Contacts of the helix formed by residues 11 - 36 (chain m) in PDB entry 5W97
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 11 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9m PRO* 3.8 2.6 + - - +
10m THR* 1.3 75.7 - - - +
12m PRO* 1.3 76.3 - - - +
13m LYS* 3.3 14.6 - - - +
14m GLU* 3.0 35.0 + - - +
15m GLN* 3.0 21.1 + - - +
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Residues in contact with PRO 12 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607a PGV 4.0 54.0 - - + +
11m SER* 1.3 87.4 - - - +
13m LYS* 1.3 60.3 + - - +
15m GLN* 3.7 4.6 - - + +
16m ALA* 3.1 23.7 + - - +
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Residues in contact with LYS 13 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11m SER* 3.3 13.0 + - - +
12m PRO* 1.3 75.9 - - - +
14m GLU* 1.3 68.7 + - + +
16m ALA* 3.2 14.4 + - - +
17m ILE* 3.3 24.4 + - + +
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Residues in contact with GLU 14 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473a TRP* 4.1 7.0 - - + -
18l LYS* 3.2 19.9 + - - +
19l TRP* 3.7 36.2 + - + -
9m PRO 3.4 3.6 - - - +
10m THR* 3.2 20.4 - - + -
11m SER* 3.0 34.4 + - - +
13m LYS* 1.3 80.0 - - + +
15m GLN* 1.3 58.5 + - - +
17m ILE* 3.0 11.0 + - + +
18m GLY* 2.9 25.5 + - - -
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Residues in contact with GLN 15 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406a ASN* 5.9 0.7 + - - -
409a TRP* 3.1 37.4 + - - +
470a PHE* 3.7 20.5 - - + -
473a TRP* 4.4 2.9 - - - -
474a GLU* 4.6 12.8 - - + +
607a PGV 3.7 43.4 - - + +
10m THR* 3.1 29.7 - - + +
11m SER 3.0 15.9 + - - +
12m PRO* 3.7 5.6 - - + +
14m GLU* 1.3 75.8 - - - +
16m ALA* 1.3 53.8 + - - +
18m GLY 3.3 0.8 + - - +
19m LEU* 2.8 37.4 + - - +
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Residues in contact with ALA 16 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607a PGV 4.5 28.7 - - + +
12m PRO 3.1 15.4 + - - +
13m LYS* 3.2 11.9 + - - +
15m GLN* 1.3 74.3 - - - +
17m ILE* 1.3 55.4 + - + +
19m LEU* 3.7 3.0 + - - +
20m SER* 2.6 36.4 + - - -
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Residues in contact with ILE 17 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19l TRP* 4.1 22.2 - - + -
22l LEU* 4.7 0.9 - - + -
13m LYS* 3.3 24.0 + - + +
14m GLU* 3.0 11.3 + - + +
16m ALA* 1.3 75.7 - - + +
18m GLY* 1.3 56.6 + - - +
20m SER* 3.0 7.2 + - - -
21m VAL* 2.7 48.7 + - + +
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Residues in contact with GLY 18 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470a PHE* 3.9 7.0 - - - -
473a TRP* 3.8 22.6 - - - -
19l TRP* 4.9 0.2 - - - -
22l LEU* 4.1 15.2 - - - +
14m GLU 2.9 13.1 + - - -
15m GLN 3.6 2.9 - - - -
17m ILE* 1.3 76.8 - - - +
19m LEU* 1.3 60.6 + - - +
21m VAL* 4.0 0.3 - - - +
22m THR* 3.0 30.9 + - - -
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Residues in contact with LEU 19 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409a TRP* 4.1 14.6 - - + -
467a LEU* 3.7 26.0 - - + -
470a PHE* 3.8 18.3 - - + -
607a PGV 4.5 29.8 - - + -
88d PHE* 3.7 22.4 - - + -
15m GLN 2.8 19.9 + - - +
16m ALA* 4.1 5.6 - - - +
18m GLY* 1.3 74.6 - - - +
20m SER* 1.3 58.4 + - - +
22m THR* 3.8 2.0 - - - -
23m PHE* 2.9 68.8 + - + +
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Residues in contact with SER 20 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607a PGV 4.1 27.6 - - - +
