Contacts of the helix formed by residues 17 - 35 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I THR* 1.3 72.0 - - - +
18I GLU* 1.3 65.1 + - - +
20I ILE* 3.4 0.5 + - - +
21I LEU* 3.0 39.7 + - + +
55I ALA* 3.6 12.1 - - + +
56I VAL* 3.9 28.1 - - + +
60I LYS* 2.9 35.3 + - - -
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Residues in contact with GLU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I THR* 3.3 6.9 + - - +
17I GLU* 1.3 78.6 - - - +
19I GLU* 1.3 60.3 + - + +
21I LEU* 4.0 3.9 - - - +
22I GLN* 3.1 51.8 + - + +
13K GLU* 4.0 16.8 - - - +
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.8 5.8 - - + +
13I GLU* 3.2 22.3 + - - +
14I ARG* 2.8 45.3 + - - +
16I THR* 3.4 17.3 + - - +
17I GLU 3.3 0.6 - - - -
18I GLU* 1.3 78.7 - - + +
20I ILE* 1.3 66.5 + - - +
22I GLN* 3.3 11.8 + - - +
23I LYS* 2.9 59.4 + - - +
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.9 24.5 - - + -
15I ASP* 3.7 22.0 - - - +
16I THR 3.1 19.0 + - - +
19I GLU* 1.3 73.9 - - - +
21I LEU* 1.3 58.8 + - - +
23I LYS* 4.1 0.2 - - - +
24I THR* 2.8 38.4 + - - +
53I LEU* 4.5 15.3 - - + -
55I ALA* 3.7 13.2 - - + +
56I VAL* 3.7 29.6 - - + +
58I PRO* 3.9 31.4 - - + -
89I ILE* 4.2 7.9 - - + -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 3.0 41.3 + - + +
18I GLU* 4.2 4.0 - - - +
20I ILE* 1.3 76.0 - - + +
22I GLN* 1.3 56.8 + - - +
25I LYS* 2.9 31.7 + - - +
56I VAL* 3.7 17.7 - - + -
57I PHE 3.9 4.3 - - - +
58I PRO 4.4 1.6 - - - +
60I LYS* 3.7 40.2 - - + -
61I ALA* 3.5 19.9 - - + +
64I GLU* 4.4 15.5 - - - +
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 3.1 46.7 + - + +
19I GLU* 3.7 10.8 - - - +
21I LEU* 1.3 75.8 - - - +
23I LYS* 1.3 78.4 + - - +
25I LYS* 3.4 6.7 + - - +
26I GLN* 2.9 51.0 + - - +
13K GLU* 5.7 8.5 + - + +
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 3.8 15.6 + - + +
11I THR 3.7 17.9 + - - +
12I VAL* 3.8 21.8 - - + +
13I GLU* 4.5 5.9 - - - +
19I GLU* 2.9 48.0 + - - +
20I ILE 4.1 0.4 - - - +
22I GLN* 1.3 88.9 + - - +
24I THR* 1.3 65.3 + - - +
26I GLN* 3.5 15.5 + - - +
27I LEU* 3.1 23.2 + - - +
89I ILE* 5.2 0.2 - - + -
109I LEU* 5.6 0.3 - - - +
110I GLU* 3.9 32.8 + - + +
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Residues in contact with THR 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 4.8 3.1 - - - -
20I ILE 2.8 22.2 + - - -
21I LEU 3.9 2.5 - - - -
23I LYS* 1.3 73.6 - - - +
25I LYS* 1.3 65.6 + - - +
27I LEU* 3.3 8.6 + - + +
28I LEU* 3.0 37.1 + - + +
47I LEU* 3.8 23.8 - - + -
58I PRO* 3.6 33.9 - - + +
61I ALA* 4.0 9.2 - - + -
89I ILE* 3.8 18.2 - - + +
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Residues in contact with LYS 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I LEU 2.9 18.3 + - - +
22I GLN* 3.7 6.5 - - - +
24I THR* 1.3 75.9 - - - +
26I GLN* 1.3 61.9 + - + +
28I LEU* 3.3 7.7 + - - +
29I GLU* 2.9 60.9 + - + +
61I ALA* 4.0 12.5 - - + +
64I GLU* 3.7 54.5 - - + +
65I LEU* 5.0 6.5 - - + -
110K GLU* 3.9 33.0 + - - +
111K LYS* 6.2 0.2 - - - -
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Residues in contact with GLN 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLN* 2.9 41.6 + - + +
23I LYS* 3.7 19.1 - - - +
25I LYS* 1.3 76.9 - - + +
27I LEU* 1.3 61.0 + - - +
29I GLU* 3.5 12.8 + - - +
30I LYS* 3.0 24.6 + - - +
109I LEU* 4.2 10.3 - - + +
110I GLU* 4.0 18.8 + - - +
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Residues in contact with LEU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLY 4.1 4.7 - - - -
