Contacts of the helix formed by residues 17 - 35 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F THR* 1.3 77.1 + - - +
18F GLU* 1.3 64.9 + - + +
20F ILE* 3.9 0.3 - - - -
21F LEU* 3.0 46.9 + - + +
55F ALA* 3.9 9.3 - - + +
56F VAL* 3.8 29.6 - - + +
60F LYS* 3.0 29.7 + - - -
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F THR* 3.2 11.9 + - + +
17F GLU* 1.3 80.2 - - + +
19F GLU* 1.3 62.5 + - - +
21F LEU* 3.9 4.1 - - - +
22F GLN* 3.0 25.7 + - - +
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 3.6 11.8 - - + -
13F GLU* 2.9 32.6 + - - +
14F ARG* 3.4 35.6 + - - +
16F THR* 3.3 22.9 - - + +
17F GLU 3.3 0.2 - - - -
18F GLU* 1.3 76.8 - - - +
20F ILE* 1.3 60.0 + - - +
22F GLN* 3.2 5.7 + - - +
23F LYS* 2.9 66.0 + - - +
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Residues in contact with ILE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.0 24.5 - - + -
14F ARG 4.4 3.1 - - - +
15F ASP* 3.4 25.8 - - - +
16F THR 3.1 20.5 + - - +
19F GLU* 1.3 73.4 - - - +
21F LEU* 1.3 62.2 + - - +
23F LYS* 4.0 0.3 - - - +
24F THR* 2.7 33.5 + - - +
53F LEU* 4.3 15.3 - - + -
55F ALA* 4.1 7.6 - - + +
56F VAL* 3.8 29.4 - - + +
58F PRO* 4.3 19.3 - - + -
89F ILE* 3.8 17.4 - - + +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 3.0 45.0 + - + +
18F GLU* 4.1 3.8 - - - +
20F ILE* 1.3 76.5 - - + +
22F GLN* 1.3 56.6 + - - +
24F THR* 4.5 0.2 - - - -
25F LYS* 2.9 30.5 + - - +
56F VAL* 4.0 12.6 - - + -
57F PHE 4.2 2.9 - - - +
58F PRO 4.6 2.2 - - - +
60F LYS* 3.6 39.5 - - + -
61F ALA* 3.6 17.1 - - + +
64F GLU* 3.3 31.5 - - - +
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Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 5.7 0.9 + - - +
18F GLU 3.0 19.4 + - - +
19F GLU* 3.7 4.3 - - - +
21F LEU* 1.3 73.3 - - - +
23F LYS* 1.3 89.4 + - - +
25F LYS* 3.1 16.3 + - - +
26F GLN* 3.0 47.8 + - - +
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR* 3.9 19.8 + - + +
11F THR 3.5 19.2 + - - +
12F VAL* 3.6 17.7 - - + +
13F GLU* 4.9 6.5 - - - +
19F GLU* 2.9 50.6 + - - +
20F ILE 4.2 0.4 - - - +
22F GLN* 1.3 98.7 - - - +
24F THR* 1.3 64.2 + - - +
26F GLN* 3.4 10.5 + - - +
27F LEU* 3.1 22.5 + - - +
109F LEU* 5.2 0.7 - - - +
110F GLU* 3.7 32.3 + - + +
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Residues in contact with THR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR* 4.5 3.3 - - - +
20F ILE* 2.7 27.4 + - - +
23F LYS* 1.3 76.4 - - - +
25F LYS* 1.3 61.7 + - - +
27F LEU* 3.1 10.6 + - + +
28F LEU* 2.9 32.8 + - + +
47F LEU* 3.9 25.6 - - + -
58F PRO* 3.7 24.1 + - + +
61F ALA* 3.8 13.7 - - + -
89F ILE* 3.7 18.7 - - + +
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU 2.9 20.0 + - - +
22F GLN* 3.6 20.5 + - - +
24F THR* 1.3 74.6 - - - +
26F GLN* 1.3 62.5 + - - +
28F LEU* 3.4 8.1 + - - +
29F GLU* 2.9 55.2 + - - +
61F ALA* 3.9 16.7 - - + +
64F GLU* 4.5 26.2 - - + +
65F LEU* 4.2 17.3 - - + -
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Residues in contact with GLN 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 3.0 49.9 + - - +
23F LYS* 3.7 20.0 - - - +
25F LYS* 1.3 79.0 + - - +
27F LEU* 1.3 67.5 + - - +
29F GLU* 3.1 16.5 + - - +
30F LYS* 2.9 25.5 + - - +
109F LEU* 4.4 10.8 - - + +
