.5 - - + -
120T TYR* 3.8 34.9 + - + -
128T VAL* 3.4 31.0 - - + -
130T GLU* 3.4 25.8 + - + +
132T GLU* 1.3 74.0 - - - +
134T LYS* 1.3 62.3 + - - +
136T GLY* 3.3 1.2 - - - +
137T GLU* 3.0 24.9 + - - +
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Residues in contact with LYS 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130T GLU* 3.2 26.7 + - - +
131T GLU* 3.0 28.6 + - - +
133T VAL* 1.3 72.1 - - - +
135T ILE* 1.3 66.7 + - + +
136T GLY 2.9 5.4 + - - -
137T GLU* 3.4 2.9 + - - +
138T LYS* 3.1 23.8 + - - +
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Residues in contact with ILE 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T ARG* 4.3 22.2 - - - +
131T GLU* 2.9 36.4 + - + +
132T GLU* 2.7 17.4 + - - +
134T LYS* 1.3 77.2 - - + +
136T GLY* 1.3 62.5 + - - +
138T LYS* 3.7 12.7 - - + +
139T LYS* 3.3 43.6 + - + +
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Residues in contact with GLY 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101T TYR* 6.1 0.5 - - - -
120T TYR* 3.5 17.0 - - - -
132T GLU 2.5 17.1 + - - -
133T VAL 3.1 5.6 + - - -
134T LYS 2.9 1.4 - - - -
135T ILE* 1.3 74.6 - - - +
137T GLU* 1.3 69.4 + - - +
139T LYS* 3.6 8.1 + - - +
140T ALA* 3.8 13.0 + - - +
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Residues in contact with GLU 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T ILE* 3.2 31.8 - - + +
8T LYS* 4.0 34.2 - - - +
101T TYR* 5.3 1.6 - - - -
116T ILE* 5.1 2.3 - - - +
118T VAL* 3.3 41.5 - - - +
120T TYR* 4.0 3.6 + - - -
133T VAL 3.0 9.9 + - - +
134T LYS* 4.4 2.2 - - - +
136T GLY* 1.3 76.8 - - - +
138T LYS* 1.3 61.6 + - - +
140T ALA* 4.3 5.6 - - - +
141T TYR* 3.3 25.1 + - - +
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Residues in contact with LYS 138 (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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134T LYS 3.1 17.0 + - - +
135T ILE* 3.7 15.7 - - + +
137T GLU* 1.3 76.2 - - - +
139T LYS* 1.3 96.4 + - - +
141T TYR* 3.6 4.1 + - - +
142T GLU* 3.3 45.5 + - - +
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Residues in contact with LYS 139 (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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35T GLN* 5.1 1.7 + - - -
135T ILE* 3.3 32.4 + - + +
136T GLY 3.6 2.0 + - - +
137T GLU 3.5 0.2 - - - -
138T LYS* 1.3 103.5 - - - +
140T ALA* 1.3 62.2 + - - +
142T GLU* 3.5 22.7 + - - +
143T PHE* 3.5 22.0 + - - +
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Residues in contact with ALA 140 (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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27T ARG* 4.1 22.4 + - - +
101T TYR* 5.7 8.7 - - + -
136T GLY 3.8 13.5 + - - +
137T GLU* 4.3 7.2 - - - +
139T LYS* 1.3 77.5 - - - +
141T TYR* 1.3 63.0 + - - +
143T PHE* 3.4 6.1 + - - +
144T TYR* 3.2 24.0 + - - +
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Residues in contact with TYR 141 (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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10T GLU* 3.4 40.5 + - + -
137T GLU 3.3 19.5 + - - +
138T LYS* 3.9 5.4 - - - +
139T LYS 3.5 0.2 - - - -
140T ALA* 1.3 75.4 - - - +
142T GLU* 1.3 62.9 + - - +
144T TYR* 3.3 16.7 + + - -
145T LYS* 3.1 60.3 + - + +
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Residues in contact with GLU 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T GLN* 4.9 7.9 + - - +
138T LYS* 3.3 31.7 + - - +
139T LYS* 3.5 37.7 + - - +
141T TYR* 1.3 80.7 - - - +
143T PHE* 1.3 63.2 + - - +
145T LYS* 3.1 10.5 + - - +
146T GLN* 3.1 22.3 + - - +
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Residues in contact with PHE 143 (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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22T ALA 4.4 1.8 - - - -
23T LEU* 3.6 15.9 - - + -
27T ARG* 3.4 41.7 - - + -
30T VAL* 3.7 20.6 - - + -
31T LEU* 3.6 46.4 - - + -
34T ALA* 3.8 15.0 - - + -
35T GLN* 3.7 25.4 - - - +
139T LYS 3.5 12.3 + - - +
140T ALA* 3.4 3.9 + - - +
141T TYR 3.3 0.4 - - - -
142T GLU* 1.3 77.0 - - - +
144T TYR* 1.3 70.1 + - - +
145T LYS 3.1 0.2 + - - -
146T GLN* 3.2 4.3 + - - +
147T VAL* 2.8 42.7 + - + +
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Residues in contact with TYR 144 (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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10T GLU* 3.8 27.5 + - + +
