Contacts of the helix formed by residues 17 - 35 (chain A) in PDB entry 2CHT
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 1.3 72.3 + - - +
18A GLU* 1.3 66.9 + - - +
19A GLU 3.0 0.7 + - - -
20A ILE* 3.0 2.1 + - - -
21A LEU* 2.9 37.4 + - + +
55A ALA* 3.5 9.4 - - + +
56A VAL* 3.4 40.0 - - + +
60A LYS* 3.3 29.0 + - - +
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Residues in contact with GLU 18 (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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16A THR* 3.6 4.8 + - + +
17A GLU* 1.3 79.2 - - - +
19A GLU* 1.3 56.5 + - - +
21A LEU* 4.4 4.2 - - - +
22A GLN* 3.0 35.2 + - + +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.7 6.1 - - + -
13A GLU* 2.9 27.7 + - - +
14A ARG* 3.1 47.2 + - - +
16A THR* 3.4 25.0 + - + +
17A GLU 3.1 0.6 - - - -
18A GLU* 1.3 75.6 - - - +
20A ILE* 1.3 65.6 + - - +
22A GLN* 3.2 6.6 + - - +
23A LYS* 3.0 51.2 + - - +
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Residues in contact with ILE 20 (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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12A VAL* 3.5 26.7 - - + -
15A ASP* 3.6 23.8 - - - +
16A THR 3.0 21.5 + - - +
17A GLU 3.7 2.7 - - - +
19A GLU* 1.3 75.0 - - - +
21A LEU* 1.3 59.1 + - - +
23A LYS* 3.8 0.9 - - - +
24A THR* 2.8 34.1 + - - -
53A LEU* 3.9 22.9 - - + -
55A ALA* 4.3 11.2 - - + +
56A VAL* 3.5 29.6 - - + +
58A PRO* 4.3 13.7 - - + -
89A ILE* 3.8 16.0 - - + +
79B MET* 6.0 0.4 - - + -
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Residues in contact with LEU 21 (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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17A GLU* 2.9 44.9 + - + +
18A GLU* 4.4 3.8 - - - +
20A ILE* 1.3 72.5 - - - +
22A GLN* 1.3 57.0 + - - +
24A THR* 4.4 0.4 - - - -
25A LYS* 2.8 33.7 + - - +
56A VAL* 3.6 19.7 - - + -
57A PHE 3.7 13.7 - - - +
58A PRO* 3.9 5.6 - - + +
60A LYS* 3.9 20.9 - - + +
61A ALA* 3.6 31.2 - - + +
64A GLU* 4.5 15.3 - - - +
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Residues in contact with GLN 22 (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 GLU* 3.0 25.6 + - + +
19A GLU* 3.7 6.2 + - - +
21A LEU* 1.3 74.1 - - - +
23A LYS* 1.3 74.0 + - - +
25A LYS* 3.4 16.4 + - - +
26A GLN* 2.9 58.8 + - - +
64A GLU* 5.7 0.9 - - - -
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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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10A THR* 3.7 19.4 + - + +
11A THR 3.5 6.7 + - - +
12A VAL* 4.0 20.2 - - + -
13A GLU* 3.3 37.0 + - - -
19A GLU* 3.0 35.9 + - - +
22A GLN* 1.3 90.3 - - - +
24A THR* 1.3 63.4 + - - +
26A GLN* 3.9 12.0 - - - +
27A LEU* 3.1 22.2 + - - +
109A LEU* 5.6 0.2 - - - +
110A GLU* 3.5 32.3 - - + +
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Residues in contact with THR 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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10A THR* 4.7 2.9 - - - -
20A ILE 2.8 22.8 + - - -
21A LEU 3.9 2.9 - - - -
23A LYS* 1.3 71.8 - - - +
25A LYS* 1.3 61.6 + - - +
27A LEU* 2.9 18.1 + - - +
28A LEU* 3.0 21.5 + - + +
47A LEU* 4.0 24.0 - - + -
58A PRO* 3.5 25.8 - - + +
61A ALA* 3.8 9.0 - - + -
89A ILE* 3.5 27.4 - - + +
91A VAL* 5.7 1.8 - - + -
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Residues in contact with LYS 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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21A LEU 2.8 19.6 + - - +
22A GLN* 3.4 28.5 + - - +
24A THR* 1.3 71.3 - - - +
26A GLN* 1.3 69.7 + - - +
28A LEU* 3.2 8.4 + - - +
29A GLU* 2.9 53.4 + - - +
61A ALA* 3.8 19.4 - - + +
64A GLU* 3.9 34.1 + - + +
65A LEU* 4.1 15.0 - - + -
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Residues in contact with GLN 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 GLN* 2.9 53.5 + - - +