110F GLU* 4.4 7.5 + - - -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLY* 4.1 5.2 - - - -
9F ALA* 3.5 34.8 - - - +
10F THR* 3.8 22.7 - - + -
23F LYS 3.1 10.3 + - - +
24F THR* 3.1 14.5 + - + +
26F GLN* 1.3 78.8 - - - +
28F LEU* 1.3 66.6 + - + +
30F LYS* 3.3 2.6 + - - +
31F ILE* 3.1 36.3 + - + +
47F LEU* 5.6 0.4 - - + -
89F ILE* 4.3 9.9 - - + +
91F VAL* 3.7 23.6 - - + +
107F VAL* 3.8 20.4 - - + +
109F LEU* 3.9 14.3 - - + +
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Residues in contact with LEU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 2.9 27.2 + - + +
25F LYS* 3.6 9.0 - - - +
27F LEU* 1.3 79.5 - - + +
29F GLU* 1.3 61.1 + - - +
31F ILE* 3.5 8.1 + - + +
32F ILE* 3.1 30.7 + - + +
45F MET* 3.7 13.5 - - + -
47F LEU* 5.4 1.1 - - + -
61F ALA 4.7 2.5 - - - +
62F VAL* 3.7 36.1 - - + +
65F LEU* 4.0 25.1 - - + -
68F TRP* 5.8 0.9 - - + -
91F VAL* 4.4 14.6 - - + -
93F MET* 3.7 28.3 - - + -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LYS* 2.9 47.4 + - - +
26F GLN* 3.1 16.7 + - - +
28F LEU* 1.3 71.7 - - - +
30F LYS* 1.3 56.8 + - - +
32F ILE* 3.2 9.7 + - + +
33F GLU* 2.9 36.7 + - - +
65F LEU* 4.1 20.0 - - + +
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F GLN 2.9 16.1 + - - +
27F LEU* 3.6 5.6 - - - +
29F GLU* 1.3 77.0 - - - +
31F ILE* 1.3 62.0 + - - +
33F GLU* 3.3 24.3 + - - +
34F GLU* 2.9 59.7 + - + +
107F VAL* 3.7 23.3 - - + -
109F LEU* 4.5 14.1 - - + -
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.3 23.8 - - + +
7F ARG 4.6 4.3 - - - +
8F GLY* 4.2 7.9 - - - +
27F LEU* 3.1 28.2 + - + +
28F LEU* 3.7 10.1 - - + +
30F LYS* 1.3 74.4 - - - +
32F ILE* 1.3 56.5 + - - +
35F ASN* 3.0 37.4 + - - +
37F THR* 4.0 1.7 + - - +
91F VAL* 3.6 34.3 - - + -
93F MET* 3.9 28.9 - - + -
107F VAL* 3.8 24.9 - - + -
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Residues in contact with ILE 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F LEU* 3.1 20.0 + - + +
29F GLU* 3.2 11.4 + - + +
31F ILE* 1.3 74.6 - - + +
33F GLU* 1.3 59.9 + - - +
36F HIS* 2.8 35.0 + - - -
37F THR* 3.5 27.6 - - - +
65F LEU* 3.9 24.5 - - + -
68F TRP* 3.6 38.1 - - + +
93F MET* 5.1 1.6 - - + -
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Residues in contact with GLU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLU* 2.9 21.8 + - - +
30F LYS* 3.3 32.1 + - - +
32F ILE* 1.3 81.2 - - - +
34F GLU* 1.3 70.9 + - - +
35F ASN 3.2 0.2 + - - -
36F HIS* 3.2 19.1 + - - -
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Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS* 2.9 50.8 + - + +
33F GLU* 1.3 87.1 - - - +
35F ASN* 1.3 65.1 + - - +
36F HIS* 3.7 7.1 + - - -
105F ARG* 3.7 37.6 - - + +
107F VAL* 4.3 13.0 - - + -
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Residues in contact with ASN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.8 25.3 - - + +
31F ILE* 3.0 27.7 + - - +
34F GLU* 1.3 80.5 - - - +
36F HIS* 1.3 71.2 + - - +
37F THR* 3.2 11.9 + - - +
99F VAL* 5.9 2.3 - - - +
104F ILE* 3.8 12.5 - - - +
105F ARG* 2.9 52.1 + - - +
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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
------------------------------------------------------------
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