Contacts of the helix formed by residues 1 - 23 (chain T) in PDB entry 2AXT
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 MET 1 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L PHE* 4.3 3.6 - - - -
3M VAL* 5.2 6.3 - - - -
8M LEU* 4.2 31.8 - - + +
2T GLU* 1.3 80.4 + - - +
3T THR* 4.1 2.4 + - - +
4T ILE* 2.8 32.1 - - + +
5T THR* 3.0 12.5 + - - -
217T LMT 2.9 58.7 + - - +
216m LMT 3.7 55.0 - - + +
5005m GLN* 5.6 3.4 - - + +
5006m LEU* 4.2 14.4 - - + -
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Residues in contact with GLU 2 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 5.8 0.7 - - - +
36L PHE* 3.4 44.6 - - + -
1M MET* 4.8 6.9 - - - +
3M VAL* 3.4 32.8 - - + +
1T MET* 1.3 102.4 + - - +
3T THR* 1.3 69.5 + - - +
4T ILE 3.0 1.3 - - - -
5T THR* 2.6 13.7 + - - -
6T TYR* 2.8 37.6 + - + +
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Residues in contact with THR 3 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.3 9.4 - - + -
71A LEU* 4.1 31.2 + - + -
72A LEU* 3.2 36.9 - - + +
75A ASN 5.6 0.9 + - - -
1T MET 4.8 0.4 + - - -
2T GLU* 1.3 79.6 - - - +
4T ILE* 1.3 58.3 + - - +
6T TYR* 3.1 10.0 + - - +
7T VAL* 2.9 35.8 + - + +
217T LMT 4.1 25.1 + - - -
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Residues in contact with ILE 4 (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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1T MET* 2.8 36.1 - - - +
3T THR* 1.3 82.6 - - - +
5T THR* 1.3 64.1 + - - +
7T VAL* 3.5 5.2 + - - +
8T PHE* 3.1 20.7 + - + +
217T LMT 2.8 50.3 + - + +
5104T BCR 3.4 35.9 - - + -
216m LMT 3.4 34.3 - - + -
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Residues in contact with THR 5 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L SER* 5.1 0.9 - - - -
36L PHE* 3.9 19.7 - - + -
8M LEU* 3.1 22.8 - - + +
11M THR* 3.8 29.4 - - + -
1T MET 3.0 15.6 + - - -
2T GLU 2.6 13.6 + - - -
4T ILE* 1.3 82.8 - - - +
6T TYR* 1.3 60.9 + - + +
8T PHE* 3.8 4.0 - - - +
9T ILE* 3.3 26.3 + - + +
216m LMT 4.1 13.2 - - + +
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Residues in contact with TYR 6 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.2 17.0 - - + -
75A ASN 4.5 3.6 - - - -
76A ASN* 3.6 30.5 - - + +
77A ILE* 3.2 33.0 - - + -
474C UNK 5.9 1.3 - - - +
29L LEU* 3.9 8.4 - - + +
32L SER* 3.1 28.7 - - - -
33L SER* 3.6 20.8 + - - -
36L PHE* 3.3 31.7 - + - +
2T GLU* 2.8 42.3 + - + +
3T THR* 3.7 8.7 - - - +
5T THR* 1.3 71.4 - - - +
7T VAL* 1.3 68.6 + - - +
8T PHE 3.0 2.7 + - - -
9T ILE* 3.5 2.2 + - + -
10T PHE* 3.1 21.2 + - - +
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Residues in contact with VAL 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 35.9 - - + -
71A LEU* 4.2 9.6 - - + -
474C UNK 6.3 1.3 - - + -
3T THR* 2.9 24.2 + - + +
4T ILE* 4.0 5.2 - - - +
6T TYR* 1.3 76.2 - - - +
8T PHE* 1.3 57.4 + - - +
10T PHE* 3.6 9.3 - - + +
11T ALA* 2.9 25.7 + - + +
217T LMT 3.8 53.4 - - + +
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Residues in contact with PHE 8 (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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25L LEU* 6.5 0.2 - - + -
15M VAL* 5.7 10.1 - - + -
16M LEU* 6.3 3.4 - - + -
4T ILE* 3.1 19.0 + - + +
5T THR* 3.8 5.2 - - + +
6T TYR 3.0 1.0 - - - -
7T VAL* 1.3 73.2 - - - +
9T ILE* 1.3 83.7 + - + +
10T PHE 2.9 0.7 - - - -
11T ALA* 2.8 16.6 + - - +
12T CYS* 2.8 34.7 + - - -
5104T BCR 3.6 52.3 - - + -
