Contacts of the helix formed by residues 28 - 50 (chain A) in PDB entry 2YGE
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 GLU 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 3.1 19.5 + - - +
27A LYS* 1.3 76.6 - - - +
29A ILE* 1.3 63.7 + - - +
30A PHE* 3.1 4.8 + - - -
31A LEU* 3.2 12.1 + - - +
32A ARG 4.1 0.5 + - - -
184A TYR* 3.3 25.2 + - + +
189A ARG* 2.6 30.4 + - - +
193A VAL* 3.6 28.1 - - + +
196A ARG* 2.8 30.6 + - - -
197A HIS* 3.0 32.1 + - + +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.7 3.4 - - + -
26A ASN* 3.3 41.3 - - - +
27A LYS 3.0 2.6 + - - +
28A GLU* 1.3 75.2 - - - +
30A PHE* 1.3 69.9 + - - +
31A LEU 3.1 0.2 - - - -
32A ARG* 3.1 30.9 + - - +
33A GLU* 3.1 18.5 + - + +
114A VAL* 4.5 7.6 - - + +
115A SER* 4.0 34.1 - - - -
117A ILE* 4.5 0.9 - - + -
126A SER* 4.1 13.9 - - - +
129A LEU* 3.9 19.1 - - + -
197A HIS* 4.6 18.2 - - + +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS 3.1 23.6 + - - +
28A GLU 3.1 4.1 - - - -
29A ILE* 1.3 80.6 - - - +
31A LEU* 1.3 84.7 + - + +
33A GLU* 3.2 3.8 + - - +
34A LEU* 3.0 46.4 + - + +
75A LEU* 4.0 23.3 - - + -
77A ILE* 4.8 0.4 - - + -
126A SER* 3.4 39.4 + - - +
127A LEU* 4.2 2.9 - - - -
129A LEU* 4.8 0.7 - - + -
130A VAL* 3.7 33.0 - - + -
175A LEU* 3.7 21.1 - - + -
184A TYR* 4.0 30.3 - + + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 3.2 10.6 + - - +
29A ILE 3.1 0.8 - - - -
30A PHE* 1.3 101.5 - - + +
32A ARG* 1.3 64.6 + - - +
34A LEU* 3.4 2.0 + - + +
35A ILE* 3.0 46.2 + - + +
66A ILE* 4.3 7.6 - - + -
75A LEU* 4.9 6.1 - - + -
77A ILE* 4.1 26.9 - - + -
184A TYR* 5.9 2.5 - - + -
190A ILE* 4.4 18.2 - - + +
193A VAL* 3.7 27.1 - - + -
194A ILE* 4.0 21.1 - - + -
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 4.1 1.4 + - - -
29A ILE* 3.1 20.0 + - - +
31A LEU* 1.3 77.6 - - - +
33A GLU* 1.3 84.6 + - - +
35A ILE* 3.8 1.6 - - - +
36A SER* 2.9 33.0 + - - -
115A SER* 2.7 40.2 + - - +
118A GLY* 5.1 0.6 - - - +
193A VAL* 5.2 1.6 - - - +
197A HIS* 3.6 50.6 + - + +
198A SER* 4.0 13.8 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.1 12.6 + - + +
30A PHE 3.5 6.5 - - - +
31A LEU 3.2 0.2 - - - -
32A ARG* 1.3 115.0 + - - +
34A LEU* 1.3 59.7 + - + +
36A SER* 3.3 7.3 + - - -
37A ASN* 2.9 36.8 + - - +
117A ILE* 4.0 11.2 - - + +
118A GLY* 3.2 31.1 + - - -
123A GLY* 3.6 18.6 - - - +
126A SER* 3.5 21.8 - - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.0 35.9 + - + +
31A LEU* 3.4 4.0 + - + +
33A GLU* 1.3 77.3 - - - +
35A ILE* 1.3 57.3 + - - +
37A ASN* 3.3 17.1 + - + +
38A ALA* 2.9 29.1 + - - +
77A ILE* 4.0 36.8 - - + +
123A GLY 4.6 2.7 - - - +