16m ALA 2.6 22.6 + - - -
17m ILE* 3.0 8.6 + - - -
19m LEU* 1.3 76.0 - - - +
21m VAL* 1.3 66.5 + - - +
23m PHE* 3.5 4.2 + - - +
24m LEU* 3.1 39.2 + - - +
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Residues in contact with VAL 21 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22l LEU* 3.9 25.8 - - + -
23l ALA* 6.0 0.7 - - - -
26l THR* 3.6 24.0 - - + +
17m ILE* 2.7 38.4 + - + +
18m GLY 4.0 0.4 - - - +
20m SER* 1.3 71.7 - - - +
22m THR* 1.3 54.8 - - - +
24m LEU* 2.7 31.0 + - + +
25m SER* 2.9 14.0 + - - -
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Residues in contact with THR 22 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466a MET 3.5 26.9 - - - +
469a VAL* 3.9 23.8 - - + +
470a PHE* 3.9 16.9 - - + +
473a TRP* 5.4 1.2 - - - +
22l LEU* 3.7 15.4 - - - +
26l THR* 4.0 6.1 - - + +
18m GLY 3.0 19.0 + - - -
19m LEU 3.9 2.2 - - - -
21m VAL* 1.3 78.6 - - - +
23m PHE* 1.3 61.6 + - + +
25m SER* 2.8 21.0 + - - +
26m PHE* 3.2 16.7 - - + -
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Residues in contact with PHE 23 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463a THR* 4.0 12.3 - - + -
466a MET* 3.7 43.1 - - + -
467a LEU* 3.7 20.0 - - + -
470a PHE* 5.3 0.4 - - + -
607a PGV 5.0 11.4 - - + -
88d PHE* 4.0 16.4 - + - -
91d PHE* 3.5 37.2 - + - -
19m LEU* 2.9 59.7 + - + +
20m SER* 4.1 4.5 - - - +
21m VAL 3.3 0.2 - - - -
22m THR* 1.3 78.3 - - + +
24m LEU* 1.3 59.3 + - + +
26m PHE* 3.6 1.8 + - - +
27m LEU* 3.1 41.1 + - + +
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Residues in contact with LEU 24 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607a PGV 5.3 11.9 - - + -
20m SER* 3.1 32.2 + - - +
21m VAL* 2.7 11.0 + - + +
23m PHE* 1.3 76.7 - - - +
25m SER* 1.3 58.7 + - - +
27m LEU* 4.6 6.7 - - + -
28m LEU* 2.8 73.6 + - + +
401m DMU 6.2 0.4 - - + -
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Residues in contact with SER 25 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26l THR* 3.2 47.4 - - - +
30l GLY* 4.4 13.9 + - - +
33l PHE* 5.4 0.3 - - - -
21m VAL* 2.9 5.9 + - - -
22m THR* 2.8 19.6 + - - -
24m LEU* 1.3 73.5 - - - +
26m PHE* 1.3 63.5 + - - +
29m PRO* 3.2 23.8 - - - +
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Residues in contact with PHE 26 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28a MET* 3.7 26.0 - - - -
462a LEU* 4.2 2.7 - - + -
465a VAL* 4.5 8.1 - - + -
466a MET* 3.6 42.6 - - + -
469a VAL* 3.5 37.0 - - + -
29l PHE* 4.2 15.0 - - + -
30l GLY* 5.3 2.0 - - - -
33l PHE* 3.4 64.4 - + + -
22m THR* 3.2 24.5 - - + -
23m PHE 3.6 1.7 + - - +
24m LEU 3.2 0.6 - - - -
25m SER* 1.3 85.0 + - - +
27m LEU* 1.3 64.3 + - + +
29m PRO* 4.2 0.5 - - - +
30m ALA* 3.7 10.2 + - - +
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Residues in contact with LEU 27 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462a LEU* 4.3 6.5 - - + -
466a MET* 3.9 17.9 - - + -
607a PGV 6.0 2.0 - - + -
91d PHE* 4.3 11.9 - - + -
95d LEU* 4.0 31.9 - - + -
33l PHE* 6.3 0.2 - - + -
23m PHE* 3.1 35.1 + - + +
24m LEU* 4.2 6.7 - - + +
26m PHE* 1.3 77.9 - - - +
28m LEU* 1.3 61.5 + - + +
30m ALA* 4.1 1.3 - - - +
31m GLY* 3.0 25.8 + - - -
401m DMU 3.4 51.7 - - + +
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Residues in contact with LEU 28 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24m LEU* 2.8 56.4 + - + +
27m LEU* 1.3 70.5 - - + +
29m PRO* 1.4 63.8 - - + +
31m GLY* 2.8 5.4 + - - -
32m TRP* 2.8 29.1 + - - +