5527b BCR 5.9 2.2 - - + -
5530b MGE 4.7 20.9 - - + -
216m LMT 4.0 31.2 - - + -
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Residues in contact with ILE 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LEU* 3.2 41.5 - - + +
28L ALA* 3.6 32.8 - - + +
29L LEU* 3.7 21.8 - - + +
32L SER* 4.4 5.4 - - - +
11M THR* 4.0 18.4 - - + -
15M VAL* 5.0 6.5 - - + -
5T THR* 3.3 17.9 - - + +
6T TYR* 3.5 2.4 + - - +
8T PHE* 1.3 84.0 - - + +
10T PHE* 1.3 61.0 + - - +
12T CYS* 3.2 10.0 + - - +
13T ILE* 3.1 22.8 + - + +
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Residues in contact with PHE 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 6.0 0.2 - + - -
49A VAL* 4.0 37.7 - - + -
53A ILE* 6.1 1.3 - - + -
559A CLA 4.2 16.6 - - + -
474C UNK 3.5 32.3 - - + -
360D MGE 3.6 31.0 - - + -
29L LEU* 4.2 6.9 - - + +
6T TYR 3.1 15.6 + - - +
7T VAL* 3.6 11.9 - - + +
8T PHE 2.8 1.4 + - - -
9T ILE* 1.3 75.7 - - - +
11T ALA* 1.3 67.2 + - - +
12T CYS 2.9 5.6 + - - -
13T ILE* 2.9 17.5 + - - +
14T ILE* 3.0 34.6 + - + +
217T LMT 4.5 14.8 - - + -
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Residues in contact with ALA 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T VAL* 2.9 18.5 + - + +
8T PHE* 2.8 7.0 + - - +
10T PHE* 1.3 73.0 - - - +
12T CYS* 1.3 61.6 + - - +
14T ILE* 3.6 2.8 + - - +
15T ALA* 3.2 22.2 + - - +
217T LMT 3.7 32.3 - - + -
5104T BCR 3.4 38.3 - - + +
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Residues in contact with CYS 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LEU* 3.7 23.9 - - + +
5213L SQD 4.9 9.5 - - + +
8T PHE* 2.8 49.5 + - - -
9T ILE* 3.3 11.9 - - - +
11T ALA* 1.3 76.4 - - - +
13T ILE* 1.3 67.8 + - - +
14T ILE 3.1 0.2 - - - -
15T ALA* 3.2 4.8 + - - +
16T LEU* 2.8 25.5 + - - +
5104T BCR 4.0 7.0 - - - -
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Residues in contact with ILE 13 (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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360D MGE 3.8 27.1 - - + -
22L LEU* 4.4 8.7 - - + -
25L LEU* 3.3 36.8 - - + +
26L VAL* 3.9 22.0 - - + -
29L LEU* 5.1 4.5 - - + -
9T ILE* 3.1 17.1 + - + +
10T PHE* 2.9 11.0 + - - +
12T CYS* 1.3 75.4 - - - +
14T ILE* 1.3 58.2 + - + +
16T LEU* 3.1 7.5 + - + +
17T PHE* 2.9 67.2 + - + -
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Residues in contact with ILE 14 (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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559A CLA 4.3 19.5 - - + -
360D MGE 5.5 0.9 - - + -
10T PHE* 3.0 46.5 + - + +
11T ALA 3.8 4.3 - - - +
13T ILE* 1.3 76.7 - - + +
15T ALA* 1.3 63.3 + - - +
17T PHE* 3.5 28.0 + - + +
18T PHE 3.4 14.0 + - - -
217T LMT 3.7 23.8 - - + -
5104T BCR 3.9 21.7 - - + +
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Residues in contact with ALA 15 (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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5213L SQD 5.2 13.7 - - + -
11T ALA 3.2 12.7 + - - +
12T CYS* 3.9 5.4 - - - +
14T ILE* 1.3 74.6 - - - +
16T LEU* 1.3 65.5 + - - +
17T PHE 3.1 0.4 - - - -
18T PHE* 3.2 5.7 + - - +
19T PHE* 3.1 40.9 + - + -
5104T BCR 3.6 37.2 - - + -
5108b PHE* 6.4 0.9 - - + -
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Residues in contact with LEU 16 (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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360D MGE 5.7 2.7 - - + +
18L TYR* 3.7 27.8 - - + +
21L LEU* 3.3 52.7 - - + +
