Contacts of the helix formed by residues 17 - 37 (chain A) in PDB entry 2CH0
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLU* 3.7 14.1 - - + +
14A THR* 3.0 43.7 + - + +
16A GLN* 1.4 80.7 - - + +
18A TYR* 1.4 54.6 + - - +
19A ASP* 3.2 11.2 + - - +
20A MET 4.8 1.0 + - - -
21A VAL* 4.3 0.2 - - - +
69A ARG* 5.4 3.6 - - - -
72A ASP* 4.8 8.5 - - - +
73A PHE* 3.2 74.3 - - + +
76A ALA* 5.8 0.7 - - + -
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 4.1 12.1 + - - +
14A THR* 2.8 34.5 + - + -
15A ARG* 4.1 23.8 - - + -
16A GLN 3.5 3.8 - - - +
17A MET* 1.4 71.8 - - - +
19A ASP* 1.4 55.7 + - - +
20A MET 3.8 0.9 - - - -
21A VAL* 3.2 20.3 + - + -
22A VAL* 2.8 44.2 + - + +
25A ILE* 4.5 15.7 - - + -
73A PHE* 4.8 4.3 - - + -
77A ASN* 2.5 37.1 + - - +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN 4.5 8.0 + - - +
17A MET 3.2 8.1 + - - +
18A TYR* 1.4 72.6 - - - +
20A MET* 1.4 59.6 + - - +
22A VAL* 3.4 9.6 - - - +
23A LYS* 3.3 17.0 - - - -
73A PHE* 6.4 0.2 - - + -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET 4.8 1.4 + - - -
18A TYR 3.8 0.2 - - - -
19A ASP* 1.4 78.9 - - - +
21A VAL* 1.4 63.2 + - - +
22A VAL 3.5 0.4 - - - -
23A LYS* 3.3 25.2 + - - +
24A ILE* 4.3 3.5 + - + -
54A LEU* 3.5 35.0 - - + -
63A MET* 3.6 37.2 - - + +
66A VAL* 3.6 30.3 - - + -
67A TRP* 3.9 16.6 - - + -
70A ALA* 3.6 24.9 - - + -
73A PHE* 5.6 5.3 - - + -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.2 31.3 + - + +
20A MET* 1.4 75.2 - - - +
22A VAL* 1.4 53.5 + - - +
23A LYS 3.3 0.7 - - - -
24A ILE* 2.9 6.4 + - + +
25A ILE* 2.8 38.1 + - + +
67A TRP* 3.6 21.1 - - + -
70A ALA* 3.9 19.7 - - + +
73A PHE* 3.8 28.9 - - + -
74A LEU* 3.5 35.0 - - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 2.8 24.2 + - + +
19A ASP* 3.4 19.5 - - - +
21A VAL* 1.4 70.0 - - - +
23A LYS* 1.4 65.4 + - + +
25A ILE* 3.6 18.8 - - + +
26A ASP* 3.1 28.6 + - - +
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Residues in contact with LYS 23 (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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19A ASP 3.3 24.9 - - - -
20A MET* 3.3 23.0 + - - +
21A VAL 3.3 0.6 - - - -
22A VAL* 1.4 82.7 - - + +
24A ILE* 1.4 57.1 + - + +
26A ASP* 3.5 7.3 - - - +
27A VAL* 3.0 31.4 + - + +
53A SER 5.2 2.9 - - - +
54A LEU* 4.7 22.3 + - - +
63A MET* 3.7 27.1 - - - +
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Residues in contact with ILE 24 (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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20A MET* 4.3 2.9 + - + +
21A VAL* 2.9 9.3 + - - +
23A LYS* 1.4 69.4 - - + +
25A ILE* 1.4 59.4 + - - +
26A ASP 3.3 0.9 - - - -
27A VAL* 3.4 3.7 - - + +
28A LEU* 3.0 52.7 + - + +
50A VAL* 3.2 36.8 - - + +
53A SER* 4.6 7.2 - - - -
54A LEU* 3.8 26.5 - - + +
67A TRP* 3.3 57.0 - - + -
74A LEU* 4.2 7.0 - - + -
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Residues in contact with ILE 25 (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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18A TYR* 4.5 26.9 - - + -
21A VAL* 2.8 25.5 + - + +
22A VAL* 3.6 28.7 - - + +
24A ILE* 1.4 70.0 - - - +
26A ASP* 1.4 58.0 + - - +
29A ARG* 3.0 38.1 + - - +
74A LEU* 3.4 28.9 - - + -
77A ASN* 5.1 5.6 - - - +
78A GLU* 3.4 32.7 - - + +
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Residues in contact with ASP 26 (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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22A VAL 3.1 21.7 + - - +
23A LYS* 3.5 8.4 - - - +
24A ILE 3.3 0.2 - - - -
25A ILE* 1.4 73.2 - - - +
27A VAL* 1.4 52.9 + - - +
29A ARG* 4.9 2.0 - - - -
30A SER* 2.6 54.8 + - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS 3.0 22.8 + - - +
24A ILE* 3.4 11.9 - - + +
26A ASP* 1.4 68.1 + - - +
28A LEU* 1.4 78.9 + - + +
30A SER* 4.1 1.3 - - - -
31A HIS* 2.9 52.7 + - + +
49A HIS* 4.2 11.0 - - + +
50A VAL* 4.8 4.7 - - + -
53A SER* 3.8 40.6 - - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.0 47.6 + - + +
25A ILE* 5.2 0.7 - - - -
27A VAL* 1.4 85.5 - - + +
29A ARG* 1.4 58.4 + - - +
