Contacts of the helix formed by residues 17 - 35 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D THR* 1.3 73.9 + - - +
18D GLU* 1.3 58.6 + - - +
20D ILE 3.9 0.2 - - - -
21D LEU* 2.9 50.7 + - + +
55D ALA* 3.5 12.9 - - + +
56D VAL* 3.7 26.8 - - + +
60D LYS* 3.2 28.4 + - - -
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 3.4 8.6 + - + +
17D GLU* 1.3 78.8 - - - +
19D GLU* 1.3 57.9 + - - +
21D LEU* 4.0 4.3 - - - +
22D GLN* 2.9 46.8 + - + +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.5 10.0 - - + +
13D GLU* 2.9 27.8 + - - +
14D ARG* 3.2 48.9 + - - +
16D THR* 3.3 21.3 + - + +
18D GLU* 1.3 77.1 - - - +
20D ILE* 1.3 63.7 + - - +
22D GLN* 4.6 3.5 - - - +
23D LYS* 3.0 64.0 + - - +
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.9 23.1 - - + -
15D ASP* 3.4 26.0 - - - +
16D THR 3.0 22.0 + - - +
19D GLU* 1.3 75.8 - - - +
21D LEU* 1.3 62.6 + - - +
24D THR* 2.8 30.9 + - - -
53D LEU* 4.1 19.3 - - + -
54D HIS 4.7 0.2 - - - +
55D ALA* 4.2 13.0 - - + +
56D VAL* 3.9 20.9 - - + +
58D PRO* 4.1 22.7 - - + -
89D ILE* 3.6 17.7 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 2.9 47.0 + - + +
18D GLU* 4.0 4.5 - - - +
20D ILE* 1.3 75.9 - - - +
22D GLN* 1.3 57.2 + - - +
24D THR* 4.7 0.2 - - - -
25D LYS* 3.0 30.0 + - - +
56D VAL* 4.2 9.2 - - + -
57D PHE 4.0 11.0 - - - +
58D PRO* 4.6 2.9 - - + +
60D LYS* 3.7 37.5 - - + -
61D ALA* 3.7 21.1 - - + +
64D GLU* 4.4 21.7 - - - +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLU* 2.9 35.4 + - + +
19D GLU* 4.2 3.4 - - - +
21D LEU* 1.3 69.7 - - - +
23D LYS* 1.3 90.7 + - - +
24D THR 3.2 0.2 + - - -
25D LYS* 3.3 8.8 + - + +
26D GLN* 3.0 45.1 + - + +
64D GLU* 5.6 0.9 - - - -
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.7 23.8 + - + +
11D THR 3.9 7.0 - - - +
12D VAL* 3.7 21.5 - - + -
13D GLU* 5.7 3.4 - - - -
19D GLU* 3.0 51.1 + - - +
20D ILE 4.4 0.4 - - - +
22D GLN* 1.3 98.4 + - - +
24D THR* 1.3 56.3 + - - +
26D GLN* 3.4 23.6 + - - +
27D LEU 3.1 21.1 + - - -
109D LEU* 5.5 0.3 - - - +
110D GLU* 4.2 28.9 - - + +
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Residues in contact with THR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 4.8 2.0 - - - -
20D ILE 2.8 20.5 + - - -
21D LEU* 3.9 2.9 - - - -
23D LYS* 1.3 74.0 - - - +
25D LYS* 1.3 65.7 + - - +
27D LEU* 3.3 7.7 + - + +
28D LEU* 3.1 31.8 + - + +
47D LEU* 4.1 19.1 - - + -
58D PRO* 3.7 32.0 - - + +
61D ALA* 3.8 9.4 - - + -
89D ILE* 3.4 24.8 - - + +
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU 3.0 17.9 + - - +
22D GLN* 3.5 8.7 - - + +
24D THR* 1.3 74.0 - - - +
26D GLN* 1.3 60.5 + - + +
28D LEU* 3.3 6.9 + - - +
29D GLU* 2.8 67.0 + - + +
61D ALA* 3.7 10.6 - - + +
64D GLU* 3.6 45.7 + - + +
65D LEU* 4.3 8.1 - - + -
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.0 38.2 + - + +
23D LYS* 3.4 36.0 - - - +
25D LYS* 1.3 77.2 - - + +
27D LEU* 1.3 62.0 + - - +
29D GLU* 4.0 11.1 - - - +
