Contacts of the helix formed by residues 17 - 35 (chain J) in PDB entry 2CHS
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 17 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J THR* 1.3 70.0 - - - +
18J GLU* 1.3 61.3 + - - +
21J LEU* 2.9 40.7 + - + +
55J ALA* 3.7 10.6 - - + +
56J VAL* 3.4 39.3 - - + +
60J LYS* 3.2 30.8 + - - +
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Residues in contact with GLU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ARG* 5.0 8.0 + - - -
16J THR* 3.6 12.1 + - - +
17J GLU* 1.3 79.7 - - - +
19J GLU* 1.3 60.2 + - - +
21J LEU* 4.1 2.6 - - - +
22J GLN* 3.0 59.5 + - - +
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Residues in contact with GLU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL* 3.6 4.3 - - + -
13J GLU* 2.8 35.5 + - - +
14J ARG* 3.3 39.6 + - - +
16J THR* 3.0 15.6 + - - +
18J GLU* 1.3 85.7 - - - +
20J ILE* 1.3 60.8 + - - +
22J GLN* 4.2 15.5 - - - +
23J LYS* 2.9 52.7 + - + +
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Residues in contact with ILE 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.0 22.7 - - + -
15J ASP* 3.3 25.8 - - - +
16J THR 2.9 27.5 + - - +
19J GLU* 1.3 72.6 - - - +
21J LEU* 1.3 61.4 + - - +
23J LYS* 4.0 0.5 - - - +
24J THR* 2.8 31.8 + - - +
53J LEU* 4.3 21.3 - - + -
55J ALA* 4.1 9.0 - - + +
56J VAL* 3.5 33.2 - - + +
58J PRO* 4.2 25.4 - - + -
89J ILE* 4.9 4.2 - - + +
79K MET* 6.2 0.2 - - + -
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J GLU* 2.9 35.7 + - + +
18J GLU* 4.2 2.0 - - - +
20J ILE* 1.3 72.2 - - + +
22J GLN* 1.3 58.0 + - - +
24J THR* 3.3 1.0 + - - -
25J LYS* 2.8 34.3 + - - +
56J VAL* 4.0 15.3 - - + -
57J PHE 4.2 4.7 - - - +
58J PRO 4.4 2.0 - - - +
60J LYS* 3.7 37.0 - - + +
61J ALA* 3.6 29.8 - - + +
64J GLU* 3.7 25.1 - - - +
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Residues in contact with GLN 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLU* 3.0 50.2 + - - +
19J GLU* 4.0 16.7 - - - +
21J LEU* 1.3 76.3 - - - +
23J LYS* 1.3 70.4 + - + +
25J LYS* 3.4 6.0 + - - +
26J GLN* 3.0 46.8 + - - +
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Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J THR* 3.8 19.0 + - + +
11J THR 3.3 17.7 + - - +
12J VAL* 3.6 20.5 - - + +
13J GLU* 4.4 5.9 + - - +
19J GLU* 2.9 53.1 + - + +
22J GLN* 1.3 84.3 - - + +
24J THR* 1.3 62.3 + - - +
26J GLN* 3.5 17.9 + - - +
27J LEU* 3.1 22.9 + - - +
89J ILE* 5.1 0.4 - - + -
109J LEU* 5.3 0.5 - - - +
110J GLU* 3.9 31.0 + - + +
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Residues in contact with THR 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J THR* 5.0 2.5 - - - -
20J ILE* 2.8 19.8 + - - +
21J LEU 3.8 2.5 - - - -
23J LYS* 1.3 75.2 - - - +
25J LYS* 1.3 65.7 + - - +
27J LEU* 3.1 9.7 + - + +
28J LEU* 2.9 35.1 + - + +
47J LEU* 4.1 24.2 - - + -
58J PRO* 3.4 36.3 - - + +
61J ALA* 3.9 9.2 - - + -
89J ILE* 4.2 16.3 - - + +
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Residues in contact with LYS 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J LEU 2.8 21.2 + - - +
22J GLN* 3.8 5.6 - - - +
24J THR* 1.3 71.8 - - - +
26J GLN* 1.3 64.5 + - + +
28J LEU* 3.3 7.9 + - - +
29J GLU* 2.9 56.1 + - + +
61J ALA* 3.9 15.2 - - + +
64J GLU* 3.8 45.8 + - + +
65J LEU* 3.8 15.1 - - + +
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Residues in contact with GLN 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J GLN* 3.0 39.8 + - - +
23J LYS* 3.9 20.0 - - - +
25J LYS* 1.3 78.9 - - + +
27J LEU* 1.3 61.1 + - - +
29J GLU* 3.8 15.0 - - - +