32A ASN* 2.7 35.0 + - - -
45A MET* 4.5 5.2 - - + -
50A VAL* 4.2 11.0 - - + -
74A LEU* 5.5 6.5 - - + -
78A GLU* 3.9 12.8 - - - +
80A ARG* 4.0 17.9 - - + +
81A VAL* 3.4 28.0 - - + +
96A TRP* 6.4 1.1 - - + -
98A TRP* 3.3 27.2 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.0 25.2 + - - +
26A ASP* 4.4 2.2 - - - +
28A LEU* 1.4 72.2 - - - +
30A SER* 1.4 57.1 + - - +
32A ASN* 3.6 16.8 - - - +
33A GLU* 3.9 10.0 + - - +
78A GLU* 3.2 29.0 + - - +
80A ARG* 3.4 31.4 - - + +
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Residues in contact with SER 30 (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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26A ASP* 2.6 43.3 + - - -
27A VAL* 4.1 3.4 - - - -
29A ARG* 1.4 73.3 - - - +
31A HIS* 1.4 65.7 + - - +
32A ASN 3.2 0.9 - - - -
33A GLU* 3.4 26.3 - - - +
34A ALA* 4.2 3.5 + - - +
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Residues in contact with HIS 31 (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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27A VAL* 2.9 33.1 + - - +
30A SER* 1.4 78.2 - - - +
32A ASN* 1.4 54.2 + - - +
33A GLU 3.6 0.3 + - - -
34A ALA* 3.6 3.9 + - - +
35A CYS* 3.1 28.9 + - - +
41A LEU* 3.4 28.4 - - + +
42A GLN* 4.7 4.8 - - + +
49A HIS* 3.3 39.4 + + - -
53A SER* 5.5 0.2 + - - -
98A TRP* 3.1 34.4 - + + -
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Residues in contact with ASN 32 (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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28A LEU 2.7 29.4 + - - +
29A ARG* 3.6 11.7 - - - +
31A HIS* 1.4 75.4 - - - +
33A GLU* 1.4 56.7 + - - +
35A CYS* 3.1 14.2 + - - +
36A GLN* 3.1 18.9 + - - +
80A ARG* 2.8 36.7 + - + +
98A TRP* 2.9 20.4 - - - +
99A ILE 3.3 6.9 - - - +
100A GLN* 3.5 3.7 - - - +
101A PRO* 3.1 31.8 - - + +
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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
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29A ARG 3.9 7.7 + - - +
30A SER* 3.4 18.7 + - - +
32A ASN* 1.4 75.3 - - - +
34A ALA* 1.4 76.8 + - - +
36A GLN* 3.3 30.7 + - - +
37A GLU* 4.2 2.3 - - - +
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Residues in contact with ALA 34 (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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30A SER 4.7 2.7 - - - +
31A HIS* 3.6 6.2 + - - +
33A GLU* 1.4 89.6 + - - +
35A CYS* 1.4 54.9 - - - +
36A GLN 3.7 0.4 - - - -
37A GLU* 3.3 11.7 - - - +
38A ASN* 2.7 33.2 + - - +
41A LEU* 3.4 18.5 - - + +
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Residues in contact with CYS 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 HIS 3.1 18.1 + - - +
32A ASN* 3.1 7.5 + - - +
34A ALA* 1.4 74.0 - - - +
36A GLN* 1.4 50.1 - - - +
37A GLU 3.2 4.9 - - - -
38A ASN* 2.7 31.3 - - - +
39A LYS 3.7 0.3 - - - +
40A ASP* 3.4 11.9 - - - -
41A LEU* 3.1 36.1 - - + +
98A TRP* 3.1 38.1 - - + +
100A GLN* 3.4 14.6 - - + +
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Residues in contact with GLN 36 (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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32A ASN 3.1 11.7 + - - +
33A GLU* 3.3 26.4 + - - +
35A CYS* 1.4 70.7 - - - +
37A GLU* 1.3 78.9 + - - +
38A ASN 3.5 2.8 - - - +
100A GLN* 3.4 20.4 - - + +
101A PRO 3.7 15.0 - - - +
102A SER* 3.6 25.3 + - - +
103A ALA* 3.0 35.3 - - - +
104A SER* 3.4 14.4 + - - -
130A PRO* 4.2 5.4 - - - +
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Residues in contact with GLU 37 (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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33A GLU 4.2 2.5 - - - +
34A ALA* 3.3 16.8 - - - +
36A GLN* 1.3 90.1 + - - +
38A ASN* 1.3 78.0 + - - +
130A PRO* 3.4 19.6 - - - +
131A HIS 4.0 9.7 + - - +
133A ASP* 3.5 37.7 + - - +
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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
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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