124A PHE* 4.3 20.0 - - - +
126A SER* 4.9 0.7 - - - +
127A LEU* 4.3 7.4 - - + -
173A LEU* 3.6 33.2 - - + -
175A LEU* 4.0 10.1 - - + -
1215A GDM 5.1 0.9 + - - -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.0 36.8 + - + +
32A ARG 3.9 2.9 - - - +
34A LEU* 1.3 76.7 - - - +
36A SER* 1.3 58.1 + - - +
38A ALA* 3.2 7.5 + - - +
39A SER* 2.8 28.4 + - - -
64A ILE* 3.9 15.6 - - + +
66A ILE* 4.2 12.3 - - + -
77A ILE* 5.0 2.9 - - + -
194A ILE* 3.8 27.4 - - + -
198A SER* 3.8 21.1 - - - +
201A VAL* 4.0 23.6 - - + -
205A ILE* 4.0 17.7 - - + -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 2.9 21.2 + - - -
33A GLU* 3.7 11.1 + - - -
34A LEU 3.3 0.2 - - - -
35A ILE* 1.3 77.6 - - - +
37A ASN* 1.3 60.2 + - - +
39A SER* 3.3 7.4 + - - -
40A ASP* 2.9 29.7 + - - +
201A VAL* 6.2 1.1 - - - -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.9 24.2 + - - +
34A LEU* 3.5 15.5 - - - +
36A SER* 1.3 78.3 + - - +
38A ALA* 1.3 59.5 + - - +
40A ASP* 3.2 5.8 + - - +
41A ALA* 2.9 29.3 + - - +
123A GLY* 5.4 0.7 - - - -
124A PHE* 3.9 34.0 + - - +
173A LEU* 5.7 0.4 - - + +
1215A GDM 3.3 62.2 + - + +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 2.9 17.2 + - - +
35A ILE* 3.4 6.3 - - - +
37A ASN* 1.3 75.8 - - - +
39A SER* 1.3 58.8 + - - +
41A ALA* 3.1 3.8 + - - +
42A LEU* 2.9 33.5 + - - +
64A ILE* 3.9 21.5 - - + -
77A ILE* 5.0 6.1 - - + -
79A ASP* 3.7 23.2 - - + +
1215A GDM 3.6 12.3 + - - +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE 2.8 19.1 + - - -
36A SER* 3.6 8.7 - - - -
37A ASN 3.2 0.2 - - - -
38A ALA* 1.3 74.2 - - - +
40A ASP* 1.3 55.3 + - - +
42A LEU* 3.3 7.7 + - - +
43A ASP* 2.8 35.4 + - - +
64A ILE* 4.0 13.6 - - - +
201A VAL* 4.3 14.3 - - - +
202A ALA* 4.8 2.6 + - - +
203A TYR* 3.5 16.8 - - - -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER 2.9 17.6 + - - +
37A ASN 3.5 4.9 - - - +
39A SER* 1.3 74.1 - - - +
41A ALA* 1.3 59.1 + - - +
43A ASP* 3.1 11.0 + - - +
44A ARG* 2.7 68.4 + - - +
1215A GDM 3.0 51.6 - - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN 2.9 10.6 + - - +
38A ALA 3.1 8.7 + - - +
40A ASP* 1.3 76.3 + - - +
42A LEU* 1.3 61.4 + - - +
44A ARG* 3.5 2.1 + - - +
45A ILE 3.3 11.6 + - - -
79A ASP* 3.8 14.6 - - - +
81A GLY* 3.3 6.2 - - - -
82A ILE* 3.0 23.2 + - + +
83A GLY 5.0 0.4 - - - +
1215A GDM 3.5 44.4 - - + +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 18.1 + - - +
39A SER 3.6 5.8 - - - +
41A ALA* 1.3 74.5 - - - +
43A ASP* 1.3 64.6 + - - +
45A ILE* 3.3 4.4 - - - +
46A ARG* 3.1 24.6 + - - +
62A LEU* 3.9 16.6 - - + +
63A PHE 3.6 27.1 - - - +
64A ILE* 3.4 33.2 - - + -
79A ASP* 4.1 2.7 - - + -