30J LYS* 3.1 25.8 + - - +
109J LEU* 4.4 9.7 - - + +
110J GLU* 5.3 3.8 + - - -
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Residues in contact with LEU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J GLY* 3.9 5.4 - - - -
9J ALA* 3.5 50.0 - - - +
10J THR* 3.9 12.8 - - + +
23J LYS 3.1 13.4 + - - +
24J THR* 3.1 12.8 + - + +
26J GLN* 1.3 74.1 - - - +
28J LEU* 1.3 65.6 + - + +
30J LYS* 3.3 4.0 + - - +
31J ILE* 3.0 26.4 + - + +
47J LEU* 6.0 0.4 - - + -
89J ILE* 4.1 11.7 - - + +
91J VAL* 4.0 22.4 - - + -
107J VAL* 3.7 23.1 - - + +
109J LEU* 3.8 15.6 - - + +
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Residues in contact with LEU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J THR* 2.9 24.1 + - + +
25J LYS* 3.6 9.6 - - - +
27J LEU* 1.3 76.1 - - + +
29J GLU* 1.3 58.4 + - - +
31J ILE* 3.0 7.8 + - + +
32J ILE* 2.9 35.6 + - + +
45J MET* 3.9 24.5 - - + -
47J LEU* 4.9 6.5 - - + -
61J ALA 4.5 4.5 - - - +
62J VAL* 3.7 34.5 - - + +
65J LEU* 3.9 26.2 - - + -
91J VAL* 4.4 15.0 - - + -
93J MET* 4.1 12.6 - - + -
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Residues in contact with GLU 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J LYS* 2.9 51.5 + - + +
26J GLN* 3.8 16.8 - - - +
28J LEU* 1.3 73.5 - - - +
30J LYS* 1.3 56.5 + - - +
32J ILE* 3.5 11.0 + - - +
33J GLU* 2.9 29.4 + - - +
65J LEU* 3.8 19.5 - - + +
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Residues in contact with LYS 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J GLN 3.1 18.5 + - - +
27J LEU* 3.5 5.4 - - - +
29J GLU* 1.3 73.8 - - - +
31J ILE* 1.4 64.2 + - - +
33J GLU* 3.3 30.2 + - - +
34J GLU* 3.0 44.1 + - - +
107J VAL* 3.9 22.4 - - + +
109J LEU* 4.0 24.0 - - + +
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Residues in contact with ILE 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 4.0 15.0 - - + +
7J ARG 4.2 7.6 - - - +
8J GLY* 4.1 12.3 - - - +
27J LEU* 3.0 19.5 + - + +
28J LEU* 3.0 9.2 + - - +
30J LYS* 1.4 72.4 - - - +
32J ILE* 1.3 66.2 + - - +
34J GLU 3.8 0.2 - - - -
35J ASN* 2.9 42.8 + - + +
37J THR* 5.0 0.7 - - - +
91J VAL* 3.5 31.4 - - + -
93J MET* 3.9 33.2 - - + -
107J VAL* 3.7 26.5 - - + -
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Residues in contact with ILE 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J LEU* 2.9 24.8 + - + +
29J GLU* 3.6 9.9 - - - +
31J ILE* 1.3 74.2 - - - +
33J GLU* 1.3 52.8 + - - +
36J HIS* 2.7 32.4 + - - -
37J THR* 3.2 32.9 + - - +
65J LEU* 3.7 27.8 - - + -
68J TRP* 3.4 39.7 - - + +
93J MET* 4.7 6.5 - - + -
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Residues in contact with GLU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J GLU 2.9 16.3 + - - +
30J LYS* 3.3 33.2 + - - +
32J ILE* 1.3 77.6 - - - +
34J GLU* 1.3 81.3 + - + +
35J ASN 3.0 1.7 + - - -
36J HIS* 3.1 22.9 + - - -
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J LYS* 3.0 29.4 + - - +
31J ILE 4.1 1.8 - - - +
33J GLU* 1.3 100.4 - - + +
35J ASN* 1.3 59.6 + - - +
36J HIS* 4.2 7.6 + - - -
105J ARG* 3.1 71.9 + - + +
106J HIS 5.1 1.4 - - - +
107J VAL* 4.0 21.1 - - + +
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Residues in contact with ASN 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 3.5 30.2 - - + +
31J ILE* 2.9 25.4 + - - +
34J GLU* 1.3 80.3 - - - +
36J HIS* 1.3 74.7 + - - +
37J THR* 3.2 15.3 + - - +
103J GLN 5.0 0.5 - - - +
104J ILE* 4.1 7.8 - - - +
105J ARG* 2.8 49.8 + - - +
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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