Contacts of the helix formed by residues 51 - 72 (chain S) in PDB entry 3H1I
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 51 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S ARG 3.8 3.1 - - - +
50S LEU* 1.3 92.4 - - + +
52S GLU* 1.3 67.4 + - - +
53S ASP* 3.1 18.0 + - - +
54S LEU* 3.3 19.0 + - + -
55S TYR* 3.2 15.8 + - - +
93S TYR* 3.3 28.7 - - + +
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Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S LEU 3.6 2.5 + - - -
51S PRO* 1.3 71.4 - - - +
53S ASP* 1.3 63.9 + - - +
55S TYR* 3.3 8.9 + - + +
56S ASN* 2.9 44.0 + - - +
9T ARG* 4.6 11.1 + - - -
11T ARG* 2.8 45.5 + - - -
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Residues in contact with ASP 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Q TYR* 5.0 4.5 - - - +
51S PRO* 3.8 13.7 - - - +
52S GLU* 1.3 77.9 - - - +
54S LEU* 1.3 79.0 + - - +
55S TYR 2.7 12.0 + - - -
56S ASN* 3.9 4.0 - - - +
57S GLU* 3.0 36.4 + - + +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S LEU* 4.2 11.8 - - + +
51S PRO* 3.3 30.3 + - + +
53S ASP* 1.3 89.2 + - - +
55S TYR* 1.3 56.4 + - - +
57S GLU* 3.9 20.2 - - - +
58S ARG* 3.4 21.8 + - - +
61S ARG* 4.0 6.1 + - - +
87S LYS* 6.4 1.1 - - + -
89S TYR* 4.4 33.8 - - + +
93S TYR* 5.3 3.8 - - + +
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Residues in contact with TYR 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S LEU* 4.0 32.1 - - + -
48S LYS* 6.0 0.2 - - - -
50S LEU* 4.1 17.7 - - + +
51S PRO 3.2 15.6 + - - +
52S GLU* 3.6 9.6 - - + +
53S ASP 2.7 5.7 + - - -
54S LEU* 1.3 72.2 - - - +
56S ASN* 1.3 80.4 + - - +
57S GLU 2.9 1.6 - - - -
58S ARG* 2.9 20.3 + - - +
59S MET* 2.9 39.9 + - + +
8T ALA* 5.6 2.6 - - - +
9T ARG* 4.2 36.4 + - + +
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Residues in contact with ASN 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Q TYR* 4.0 23.8 + - + +
52S GLU* 2.9 46.1 + - - +
53S ASP* 4.0 2.0 - - - +
55S TYR* 1.3 89.8 - - - +
57S GLU* 1.3 61.4 + - - +
59S MET* 3.3 8.5 - - - +
60S PHE* 3.0 23.4 + - - +
9T ARG* 5.2 2.3 - - - +
10T VAL* 5.0 1.7 - - - -
11T ARG* 3.6 41.4 + - - +
12T HIS* 4.8 5.6 + - - +
13T ILE* 5.2 0.7 - - - +
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Residues in contact with GLU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Q TYR* 3.4 33.6 + - + +
53S ASP* 3.0 35.5 + - - +
54S LEU* 3.9 20.2 - - - +
55S TYR 2.9 0.8 - - - -
56S ASN* 1.3 75.2 - - - +
58S ARG* 1.3 67.7 + - - +
60S PHE* 3.1 6.3 + - - +
61S ARG* 2.9 42.4 + - - +
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Residues in contact with ARG 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212P ILE* 5.9 1.6 - - - +
213P SER* 5.0 1.6 - - - +
34S ASP 4.0 5.9 + - - -
35S ASP* 3.5 18.3 + - - +
37S LEU* 5.7 3.0 + - - +
39S GLU* 3.2 29.5 + - - +
43S VAL* 5.9 0.8 - - - +
47S LEU* 3.7 38.6 - - - +
50S LEU* 4.7 6.5 - - + -
54S LEU 3.4 9.3 + - - +
55S TYR* 2.9 23.0 + - - +
57S GLU* 1.3 73.9 - - - +
59S MET* 1.3 74.2 + - - +
61S ARG* 3.0 37.8 + - - +
62S ILE* 3.1 36.4 + - + +
89S TYR* 3.3 31.5 + - + +
90S LEU* 5.5 0.6 - - - +
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Residues in contact with MET 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213P SER* 4.7 10.5 - - - +
