Contacts of the helix formed by residues 17 - 35 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G THR* 1.3 70.8 + - - +
18G GLU* 1.3 64.5 + - - +
20G ILE* 4.0 0.3 - - - +
21G LEU* 3.0 38.5 + - + +
55G ALA* 3.3 15.4 - - + +
56G VAL* 3.7 31.4 - - + +
60G LYS* 3.3 25.0 + - - +
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Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ARG* 3.1 28.1 + - - -
16G THR* 3.5 8.8 + - - +
17G GLU* 1.3 77.5 - - - +
19G GLU* 1.3 73.1 + - - +
21G LEU* 4.0 4.9 - - - +
22G GLN* 3.1 54.1 + - - +
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Residues in contact with GLU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G VAL* 3.7 5.5 - - + -
13G GLU* 3.0 27.7 + - - +
14G ARG* 3.2 38.5 + - - +
16G THR* 3.3 18.6 + - + +
17G GLU 3.3 0.4 - - - -
18G GLU* 1.3 90.9 + - - +
20G ILE* 1.3 64.7 + - - +
22G GLN* 4.2 11.2 - - - +
23G LYS* 3.0 52.0 + - + +
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Residues in contact with ILE 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G VAL* 4.0 21.5 - - + -
15G ASP* 3.4 25.6 - - - +
16G THR 2.8 28.2 + - - +
19G GLU* 1.3 70.2 - - - +
21G LEU* 1.3 62.8 + - - +
23G LYS* 4.0 0.5 - - - +
24G THR* 2.8 29.5 + - - -
53G LEU* 4.6 13.7 - - + -
55G ALA* 3.6 14.1 - - + +
56G VAL* 3.5 30.5 - - + +
58G PRO* 4.0 24.7 - - + -
89G ILE* 4.0 17.9 - - + +
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 3.0 33.3 + - + +
18G GLU* 4.1 4.3 - - - +
20G ILE* 1.3 77.2 - - - +
22G GLN* 1.3 61.8 + - - +
25G LYS* 3.0 27.0 + - - +
56G VAL* 3.9 16.6 - - + -
57G PHE 4.2 3.1 - - - +
58G PRO* 4.5 2.0 - - + +
60G LYS* 3.7 41.7 - - + -
61G ALA* 3.7 18.2 - - + +
64G GLU* 3.7 21.1 - - - +
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU* 3.1 43.6 + - - +
19G GLU* 3.6 8.7 - - - +
21G LEU* 1.3 75.8 - - - +
23G LYS* 1.3 77.2 + - + +
25G LYS* 3.6 6.1 - - - +
26G GLN* 2.9 46.3 + - + +
64G GLU* 6.1 0.2 - - - -
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Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 3.9 18.4 + - + +
11G THR 3.5 21.1 + - - +
12G VAL* 3.7 17.6 - - + +
13G GLU* 4.9 1.8 - - - +
19G GLU* 3.0 39.5 + - + +
20G ILE 4.2 0.2 - - - +
22G GLN* 1.3 92.9 - - - +
24G THR* 1.3 59.4 + - - +
26G GLN* 3.4 19.1 + - - +
27G LEU* 2.9 28.8 + - - +
89G ILE* 5.1 0.2 - - + -
109G LEU* 5.5 0.2 - - - +
110G GLU* 3.6 34.3 + - + +
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Residues in contact with THR 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 4.9 2.9 - - - -
20G ILE 2.8 19.1 + - - -
23G LYS* 1.3 71.7 - - - +
25G LYS* 1.3 65.4 + - - +
27G LEU* 3.1 8.3 + - + +
28G LEU* 2.9 36.1 + - + +
47G LEU* 4.3 15.5 - - + -
58G PRO* 3.6 31.9 - - + +
61G ALA* 3.5 23.3 - - + -
89G ILE* 3.8 15.3 - - + +
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Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU 3.0 20.1 + - - +
22G GLN* 3.6 4.9 - - - +
24G THR* 1.3 74.9 - - - +
26G GLN* 1.3 58.5 + - + +
28G LEU* 3.4 6.2 + - - +
29G GLU* 2.9 60.4 + - - +
61G ALA* 4.0 8.9 - - + +
64G GLU* 3.5 46.9 + - - +
65G LEU* 4.0 15.9 - - + -
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Residues in contact with GLN 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 5.5 0.8 + - - -
22G GLN* 2.9 33.8 + - + +
23G LYS* 3.7 21.1 + - - +
25G LYS* 1.3 76.9 - - - +
27G LEU* 1.3 61.0 + - - +
29G GLU* 4.1 9.4 + - - +
30G LYS* 3.2 22.9 + - - +