30D LYS* 3.1 23.7 + - - +
109D LEU* 4.1 11.1 - - + +
110D GLU* 4.4 8.5 + - - +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLY* 4.0 7.2 - - - -
9D ALA* 3.5 51.1 - - - +
10D THR* 4.0 14.1 - - + +
23D LYS 3.1 11.5 + - - +
24D THR* 3.3 9.2 + - + +
26D GLN* 1.3 77.1 - - - +
28D LEU* 1.3 60.1 + - + +
30D LYS* 3.2 5.2 + - - +
31D ILE* 3.0 37.1 + - + +
47D LEU* 5.7 1.6 - - + -
89D ILE* 4.1 9.9 - - + +
90D ARG 5.3 0.2 - - - -
91D VAL* 4.1 12.6 - - + -
107D VAL* 3.6 23.8 - - + +
109D LEU* 3.9 12.5 - - + +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D THR* 3.1 30.1 + - + +
25D LYS* 3.6 4.5 - - - +
27D LEU* 1.3 77.7 - - + +
29D GLU* 1.3 65.2 + - - +
31D ILE* 3.2 6.5 + - + +
32D ILE* 3.0 32.2 + - + +
45D MET* 3.8 22.9 - - - -
47D LEU* 4.9 5.4 - - + -
61D ALA* 4.7 2.7 - - + -
62D VAL* 3.7 33.7 - - + +
65D LEU* 3.9 23.8 - - + -
91D VAL* 4.1 22.9 - - + -
93D MET* 4.3 9.6 - - + -
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 2.8 61.1 + - - +
26D GLN* 4.0 10.0 - - - +
28D LEU* 1.3 72.1 - - - +
30D LYS* 1.3 60.8 + - - +
32D ILE* 3.9 8.6 - - + +
33D GLU* 3.2 28.2 + - - +
64D GLU 5.3 0.5 - - - +
65D LEU* 3.9 17.9 - - + +
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN 3.1 14.6 + - - +
27D LEU 3.3 9.4 - - - +
29D GLU* 1.3 73.7 - - - +
31D ILE* 1.3 64.6 + - - +
32D ILE 3.3 0.2 + - - -
33D GLU* 3.3 20.7 + - - +
34D GLU* 2.9 55.7 + - - +
107D VAL* 3.5 25.1 - - + -
109D LEU* 4.3 17.0 - - + -
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.9 28.7 - - + +
7D ARG 4.6 1.3 - - - +
8D GLY* 4.0 10.5 - - - +
27D LEU* 3.0 30.1 + - + +
28D LEU* 3.2 13.2 + - + +
30D LYS* 1.3 73.6 - - - +
32D ILE* 1.3 59.5 + - - +
34D GLU 3.3 0.3 + - - -
35D ASN* 2.9 38.3 + - - +
37D THR* 5.0 0.7 - - - +
91D VAL* 3.6 31.9 - - + -
93D MET* 4.1 25.6 - - + -
107D VAL* 3.8 25.6 - - + +
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 3.0 20.5 + - + +
29D GLU* 3.9 7.6 - - - +
31D ILE* 1.3 75.6 - - - +
33D GLU* 1.3 56.0 + - - +
36D HIS* 2.6 38.0 + - - -
37D THR* 3.2 32.7 + - - +
65D LEU* 3.9 19.5 - - + -
68D TRP* 3.3 43.1 - - + +
93D MET* 4.5 5.8 - - + -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.2 17.5 + - - +
30D LYS* 3.7 25.1 + - - +
32D ILE* 1.3 81.9 - - - +
34D GLU* 1.3 64.8 + - - +
36D HIS* 3.9 13.4 + - - +
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 2.9 50.1 + - - +
31D ILE* 4.4 0.4 - - - -
33D GLU* 1.3 80.2 - - + +
35D ASN* 1.3 73.4 + - - +
36D HIS* 3.4 18.4 + - - -
105D ARG* 3.4 41.3 + - + +
106D HIS 5.1 1.4 - - - +
107D VAL* 3.9 17.8 - - + +
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.8 27.9 - - + +
31D ILE* 2.9 27.4 + - - +
34D GLU* 1.3 81.7 - - - +
36D HIS* 1.3 79.3 + - - +
37D THR* 3.2 13.1 + - - +
103D GLN 5.0 0.3 - - - +
104D ILE* 4.0 7.6 - - - +
105D ARG* 2.9 47.8 + - - +
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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