Contacts of the helix formed by residues 17 - 35 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H THR* 1.3 72.1 + - - +
18H GLU* 1.3 63.3 + - - +
20H ILE* 3.3 0.3 + - - +
21H LEU* 3.1 40.0 + - + +
55H ALA* 3.4 11.7 - - + +
56H VAL* 3.8 34.2 - - + +
60H LYS* 3.4 28.4 + - - -
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 4.4 11.0 + - - -
16H THR* 3.1 26.0 + - - +
17H GLU* 1.3 78.2 - - - +
19H GLU* 1.3 85.4 + - - +
21H LEU* 4.1 3.6 - - - +
22H GLN* 3.1 39.3 + - - +
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Residues in contact with GLU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.6 9.9 - - + -
13H GLU* 3.0 27.8 + - - +
14H ARG* 3.1 50.6 + - - +
16H THR* 3.3 23.6 + - + -
18H GLU* 1.3 85.9 + - - +
20H ILE* 1.3 64.7 + - - +
22H GLN* 3.2 7.4 + - - +
23H LYS* 3.0 59.1 + - - +
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Residues in contact with ILE 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 4.1 21.8 - - + -
15H ASP* 3.6 23.8 - - - +
16H THR 2.9 15.4 + - - +
17H GLU 3.9 2.7 - - - +
19H GLU* 1.3 75.1 - - - +
21H LEU* 1.3 57.4 + - - +
23H LYS* 3.5 1.2 + - - +
24H THR* 2.7 35.9 + - - -
53H LEU* 4.3 13.9 - - + -
55H ALA* 3.6 20.2 - - + +
56H VAL* 3.8 24.7 - - + +
58H PRO* 3.9 24.0 - - + -
89H ILE* 3.9 22.2 - - + +
79I MET* 6.2 0.7 - - + -
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Residues in contact with LEU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.1 30.3 + - + +
18H GLU* 4.4 3.8 - - - +
20H ILE* 1.3 79.3 - - + +
22H GLN* 1.3 56.0 + - - +
24H THR* 4.3 0.7 - - - -
25H LYS* 3.0 30.8 + - - +
56H VAL* 3.7 18.4 - - + -
57H PHE 4.0 1.8 - - - +
58H PRO 4.0 8.7 - - - +
60H LYS* 3.9 35.7 - - + -
61H ALA* 3.7 32.4 - - + +
64H GLU* 6.0 4.5 - - + -
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Residues in contact with GLN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 3.1 34.6 + - - +
19H GLU* 3.2 9.6 + - - +
21H LEU* 1.3 74.2 - - - +
23H LYS* 1.3 75.2 + - + +
25H LYS* 3.9 4.2 - - - +
26H GLN* 3.1 45.7 + - + +
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Residues in contact with LYS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 4.1 18.3 + - + +
11H THR 3.7 13.9 - - - +
12H VAL* 3.5 26.5 - - + +
13H GLU* 5.1 3.6 - - - +
14H ARG* 5.1 1.0 - - - +
19H GLU* 3.0 47.8 + - - +
20H ILE 3.9 0.9 - - - +
22H GLN* 1.3 84.4 - - - +
24H THR* 1.3 56.8 + - - +
26H GLN* 3.3 17.1 + - - +
27H LEU* 2.9 29.1 + - - +
109H LEU* 5.4 0.2 - - - +
110H GLU* 3.6 33.2 - - + -
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Residues in contact with THR 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 4.6 3.6 - - - +
20H ILE 2.7 24.1 + - - -
21H LEU* 3.9 3.8 - - - -
23H LYS* 1.3 74.8 - - - +
25H LYS* 1.3 66.1 + - - +
27H LEU* 3.2 10.1 + - + +
28H LEU* 3.0 36.3 + - + +
47H LEU* 4.7 13.7 - - + -
58H PRO* 3.7 30.1 - - + +
61H ALA* 4.0 10.5 - - + -
89H ILE* 3.7 21.1 - - + +
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Residues in contact with LYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU 3.0 20.5 + - - +
22H GLN* 3.9 4.3 - - - +
24H THR* 1.3 76.5 - - - +
26H GLN* 1.3 60.6 + - + +
28H LEU* 3.7 8.2 - - - +
29H GLU* 2.8 66.9 + - + +
61H ALA* 4.1 12.7 - - + +
64H GLU* 4.6 26.5 - - + +
65H LEU* 4.7 12.8 - - + +
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Residues in contact with GLN 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 3.1 42.5 + - + +