109G LEU* 4.0 16.0 - - + +
110G GLU* 3.7 20.4 + - - +
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLY* 3.9 8.5 - - - +
9G ALA* 3.5 35.2 - - - +
10G THR* 4.0 14.1 - - + +
23G LYS 2.9 15.0 + - - +
24G THR* 3.1 10.5 + - + +
26G GLN* 1.3 71.5 - - - +
28G LEU* 1.3 68.3 + - + +
30G LYS* 3.2 5.5 + - - +
31G ILE* 3.0 31.8 + - + +
47G LEU* 6.1 0.9 - - + -
89G ILE* 4.3 9.6 - - + +
90G ARG 5.2 0.2 - - - -
91G VAL* 3.9 13.9 - - + +
107G VAL* 3.4 38.6 - - + +
109G LEU* 3.9 11.2 - - + +
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Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G THR* 2.9 33.1 + - + +
25G LYS* 3.8 4.3 - - - +
27G LEU* 1.3 76.7 - - + +
29G GLU* 1.3 56.9 + - - +
31G ILE* 3.0 9.1 + - - +
32G ILE* 2.9 35.0 + - + +
45G MET* 3.7 26.9 - - + -
47G LEU* 4.7 6.1 - - + -
61G ALA 4.5 3.4 - - - +
62G VAL* 3.7 33.9 - - + +
65G LEU* 4.0 23.8 - - + -
68G TRP* 6.2 0.7 - - + -
91G VAL* 4.2 14.6 - - + -
93G MET* 4.1 13.9 - - + -
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Residues in contact with GLU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LYS* 2.9 47.5 + - - +
26G GLN* 4.1 7.0 + - - +
28G LEU* 1.3 68.4 - - - +
30G LYS* 1.3 64.8 + - - +
32G ILE* 4.0 8.4 - - + +
33G GLU* 3.1 24.3 + - - +
65G LEU* 3.6 30.3 - - + +
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Residues in contact with LYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLN 3.2 16.1 + - - +
27G LEU 3.2 4.9 + - - +
29G GLU* 1.3 76.6 - - - +
31G ILE* 1.3 64.6 + - - +
33G GLU* 3.3 25.2 + - - +
34G GLU* 2.9 50.9 + - - +
107G VAL* 3.6 27.8 - - + -
109G LEU* 4.5 15.7 - - + -
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Residues in contact with ILE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.7 26.0 - - + +
7G ARG 4.3 13.5 - - - +
8G GLY* 4.3 1.1 - - - -
27G LEU* 3.0 24.9 + - + +
28G LEU* 3.0 10.1 + - - +
30G LYS* 1.3 75.0 - - - +
32G ILE* 1.3 57.6 - - - +
35G ASN* 2.8 41.2 + - + +
37G THR* 5.0 0.7 - - - +
91G VAL* 3.5 31.6 - - + -
93G MET* 3.6 32.5 - - + -
107G VAL* 4.1 21.3 - - + -
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Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 2.9 18.9 + - + +
29G GLU* 4.0 8.5 - - + +
31G ILE* 1.3 76.3 - - + +
33G GLU* 1.3 55.4 + - - +
35G ASN 3.0 0.2 + - - -
36G HIS* 2.6 36.7 + - - -
37G THR* 3.2 35.7 - - + +
65G LEU* 3.6 25.8 - - + -
68G TRP* 3.5 36.6 - - + +
93G MET* 5.3 3.1 - - + -
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Residues in contact with GLU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G GLU 3.1 18.4 + - - +
30G LYS* 3.3 34.9 + - - +
32G ILE* 1.3 73.2 - - - +
34G GLU* 1.3 64.3 + - + +
36G HIS* 3.1 28.4 + - - -
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LYS* 2.9 45.9 + - - +
31G ILE 4.0 2.2 - - - +
33G GLU* 1.3 80.8 - - + +
35G ASN* 1.3 65.7 + - - +
36G HIS* 3.9 10.4 + - - -
105G ARG* 2.7 66.9 + - + +
106G HIS 5.2 0.5 - - - +
107G VAL* 3.5 21.4 - - + +
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Residues in contact with ASN 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.7 30.9 - - + +
31G ILE* 2.8 29.4 + - - +
34G GLU* 1.3 82.8 - - - +
36G HIS* 1.3 75.7 + - - +
37G THR* 3.5 13.2 + - - +
99G VAL* 5.8 3.8 - - - +
103G GLN 5.0 0.2 - - - +
104G ILE* 4.0 6.9 - - - +
105G ARG* 2.9 48.0 + - - +
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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