80A SER* 3.5 30.1 - - - +
81A GLY* 3.8 7.2 - - - +
203A TYR* 3.5 30.6 - - + -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 2.8 24.0 + - - +
40A ASP* 3.1 13.3 + - - +
42A LEU* 1.3 72.5 - - - +
44A ARG* 1.3 71.0 + - - +
46A ARG* 3.6 14.9 + - - +
47A TYR* 2.8 33.3 + - - +
202A ALA* 5.5 1.0 - - - +
203A TYR* 2.5 35.2 + - - -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 2.7 54.2 + - - +
41A ALA 3.6 7.0 - - - +
42A LEU 3.2 0.2 - - - -
43A ASP* 1.3 91.2 + - - +
45A ILE* 1.3 58.4 + - - +
47A TYR* 3.3 5.4 + - - +
48A LYS* 2.9 30.8 + - - +
82A ILE* 3.9 21.2 - - + +
1215A GDM 3.5 44.2 + - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.3 7.9 + - - +
42A LEU* 3.3 12.8 - - - +
44A ARG* 1.3 78.9 - - - +
46A ARG* 1.3 59.9 + - - +
48A LYS* 4.1 15.7 - - + -
49A SER* 2.8 28.1 + - - -
55A GLN* 3.9 27.4 - - + +
56A LEU* 4.1 9.0 - - + -
62A LEU* 4.2 14.4 - - + -
80A SER 4.0 6.3 - - - +
81A GLY* 3.9 13.7 - - - -
82A ILE* 3.8 23.0 - - + +
141A ASN* 4.5 0.9 - - - +
169A ARG* 3.7 33.0 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 3.1 15.5 + - - +
43A ASP* 3.6 15.4 + - - +
45A ILE* 1.3 76.8 - - - +
47A TYR* 1.3 64.4 + - - +
49A SER* 2.6 26.6 + - - +
50A LEU* 3.4 13.2 + - + +
56A LEU* 5.0 4.3 - - + -
62A LEU* 4.1 25.1 - - + -
202A ALA* 5.3 6.6 - - - +
203A TYR* 3.1 29.5 + - - -
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Residues in contact with TYR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP 2.8 17.1 + - - +
44A ARG* 3.8 5.8 - - - +
46A ARG* 1.3 73.4 - - - +
48A LYS* 1.3 71.7 + - - +
50A LEU* 3.0 45.9 + - + +
51A SER* 5.8 0.2 - - - -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG 2.9 17.9 + - - +
45A ILE* 3.6 15.7 - - + +
47A TYR* 1.3 82.8 - - - +
49A SER* 1.3 61.6 + - - +
50A LEU 3.0 1.7 + - - -
51A SER* 3.2 12.3 + - - -
52A ASP* 3.3 14.7 + - + +
55A GLN* 3.8 37.9 - - + +
82A ILE* 3.7 24.0 - - + +
142A ASP* 5.2 9.4 - - - -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE 2.8 15.2 + - - -
46A ARG* 2.6 27.0 + - - +
48A LYS* 1.3 75.9 - - - +
50A LEU* 1.3 63.8 + - - +
51A SER 3.2 1.6 + - - -
52A ASP 3.4 15.0 - - - -
53A PRO* 3.3 23.6 - - - +
55A GLN* 4.9 3.4 - - - -
56A LEU* 3.7 33.2 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.7 13.5 - - + +
47A TYR* 3.0 46.6 + - + +
48A LYS 3.0 1.0 + - - -
49A SER* 1.3 80.2 + - - +
51A SER* 1.3 62.3 + - - +
53A PRO* 4.9 2.4 - - - +
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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) + - + + + + + -
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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