Contacts of the helix formed by residues 17 - 35 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L THR* 1.3 70.3 + - - +
18L GLU* 1.3 61.8 + - - +
20L ILE* 3.3 1.4 + - - +
21L LEU* 3.0 39.9 + - + +
55L ALA* 3.7 16.2 - - + +
56L VAL* 3.5 36.1 - - + +
60L LYS* 3.1 28.3 + - - -
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Residues in contact with GLU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L THR* 3.4 9.0 - - + +
17L GLU* 1.3 78.8 - - - +
19L GLU* 1.3 57.6 + - - +
21L LEU* 3.9 3.3 - - - +
22L GLN* 2.9 44.8 + - - +
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L VAL* 3.7 9.2 - - + -
13L GLU* 3.0 25.2 + - - +
14L ARG* 2.8 41.6 + - - +
16L THR* 3.3 19.5 - - + +
18L GLU* 1.3 78.1 - - - +
20L ILE* 1.3 62.4 + - - +
22L GLN* 4.0 17.5 - - - +
23L LYS* 3.0 50.5 + - + +
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Residues in contact with ILE 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L VAL* 4.1 23.6 - - + -
14L ARG 4.8 0.2 - - - +
15L ASP* 3.5 24.2 - - - +
16L THR 3.1 20.2 + - - +
17L GLU 3.3 0.2 + - - -
19L GLU* 1.3 75.1 - - - +
21L LEU* 1.3 61.3 + - - +
24L THR* 2.7 31.4 + - - -
53L LEU* 4.2 18.4 - - + -
55L ALA* 4.2 1.6 - - + +
56L VAL* 3.5 46.4 - - + +
58L PRO* 4.2 16.4 - - + -
89L ILE* 4.1 15.1 - - + +
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Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLU* 3.0 35.4 + - + +
18L GLU* 4.0 3.4 - - - +
20L ILE* 1.3 74.7 - - - +
22L GLN* 1.3 60.8 + - - +
25L LYS* 3.0 30.8 + - - +
56L VAL* 3.9 16.2 - - + -
57L PHE 4.0 3.8 - - - +
58L PRO* 4.2 3.6 - - + +
60L LYS* 3.9 35.7 - - + +
61L ALA* 3.5 34.4 - - + +
64L GLU* 5.6 7.6 - - - +
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Residues in contact with GLN 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 2.9 32.0 + - + +
19L GLU* 3.9 14.6 - - - +
21L LEU* 1.3 74.2 - - - +
23L LYS* 1.3 77.6 + - - +
25L LYS* 3.4 6.8 + - - +
26L GLN* 2.9 47.0 + - - +
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L THR* 4.1 16.7 + - + +
11L THR 3.9 10.8 - - - +
12L VAL* 3.8 22.2 - - + -
19L GLU* 3.0 39.9 + - - +
20L ILE 4.4 0.4 - - - +
22L GLN* 1.3 89.4 + - - +
24L THR* 1.3 65.7 + - - +
26L GLN* 3.2 23.0 + - - +
27L LEU* 2.9 23.4 + - - +
89L ILE* 5.1 0.4 - - + -
109L LEU* 5.6 0.2 - - - +
110L GLU* 3.1 34.5 + - + +
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Residues in contact with THR 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L THR* 4.5 3.1 - - - +
20L ILE 2.7 22.5 + - - -
23L LYS* 1.3 76.7 - - - +
25L LYS* 1.3 61.8 + - - +
27L LEU* 3.3 9.8 + - + +
28L LEU* 2.9 33.8 + - + +
47L LEU* 4.1 23.1 - - + -
58L PRO* 3.6 27.8 - - + +
61L ALA* 3.9 13.0 - - + -
89L ILE* 3.5 21.6 - - + +
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Residues in contact with LYS 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU 3.0 19.3 + - - +
22L GLN* 3.6 6.5 - - - +
24L THR* 1.3 73.6 - - - +
26L GLN* 1.3 64.5 + - - +
28L LEU* 3.1 6.6 + - - +
29L GLU* 2.8 64.0 + - - +
61L ALA* 3.9 14.4 - - + +
64L GLU* 3.6 50.9 + - + +
65L LEU* 4.4 11.4 - - + -
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Residues in contact with GLN 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L GLN* 2.9 32.1 + - - +
23L LYS* 3.2 41.1 + - - +
25L LYS* 1.3 72.3 - - + +
27L LEU* 1.3 62.6 + - - +
29L GLU* 3.4 11.9 + - - +
30L LYS* 3.0 24.1 + - - +
109L LEU* 4.2 9.5 - - + +
110L GLU* 4.5 5.1 + - - +
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Residues in contact with LEU 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L GLY* 4.2 3.4 - - - -