9I ALA* 3.8 33.2 - - - +
10I THR* 3.9 22.2 - - + +
23I LYS 3.1 14.6 + - - +
24I THR* 3.3 10.1 + - + +
26I GLN* 1.3 75.9 - - - +
28I LEU* 1.3 65.4 + - + +
30I LYS* 3.1 3.1 + - - +
31I ILE* 3.0 38.3 + - + +
47I LEU* 6.6 0.2 - - + -
89I ILE* 4.4 10.3 - - + +
91I VAL* 4.1 13.7 - - + -
107I VAL* 3.8 30.3 - - + +
109I LEU* 3.8 12.9 - - + +
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Residues in contact with LEU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I THR* 3.0 39.6 + - + +
25I LYS* 3.9 6.3 - - - +
27I LEU* 1.3 74.3 - - + +
29I GLU* 1.3 56.7 + - - +
31I ILE* 3.4 7.7 + - + +
32I ILE* 2.9 37.2 + - + +
45I MET* 4.2 22.7 - - + -
47I LEU* 4.8 2.7 - - + -
61I ALA 4.8 0.2 - - - -
62I VAL* 3.8 30.5 - - + +
65I LEU* 3.8 27.8 - - + -
68I TRP* 6.3 0.4 - - + -
91I VAL* 4.3 21.5 - - + -
93I MET* 4.8 8.5 - - + -
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Residues in contact with GLU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LYS* 2.9 53.6 + - + +
26I GLN* 3.7 12.3 - - - +
28I LEU* 1.3 76.1 - - - +
30I LYS* 1.3 59.0 + - - +
32I ILE* 3.6 7.7 + - - +
33I GLU* 3.0 32.0 + - - +
65I LEU* 3.8 25.7 - - + +
110K GLU* 4.9 4.6 - - - +
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Residues in contact with LYS 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I GLN 3.0 14.3 + - - +
27I LEU 3.1 7.4 + - - +
29I GLU* 1.3 71.7 - - - +
31I ILE* 1.3 60.2 + - - +
33I GLU* 2.9 35.7 + - - +
34I GLU* 2.8 61.3 + - - +
107I VAL* 4.0 21.8 - - + -
109I LEU* 4.3 16.6 - - + -
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Residues in contact with ILE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 4.1 15.5 - - + +
7I ARG 4.1 6.5 - - - +
8I GLY* 3.8 15.0 - - - -
27I LEU* 3.0 19.7 + - + +
28I LEU* 3.5 11.9 - - + +
30I LYS* 1.3 74.1 - - - +
32I ILE* 1.3 63.0 + - - +
35I ASN* 2.9 40.6 + - + +
37I THR* 5.2 0.4 - - - +
91I VAL* 3.6 32.8 - - + -
93I MET* 4.1 26.9 - - + -
107I VAL* 3.8 24.8 - - + +
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Residues in contact with ILE 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU* 2.9 27.8 + - + +
29I GLU* 3.8 6.1 - - - +
31I ILE* 1.3 72.4 - - - +
33I GLU* 1.3 54.9 + - - +
36I HIS* 2.7 34.2 + - - -
37I THR* 3.2 34.7 + - - +
65I LEU* 3.9 28.5 - - + -
68I TRP* 3.5 40.6 - - + +
93I MET* 4.8 5.2 - - + -
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Residues in contact with GLU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I GLU* 3.0 19.3 + - - +
30I LYS* 2.9 42.4 + - - +
32I ILE* 1.3 79.2 - - - +
34I GLU* 1.3 65.2 + - + +
36I HIS* 3.6 17.2 + - - -
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Residues in contact with GLU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I LYS* 2.8 52.3 + - + +
33I GLU* 1.3 76.7 - - + +
35I ASN* 1.3 64.4 + - - +
36I HIS* 3.5 14.3 + - - -
105I ARG* 3.9 38.5 - - + +
107I VAL* 4.0 16.7 - - + +
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Residues in contact with ASN 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 3.8 23.8 - - + +
31I ILE* 2.9 29.3 + - - +
34I GLU* 1.3 78.2 - - - +
36I HIS* 1.3 79.8 + - - +
37I THR* 3.3 14.8 + - - +
99I VAL* 6.2 0.3 - - - +
103I GLN 4.9 0.2 - - - +
104I ILE* 3.9 11.5 - - + +
105I ARG* 2.9 51.6 + - - +
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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