401m DMU 3.4 40.3 + - + +
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Residues in contact with PRO 29 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30l GLY 5.5 1.1 - - - +
33l PHE* 6.4 0.7 - - + -
34l ALA* 4.2 25.6 - - + -
37l PHE* 5.5 0.9 - - - -
38l PHE* 4.7 10.8 - - + -
24m LEU 3.8 1.1 - - - +
25m SER* 3.2 26.7 - - - +
26m PHE 4.2 1.1 - - - +
27m LEU 3.9 0.2 - - - -
28m LEU* 1.4 93.4 - - + +
30m ALA* 1.3 63.4 + - - +
32m TRP* 3.5 14.2 + - + +
33m VAL* 3.2 28.7 + - - +
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Residues in contact with ALA 30 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33l PHE* 4.0 5.6 - - + -
37l PHE* 3.6 42.5 - - + -
26m PHE 3.7 17.6 + - - +
27m LEU 3.8 2.4 + - - +
28m LEU 3.3 0.6 - - - -
29m PRO* 1.3 81.4 - - - +
31m GLY* 1.3 57.7 + - - +
33m VAL* 3.4 1.9 + - - +
34m LEU* 2.9 41.0 + - + +
401m DMU 4.4 9.2 - - + -
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Residues in contact with GLY 31 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98d TRP* 3.5 20.9 - - - -
27m LEU 3.0 13.6 + - - -
28m LEU 2.8 8.3 + - - -
30m ALA* 1.3 74.1 - - - +
32m TRP* 1.3 54.4 + - - -
34m LEU* 4.4 0.4 - - - -
35m TYR* 2.7 38.6 + - - +
401m DMU 3.9 19.7 - - - +
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Residues in contact with TRP 32 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38l PHE* 4.6 27.4 - + - -
41l ARG* 6.2 5.8 - - - -
28m LEU 2.8 17.1 + - - +
29m PRO* 3.7 10.3 - - + +
31m GLY* 1.3 72.3 - - - +
33m VAL* 1.3 65.1 + - + +
36m HIS* 2.7 63.9 + + + -
40m TYR* 4.9 6.3 + - - -
401m DMU 3.5 20.8 - - - +
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Residues in contact with VAL 33 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37l PHE* 3.6 39.7 - - + +
38l PHE* 3.6 35.0 - - + -
40l VAL* 5.8 1.3 - - + -
41l ARG* 4.3 17.9 - - + +
29m PRO 3.2 13.9 + - - +
30m ALA 3.7 6.7 - - - +
32m TRP* 1.3 81.0 - - + +
34m LEU* 1.3 62.7 + - - +
36m HIS 3.4 6.4 + - - -
37m LEU* 3.7 15.5 + - + +
40m TYR* 3.7 23.0 - - + -
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Residues in contact with LEU 34 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36a LEU* 4.9 7.4 - - + -
39a ALA* 5.3 6.5 - - + -
47a LEU* 5.1 8.5 - - + -
98d TRP* 4.4 1.6 - - + -
99d GLU* 6.5 0.7 - - + -
102d TYR 4.2 1.2 - - - +
103d VAL* 3.8 42.7 - - + +
37l PHE* 4.2 22.9 - - + -
30m ALA 2.9 27.4 + - - +
31m GLY* 3.7 4.0 - - - +
32m TRP 3.2 0.2 - - - -
33m VAL* 1.3 75.9 - - - +
35m TYR* 1.3 65.9 + - - +
37m LEU* 3.3 31.6 - - + +
401m DMU 3.8 35.4 - - + -
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Residues in contact with TYR 35 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98d TRP* 4.3 4.1 - - + -
102d TYR* 3.8 40.1 - + + +
31m GLY 2.7 22.3 + - - +
32m TRP 3.6 4.3 - - - +
34m LEU* 1.3 73.3 - - - +
36m HIS* 1.3 82.8 + + + +
37m LEU 3.0 6.8 + - - -
38m ASP* 3.8 11.4 + - - +
39m ASN* 5.5 3.1 + - - -
401m DMU 3.0 72.0 + - - -
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Residues in contact with HIS 36 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32m TRP* 2.7 52.2 + + - +
33m VAL 3.7 2.9 - - - -
34m LEU 3.3 0.4 - - - -
35m TYR* 1.3 96.6 - + - +
37m LEU* 1.3 56.5 + - - +
38m ASP 3.7 1.8 - - - -
39m ASN* 3.5 31.8 - - - +
40m TYR* 3.1 43.3 - + + +
401m DMU 3.6 23.4 + - - -
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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