22L LEU* 3.4 29.4 - - + +
25L LEU* 4.3 6.3 - - + -
5213L SQD 4.0 16.5 - - + +
12T CYS 2.8 18.8 + - - +
13T ILE* 3.3 7.0 - - - +
15T ALA* 1.3 79.1 - - - +
17T PHE* 1.3 57.5 + - + +
19T PHE* 4.6 0.7 - - - +
20T ALA* 3.0 28.9 + - + +
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Residues in contact with PHE 17 (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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558A CLA 3.9 21.5 - - + -
559A CLA 5.5 4.0 - - + -
360D MGE 3.6 68.2 - - + -
22L LEU* 4.0 11.9 - - + -
13T ILE* 2.9 44.7 + - + -
14T ILE* 3.5 31.6 - - + +
15T ALA 3.1 0.2 - - - -
16T LEU* 1.3 78.1 - - + +
18T PHE* 1.3 68.3 + - - +
20T ALA* 3.4 4.0 + - - +
21T ILE* 3.2 27.5 + - - +
5104T BCR 3.7 15.3 - - + -
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Residues in contact with PHE 18 (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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5212A SQD 5.4 0.9 - - - -
14T ILE 3.4 2.0 + - - -
15T ALA* 3.2 9.1 + - - +
17T PHE* 1.3 80.3 - - - +
19T PHE* 1.3 86.9 + + - +
22T PHE* 2.9 57.6 + + - +
23T PHE* 3.7 24.9 - + - -
5104T BCR 3.4 55.1 - - + +
5108b PHE* 3.8 26.7 - + - -
5109b LEU* 4.5 3.4 - - + -
5112b CYS* 3.9 12.8 - - - -
5529b BCR 3.7 29.4 - - + -
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Residues in contact with PHE 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L TYR* 3.4 21.4 + - + +
5213L SQD 3.6 76.3 - - + -
15T ALA* 3.1 28.4 + - + +
16T LEU* 4.1 3.1 - - - +
18T PHE* 1.3 98.5 - + - +
20T ALA* 1.3 56.9 + - - +
23T PHE* 2.9 57.1 + + + +
5108b PHE* 4.7 4.7 - + - -
5527b BCR 3.3 34.1 - - + -
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Residues in contact with ALA 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D ILE* 3.1 15.5 - - + +
360D MGE 3.6 41.7 - - + +
18L TYR* 4.1 20.2 - - + -
16T LEU* 3.0 21.1 + - + +
17T PHE 3.9 3.8 - - - +
18T PHE 3.3 0.2 - - - -
19T PHE* 1.3 77.4 - - - +
21T ILE* 1.3 58.1 + - - +
24T ARG* 3.6 17.6 - - - +
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Residues in contact with ILE 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 3.5 33.3 + - - +
28A LEU* 4.7 2.9 - - + -
473C ASP 4.4 1.0 - - - +
258D GLY* 4.1 18.6 - - - +
259D ILE* 3.6 22.4 - - + -
360D MGE 4.5 17.9 - - + -
17T PHE 3.3 16.8 - - - +
18T PHE 3.1 2.8 + - - +
20T ALA* 1.3 79.4 - - - +
22T PHE* 1.3 83.9 + - + +
23T PHE 3.2 6.6 + - - -
24T ARG* 3.9 12.5 - - - +
5104T BCR 3.7 32.8 - - + -
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Residues in contact with PHE 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 3.8 26.2 - - + +
28A LEU* 4.0 14.4 - - + -
5212A SQD 3.8 22.2 - - - -
473C ASP* 5.9 2.7 - - - -
18T PHE* 2.9 36.1 + + + +
19T PHE 3.9 0.4 - - - -
21T ILE* 1.3 90.9 - - + +
23T PHE* 1.3 84.3 + - + +
24T ARG 3.9 0.2 - - - -
5104T BCR 3.5 45.8 - - + -
5529b BCR 3.6 33.6 - - + +
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Residues in contact with PHE 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L ARG* 3.2 8.3 + - - -
18L TYR* 2.8 18.7 + - - +
5213L SQD 3.1 78.2 - - - +
18T PHE* 3.7 29.4 - + - -
19T PHE* 2.9 37.6 + + + +
21T ILE 3.2 0.2 - - - -
22T PHE* 1.3 91.4 - - + +
24T ARG* 1.3 66.0 + - - +
5112b CYS* 4.6 6.1 - - + -
5115b TRP* 5.5 2.0 - + + -
5116b VAL* 5.2 7.4 - - + -
5527b BCR 4.5 14.6 - - + -
5529b BCR 4.0 19.1 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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