9L ALA* 3.5 37.5 - - - +
10L THR* 3.7 23.3 - - + +
23L LYS 2.9 13.1 + - - +
24L THR* 3.6 10.1 - - + +
26L GLN* 1.3 74.9 - - - +
28L LEU* 1.3 62.8 + - + +
30L LYS* 3.1 4.9 + - - +
31L ILE* 3.1 27.3 + - + +
47L LEU* 6.2 0.7 - - + -
89L ILE* 4.3 10.1 - - + +
91L VAL* 3.8 28.7 - - + -
107L VAL* 3.8 16.6 - - + +
109L LEU* 3.6 22.8 - - + +
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Residues in contact with LEU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L THR* 2.9 39.3 + - + +
25L LYS* 3.8 4.3 - - - +
27L LEU* 1.3 71.1 - - + +
29L GLU* 1.3 63.2 + - - +
31L ILE* 3.3 12.8 + - + +
32L ILE* 3.1 31.8 + - + +
45L MET* 4.2 22.7 - - + -
47L LEU* 5.3 2.5 - - + -
61L ALA* 4.8 2.2 - - + -
62L VAL* 3.8 33.2 - - + +
65L LEU* 4.2 23.3 - - + -
68L TRP* 6.3 1.1 - - + -
91L VAL* 4.3 21.1 - - + -
93L MET* 5.5 4.9 - - - -
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Residues in contact with GLU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LYS* 2.8 56.3 + - - +
26L GLN* 3.7 10.9 - - - +
28L LEU* 1.3 77.0 - - - +
30L LYS* 1.3 56.8 + - - +
32L ILE* 3.5 9.1 + - + +
33L GLU* 3.0 29.9 + - - +
64L GLU 5.4 0.5 - - - +
65L LEU* 4.0 20.3 - - + +
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Residues in contact with LYS 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L GLN 3.0 13.5 + - - +
27L LEU 3.4 8.5 - - - +
29L GLU* 1.3 74.3 - - - +
31L ILE* 1.3 59.0 + - - +
33L GLU* 3.1 33.8 + - - +
34L GLU* 2.9 59.1 + - + +
107L VAL* 3.8 23.1 - - + -
109L LEU* 4.2 15.9 - - + -
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Residues in contact with ILE 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L ILE* 3.7 19.1 - - + +
7L ARG 4.3 6.3 - - - +
8L GLY* 4.1 12.3 - - - +
27L LEU* 3.1 17.2 + - + +
28L LEU* 3.6 13.9 - - + +
30L LYS* 1.3 74.0 - - - +
32L ILE* 1.3 59.1 + - + +
35L ASN* 2.8 37.6 + - - +
91L VAL* 3.7 36.1 - - + -
93L MET* 3.6 34.8 - - + -
107L VAL* 4.0 23.6 - - + -
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Residues in contact with ILE 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L LEU* 3.1 20.8 + - + +
29L GLU* 3.7 8.5 - - + +
31L ILE* 1.3 79.8 - - + +
33L GLU* 1.3 55.2 + - - +
36L HIS* 2.6 37.1 + - - -
37L THR* 3.5 33.4 - - - +
65L LEU* 4.0 25.6 - - + -
68L TRP* 3.7 36.8 - - + +
93L MET* 5.5 1.3 - - - -
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Residues in contact with GLU 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLU 3.0 17.3 + - - +
30L LYS* 3.1 43.3 + - - +
32L ILE* 1.3 78.2 - - - +
34L GLU* 1.3 68.5 + - - +
35L ASN 3.2 0.3 + - - -
36L HIS* 3.4 21.8 + - - +
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Residues in contact with GLU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L LYS* 2.9 46.1 + - + +
31L ILE 3.8 3.6 - - - +
33L GLU* 1.3 80.1 - - + +
35L ASN* 1.3 61.6 + - - +
36L HIS* 4.0 12.0 + - - -
105L ARG* 3.8 40.1 - - + +
107L VAL* 3.9 17.9 - - + -
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Residues in contact with ASN 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L ILE* 3.7 26.3 - - + +
31L ILE* 2.8 23.0 + - - +
34L GLU* 1.3 77.8 - - - +
36L HIS* 1.3 74.9 + - - +
37L THR* 3.2 18.9 + - - +
99L VAL* 6.0 2.6 - - - +
103L GLN 5.1 0.3 - - - +
104L ILE* 3.8 11.6 - - - +
105L ARG* 2.8 49.8 + - - +
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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
------------------------------------------------------------
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