23H LYS* 3.6 16.8 + - - +
24H THR 3.3 0.2 - - - -
25H LYS* 1.3 79.2 - - + +
27H LEU* 1.3 59.7 + - - +
29H GLU* 3.5 13.8 + - - +
30H LYS* 3.3 21.5 + - - +
109H LEU* 4.2 13.5 - - + +
110H GLU* 5.7 2.8 + - - -
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLY* 4.0 6.1 - - - +
9H ALA* 3.7 35.0 - - - +
10H THR* 4.1 22.4 - - + +
23H LYS 2.9 13.7 + - - +
24H THR* 3.2 11.0 + - + +
26H GLN* 1.3 70.8 - - - +
28H LEU* 1.3 69.2 + - + +
30H LYS* 3.1 5.7 + - - +
31H ILE* 3.1 26.4 + - + +
47H LEU* 5.8 1.1 - - + -
89H ILE* 4.6 8.3 - - + +
90H ARG 5.1 0.9 - - - -
91H VAL* 3.5 30.3 - - + +
107H VAL* 3.9 23.1 - - + +
109H LEU* 3.9 13.0 - - + +
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H THR* 3.0 33.6 + - + +
25H LYS* 3.7 4.7 - - - +
27H LEU* 1.3 76.9 - - + +
29H GLU* 1.3 62.7 + - - +
31H ILE* 3.1 9.0 + - + +
32H ILE* 3.0 28.5 + - + +
45H MET* 3.6 28.0 - - + -
47H LEU* 4.9 3.8 - - + -
61H ALA 4.5 2.7 - - - +
62H VAL* 3.7 31.0 - - + +
65H LEU* 3.9 27.4 - - + -
68H TRP* 5.9 0.2 - - + -
91H VAL* 4.3 15.0 - - + -
93H MET* 4.1 14.1 - - + -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LYS* 2.8 55.1 + - - +
26H GLN* 3.6 12.8 - - - +
28H LEU* 1.3 75.7 - - - +
30H LYS* 1.3 57.7 + - + +
32H ILE* 3.3 10.2 + - + +
33H GLU* 2.9 31.0 + - - +
65H LEU* 4.2 17.3 - - + +
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Residues in contact with LYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLN 3.3 8.8 + - - +
27H LEU 3.1 8.5 + - - +
29H GLU* 1.3 76.2 - - + +
31H ILE* 1.3 64.8 + - - +
33H GLU* 3.2 35.7 + - - +
34H GLU* 3.0 38.8 + - + +
107H VAL* 3.8 24.7 - - + -
109H LEU* 4.7 14.4 - - + -
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Residues in contact with ILE 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 3.6 30.5 - - + +
7H ARG 4.4 6.5 - - - +
8H GLY* 4.1 10.5 - - - +
27H LEU* 3.1 17.4 + - + +
28H LEU* 3.1 8.6 + - - +
30H LYS* 1.3 75.5 - - - +
32H ILE* 1.3 59.5 + - - +
35H ASN* 3.0 37.5 + - - +
37H THR* 5.0 0.9 - - - +
91H VAL* 3.5 38.1 - - + -
93H MET* 4.0 26.2 - - + -
107H VAL* 3.7 24.5 - - + -
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Residues in contact with ILE 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 3.0 25.4 + - + +
29H GLU* 3.4 10.5 - - + +
31H ILE* 1.3 72.6 - - - +
33H GLU* 1.3 57.1 + - - +
36H HIS* 2.7 37.3 + - - -
37H THR* 3.3 30.3 + - - +
65H LEU* 4.0 20.4 - - + -
68H TRP* 3.7 37.5 - - + +
93H MET* 4.7 6.3 - - + -
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Residues in contact with GLU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 2.9 21.1 + - - +
30H LYS* 3.2 39.8 + - - +
32H ILE* 1.3 74.6 - - - +
34H GLU* 1.3 71.9 + - - +
35H ASN 3.4 0.2 + - - -
36H HIS* 3.8 7.7 + - - +
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LYS* 3.0 34.2 + - + +
33H GLU* 1.3 93.6 - - - +
35H ASN* 1.3 73.2 + - - +
105H ARG* 3.9 38.8 + - + +
107H VAL* 4.4 12.3 - - + -
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Residues in contact with ASN 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 4.0 17.1 - - + +
31H ILE* 3.0 34.7 + - - +
34H GLU* 1.3 83.2 - - - +
36H HIS* 1.3 73.8 + - - +
37H THR* 3.3 12.6 + - - +
99H VAL* 5.8 1.7 - - - +
103H GLN 4.5 1.0 - - - +
104H ILE* 3.8 11.0 - - + +
105H ARG* 2.8 50.2 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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