11T GLU 3.2 20.6 + - - -
12T SER* 4.5 9.6 - - - -
19T LEU* 4.5 11.8 - - + +
23T LEU* 4.0 36.3 - - + -
140T ALA 3.2 13.1 + - - +
141T TYR* 3.4 35.2 - + - +
143T PHE* 1.3 78.6 - - - +
145T LYS* 1.3 71.5 + - + +
147T VAL* 3.3 1.7 + - - +
148T GLU* 2.7 67.9 + - + +
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Residues in contact with LYS 145 (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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141T TYR* 3.1 44.3 + - + +
142T GLU* 3.1 10.2 + - - +
144T TYR* 1.3 101.4 + - + +
146T GLN* 1.3 63.0 + - - +
148T GLU* 3.0 28.9 + - - +
149T GLU* 3.2 23.9 + - - +
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Residues in contact with GLN 146 (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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34T ALA* 2.5 48.6 + - - +
35T GLN* 3.5 23.2 + - - +
37T HIS* 6.3 0.4 - - - -
142T GLU 3.1 11.9 + - - +
143T PHE* 3.6 5.7 - - - +
145T LYS* 1.3 79.3 - - - +
147T VAL* 1.3 59.6 + - - +
149T GLU* 4.0 6.9 - - - +
150T TYR* 3.3 22.7 + - - +
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Residues in contact with VAL 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T LEU* 5.4 1.3 - - + -
22T ALA* 3.8 28.7 - - + -
23T LEU* 4.1 12.6 - - + -
30T VAL* 3.4 28.0 - - + -
34T ALA* 4.2 6.5 - - + -
143T PHE* 2.8 38.3 + - + +
144T TYR 3.7 3.1 - - - +
146T GLN* 1.3 73.1 - - - +
148T GLU* 1.3 66.1 + - - +
149T GLU 2.9 2.1 + - - -
150T TYR* 3.2 6.9 + - + -
151T LEU* 2.9 42.2 + - + +
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Residues in contact with GLU 148 (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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11T GLU 4.3 0.3 - - - +
12T SER* 3.1 22.1 + - - +
13T PRO* 3.5 21.0 - - + +
14T ILE* 3.6 18.2 - - + +
19T LEU* 5.3 2.4 - - + +
144T TYR* 2.7 50.8 + - + +
145T LYS* 3.0 38.2 + - - +
147T VAL* 1.3 71.2 - - - +
149T GLU* 1.3 56.3 + - - +
151T LEU* 4.8 1.3 - - - -
152T ALA* 3.2 27.1 + - + +
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Residues in contact with GLU 149 (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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145T LYS 3.2 16.2 + - - +
146T GLN* 4.0 8.7 - - - +
147T VAL 3.0 0.8 - - - -
148T GLU* 1.3 75.0 - - - +
150T TYR* 1.3 72.4 + - - +
152T ALA* 3.3 7.6 + - + +
153T ALA* 3.2 28.2 + - - +
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Residues in contact with TYR 150 (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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33T LYS* 6.1 7.2 - - + -
146T GLN 3.3 14.7 + - - +
147T VAL* 3.2 7.5 + - + +
149T GLU* 1.3 87.3 + - - +
151T LEU* 1.3 59.9 + - + +
153T ALA* 3.1 17.8 + - + -
154T ASN* 3.2 41.0 + - - +
157T VAL* 4.5 29.1 - - + +
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Residues in contact with LEU 151 (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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14T ILE* 3.6 31.6 - - + -
18T ARG* 3.0 62.9 + - + +
19T LEU* 4.5 6.3 - - + -
22T ALA* 4.3 1.1 - - + -
147T VAL* 2.9 37.9 + - + +
150T TYR* 1.3 79.3 - - + +
152T ALA* 1.3 65.9 + - - +
153T ALA 3.3 0.9 + - - -
154T ASN 3.8 8.3 + - - +
155T PRO* 3.8 1.9 - - - +
157T VAL* 4.0 14.8 - - + +
158T PHE* 3.9 27.6 - - + -
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Residues in contact with ALA 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T PRO* 5.9 4.3 - - + -
14T ILE* 3.6 12.7 - - + +
18T ARG* 4.9 0.7 - - - +
148T GLU* 3.2 21.0 + - + +
149T GLU* 3.3 7.8 + - + +
151T LEU* 1.3 76.7 - - - +
153T ALA* 1.3 58.3 + - - +
155T PRO* 4.2 8.3 - - - +
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Residues in contact with ALA 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149T GLU* 3.2 24.3 + - - +
150T TYR* 3.1 7.1 + - + +
152T ALA* 1.3 77.9 - - - +
154T ASN* 1.3 74.0 + - - +
155T PRO* 3.6 6.7 - - - +
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Residues in contact with ASN 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T ARG* 3.3 6.9 + - - -
150T TYR* 3.2 39.0 + - + +
151T LEU 3.8 2.9 - - - +
153T ALA* 1.3 91.7 + - - +
155T PRO* 1.3 59.3 - - - +
156T GLU* 2.7 32.9 + - - +
157T VAL* 3.1 22.9 + - + +
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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