23A LYS* 3.9 16.1 - - - +
24A THR 3.3 0.2 - - - -
25A LYS* 1.3 83.2 - - - +
27A LEU* 1.3 63.4 + - - +
29A GLU* 4.0 14.8 - - - +
30A LYS* 3.3 19.8 + - - +
109A LEU* 4.1 10.4 - - + +
110A GLU* 4.6 6.1 - - - +
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Residues in contact with LEU 27 (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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9A ALA* 3.9 20.0 - - - +
10A THR* 3.9 25.8 - - + +
23A LYS 3.1 13.0 + - - +
24A THR* 2.9 12.3 + - - +
26A GLN* 1.3 73.8 - - - +
28A LEU* 1.3 64.7 + - - +
30A LYS* 3.1 7.6 + - - +
31A ILE* 2.9 35.3 + - + +
89A ILE* 4.3 4.3 - - + +
91A VAL* 3.5 26.5 - - + -
107A VAL* 3.5 41.1 - - + +
109A LEU* 3.9 12.5 - - + +
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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 THR* 3.0 28.9 + - + +
25A LYS* 3.6 8.3 - - - +
27A LEU* 1.3 75.0 - - - +
29A GLU* 1.3 57.1 + - - +
31A ILE* 2.8 39.0 + - + +
32A ILE* 2.9 21.9 + - + +
45A MET* 3.8 24.0 - - + -
47A LEU* 4.7 2.0 - - + -
62A VAL* 3.7 33.2 - - + +
65A LEU* 3.9 20.9 - - + -
68A TRP* 6.0 1.1 - - + -
91A VAL* 4.4 12.1 - - + -
93A MET* 5.1 7.4 - - - -
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Residues in contact with GLU 29 (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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25A LYS* 2.9 50.1 + - - +
26A GLN* 4.0 13.4 - - - +
28A LEU* 1.3 69.5 - - - +
30A LYS* 1.3 57.1 + - - +
32A ILE* 3.7 10.7 - - - +
33A GLU* 2.9 30.5 + - - +
65A LEU* 3.8 16.4 - - + +
22F GLN* 5.5 2.8 - - - +
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Residues in contact with LYS 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 GLN 3.3 10.5 + - - +
27A LEU 3.1 11.0 + - - +
29A GLU* 1.3 76.1 - - - +
31A ILE* 1.3 61.3 + - - +
33A GLU* 3.5 30.3 - - - +
34A GLU* 2.8 50.6 + - + +
107A VAL* 3.9 22.1 - - + +
109A LEU* 4.2 22.6 - - + +
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Residues in contact with ILE 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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6A ILE* 3.6 31.0 - - + +
7A ARG 4.8 0.4 - - - +
8A GLY* 4.3 8.7 - - - +
27A LEU* 2.9 27.0 + - + +
28A LEU* 2.8 25.3 + - + +
30A LYS* 1.3 68.9 - - - +
32A ILE* 1.3 67.1 + - + +
35A ASN* 2.9 36.5 + - - +
37A THR* 3.9 0.4 + - - -
91A VAL* 3.7 29.8 - - + -
93A MET* 3.7 21.5 - - + -
107A VAL* 4.0 22.0 - - + +
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Residues in contact with ILE 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* 3.1 25.8 - - + +
29A GLU* 3.7 8.5 - - - +
31A ILE* 1.3 77.9 - - + +
33A GLU* 1.3 51.7 + - - +
36A HIS* 2.7 31.9 + - - -
37A THR* 3.1 38.4 + - - +
65A LEU* 4.0 21.1 - - + -
68A TRP* 3.6 40.8 - - + +
93A MET* 5.3 3.4 - - - -
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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 GLU 2.9 21.4 + - - +
30A LYS* 3.5 26.5 - - - +
31A ILE 3.2 0.2 - - - -
32A ILE* 1.3 77.2 - - - +
34A GLU* 1.3 84.3 + - - +
35A ASN 3.1 1.6 + - - -
36A HIS* 3.2 21.4 + - - +
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Residues in contact with GLU 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 LYS* 2.8 38.7 + - + +
33A GLU* 1.3 94.6 - - - +
35A ASN* 1.3 70.7 + - - +
36A HIS* 3.8 14.4 + - - -
105A ARG* 3.9 46.3 + - + +
107A VAL* 3.9 17.2 - - + +
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Residues in contact with ASN 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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6A ILE* 3.7 25.0 - - + +
31A ILE* 2.9 23.8 + - - +
34A GLU* 1.3 80.1 - - - +
36A HIS* 1.3 80.3 + - - +
37A THR* 3.2 16.4 + - - +
103A GLN 5.0 0.2 - - - +
104A ILE* 3.9 7.8 - - - +
105A ARG* 2.8 50.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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