216P SER* 3.2 32.8 - - - +
55S TYR* 2.9 29.6 + - + +
56S ASN* 3.3 14.4 - - - +
58S ARG* 1.3 83.7 - - - +
60S PHE* 1.3 54.9 + - - +
62S ILE* 2.6 37.4 + - + +
63S LYS* 2.8 11.4 + - - -
8T ALA* 4.9 9.0 - - + -
9T ARG 3.7 10.8 - - - +
10T VAL* 3.6 33.4 - - + -
11T ARG 6.0 0.4 - - - +
13T ILE* 4.8 8.3 - - + -
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Residues in contact with PHE 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235Q MET* 3.1 33.9 - - + -
236Q ALA* 3.7 15.3 - - - -
237Q TYR* 3.2 55.9 - + + -
56S ASN 3.0 10.0 + - - +
57S GLU 3.6 7.0 - - - +
59S MET* 1.3 79.8 - - - +
61S ARG* 1.3 69.2 + - + +
63S LYS 4.3 1.1 - - - +
64S ARG* 2.9 46.4 + - + +
13T ILE* 3.7 30.0 - - + +
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Residues in contact with ARG 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S GLY 4.0 14.4 - - - +
31S LEU* 3.5 9.8 - - + +
32S MET* 3.9 14.7 - - - +
35S ASP* 2.9 29.2 + - - +
54S LEU* 4.0 4.8 + - - +
57S GLU* 2.9 37.7 + - - +
58S ARG* 3.0 29.8 - - - +
60S PHE* 1.3 80.3 - - + +
62S ILE* 1.3 55.1 + - - +
64S ARG* 3.3 31.2 + - - +
65S ALA 3.2 18.0 + - - -
89S TYR* 2.7 40.4 - - - -
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Residues in contact with ILE 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212P ILE* 4.0 28.0 - - + -
213P SER* 3.9 23.3 - - - +
216P SER* 4.0 7.9 - - - +
31S LEU* 4.2 7.2 - - + -
35S ASP* 4.5 11.9 - - - +
58S ARG* 3.1 51.8 + - + +
59S MET* 2.6 22.6 + - + +
61S ARG* 1.3 69.0 - - + +
63S LYS* 1.3 51.9 + - - +
64S ARG 2.7 6.0 + - - -
65S ALA* 2.7 27.8 + - - +
66S LEU* 2.7 23.3 + - + +
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Residues in contact with LYS 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244N ARG* 6.0 2.4 - - - +
216P SER* 3.4 33.0 + - - +
217P ASP* 3.5 23.7 + - + +
233Q ARG* 3.9 7.3 + - - +
235Q MET* 3.1 19.9 - - + +
59S MET 2.8 14.7 + - - +
60S PHE* 3.2 9.8 + - - +
62S ILE* 1.3 74.0 - - - +
64S ARG* 1.3 57.5 + - - +
66S LEU* 4.0 9.7 - - - +
67S ASP* 3.5 11.8 + - - +
10T VAL* 5.6 3.1 - - + -
13T ILE* 3.4 41.3 - - + -
15T THR* 3.9 17.7 - - - +
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Residues in contact with ARG 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235Q MET* 3.1 21.8 - - + +
29S TYR 2.9 26.4 + - - -
30S GLY* 3.4 18.8 + - - -
60S PHE* 2.9 35.7 + - + +
61S ARG* 3.3 36.6 + - - +
62S ILE 2.8 0.6 - - - -
63S LYS* 1.3 75.6 - - - +
65S ALA* 1.3 57.9 + - - +
66S LEU 3.1 1.1 - - - -
67S ASP* 3.2 4.0 + - + +
68S LEU* 2.8 42.3 + - + +
75S LEU* 4.1 28.1 - - - +
79S GLN* 5.8 1.2 - - - +
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Residues in contact with ALA 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P LEU* 3.7 16.6 - - + +
212P ILE* 4.9 2.0 - - + -
29S TYR* 3.7 8.3 - - + +
31S LEU* 3.4 37.9 - - + -
61S ARG 3.2 3.2 + - - +
62S ILE* 2.7 14.2 + - - +
64S ARG* 1.3 74.8 - - - +
66S LEU* 1.3 57.7 + - - +
68S LEU* 3.1 15.8 - - - +
69S SER* 2.8 29.3 + - - -
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Residues in contact with LEU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P SER* 4.1 3.8 - - - +
27P ASN* 3.4 23.3 - - - +
208P ASN* 4.5 10.8 - - - +
210P LEU* 3.7 21.3 - - + -
212P ILE* 4.7 4.7 - - + -
213P SER 4.2 6.5 - - - +
214P SER* 4.1 22.4 - - - +
216P SER* 4.5 2.7 - - - +
217P ASP* 3.7 36.8 - - + +
62S ILE* 2.7 28.8 + - + +
63S LYS* 4.2 5.2 - - - +
65S ALA* 1.3 73.3 - - - +
67S ASP* 1.3 67.2 + - - +
68S LEU 2.9 2.1 + - - -
69S SER* 3.0 4.2 + - - -
70S LEU* 2.9 27.4 + - - +
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Residues in contact with ASP 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233Q ARG* 2.8 43.3 + - - +
234Q LYS* 5.7 0.2 - - - -
235Q MET* 3.9 16.7 - - - +
63S LYS 3.5 12.0 + - - +
64S ARG* 3.2 10.0 + - + +
66S LEU* 1.3 78.2 - - - +
68S LEU* 1.3 69.1 + - - +
70S LEU* 3.2 6.7 - - - +
71S LYS* 2.6 65.2 + - - +
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Residues in contact with LEU 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S TYR* 3.4 48.0 - - + +
64S ARG* 2.8 28.6 + - + +
65S ALA* 3.1 7.4 - - - +
66S LEU 2.9 0.6 + - - -
67S ASP* 1.3 78.3 + - - +
69S SER* 1.3 54.2 + - - +
70S LEU 2.4 3.7 + - - -
71S LYS* 2.3 41.6 + - + +
72S HIS 3.0 5.0 + - - -
73S ARG* 3.4 27.4 - - + +
74S ILE* 4.0 20.4 - - - +
75S LEU* 4.2 17.3 - - + +
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Residues in contact with SER 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P ASN* 3.9 17.2 + - - +
209P PRO* 4.0 16.5 - - - +
210P LEU* 3.7 27.3 - - - +
3007P PEE 4.9 7.8 - - - -
29S TYR* 3.8 18.6 + - - -
65S ALA 2.8 14.8 + - - -
66S LEU 3.7 3.8 - - - -
68S LEU* 1.3 73.5 - - - +
70S LEU* 1.3 58.1 + - - +
71S LYS 3.4 0.4 - - - -
72S HIS* 3.8 22.4 + - - +
73S ARG 4.9 0.2 - - - -
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Residues in contact with LEU 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P SER* 3.6 30.7 - - - +
27P ASN* 4.0 5.8 - - - +
227Q TRP* 4.5 13.1 - - + -
230Q LEU* 3.1 49.1 - - + +
231Q LYS* 3.0 25.3 + - + +
233Q ARG* 3.0 32.5 - - - +
66S LEU 2.9 7.7 + - - +
67S ASP* 3.2 21.1 - - - +
68S LEU 2.4 14.5 + - - -
69S SER* 1.3 70.0 - - - +
71S LYS* 1.3 59.8 + - + +
72S HIS* 3.3 2.9 + - - -
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Residues in contact with LYS 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230Q LEU 2.9 26.2 + - - +
231Q LYS* 2.7 39.6 + - + +
232Q SER 4.4 0.2 - - - -
233Q ARG* 2.8 24.5 + - - +
3003Q CDL 4.8 2.6 + - - -
13R TYR* 5.9 1.6 - - - -
67S ASP* 2.6 50.7 + - - +
68S LEU* 2.3 29.6 + - + +
70S LEU* 1.3 73.8 - - + +
72S HIS* 1.3 70.5 + - - +
73S ARG* 3.4 29.8 + - + -
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Residues in contact with HIS 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P SER* 5.2 5.2 - - - -
3004P CDL 3.6 32.8 + - - -
3007P PEE 4.8 10.5 + - - -
231Q LYS* 3.5 19.5 + - - -
3003Q CDL 3.5 41.3 + - - +
29S TYR* 5.9 1.6 - - - -
68S LEU 3.0 3.4 + - - -
69S SER* 3.8 15.7 + - - +
70S LEU 3.3 3.8 + - - -
71S LYS* 1.3 78.8 - - - +
73S ARG* 1.3 69.0 + - - +
39T ARG* 3.9 16.7 + - - -
40T ARG* 3.0 41.1 + - - +
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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) + - + + + + + -
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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