Contacts of the helix formed by residues 28 - 43 (chain C) in PDB entry 2H8C
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 SER 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ARG* 2.4 32.2 + - - +
17C TYR 3.0 11.6 + - - -
18C TYR* 3.5 6.1 - - - -
19C ARG* 4.4 5.8 - - - +
27C VAL* 1.3 81.2 - - - +
29C ALA* 1.3 67.4 + - - +
30C GLU* 3.0 15.4 + - - +
31C GLY 3.4 4.7 + - - -
32C GLN* 2.8 29.5 + - - +
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER* 1.3 76.0 + - - +
30C GLU* 1.3 60.9 + - + +
32C GLN* 3.1 8.9 - - - +
33C ALA* 2.8 27.3 + - - +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PRO* 3.9 22.3 - - + +
16C ARG* 4.5 15.4 - - + +
28C SER* 3.0 7.8 + - - +
29C ALA* 1.3 79.1 - - + +
31C GLY* 1.3 63.9 + - - +
33C ALA* 3.8 8.4 - - + +
34C TYR* 3.2 23.7 + - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 3.5 55.5 - - - +
27C VAL* 5.3 1.6 - - - -
28C SER* 3.4 9.3 + - - -
29C ALA 3.1 1.2 - - - -
30C GLU* 1.3 76.6 - - - +
32C GLN* 1.3 67.1 + - - +
34C TYR* 3.6 0.3 - - - +
35C ARG* 3.6 17.2 + - - -
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.6 6.3 - - + +
28C SER 2.8 16.9 + - - +
29C ALA* 3.1 12.8 - - - +
31C GLY* 1.3 69.7 - - - +
33C ALA* 1.3 52.7 + - - +
35C ARG* 2.6 54.8 + - - +
36C ASP* 2.3 43.2 + - - +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 2.8 18.7 + - - +
30C GLU* 3.4 10.2 + - + +
32C GLN* 1.3 71.8 - - - +
34C TYR* 1.3 63.0 + - - +
36C ASP* 3.2 15.3 - - - +
37C ASN* 3.1 21.1 + - - +
40C ARG* 4.6 2.1 + - - -
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.1 10.6 - - - +
9C PRO* 2.7 48.3 + - + -
10C TRP 4.1 6.3 - - - -
11C PRO* 3.6 22.2 - - + -
12C PRO* 4.2 12.1 - - + -
17C TYR* 3.6 24.5 - + + -
30C GLU 3.2 11.0 + - - +
31C GLY 3.6 8.7 - - - +
32C GLN 2.8 3.6 + - - -
33C ALA* 1.3 72.6 - - - +
35C ARG* 1.3 67.9 + - - +
37C ASN* 2.7 11.8 + - + +
38C VAL* 2.6 48.1 + - + +
77C ALA* 4.5 7.0 - - + -
78C ALA* 5.1 3.3 - - - -
81C ALA* 4.0 11.1 - - + +
110C LEU* 4.0 11.3 - - - +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.7 17.8 + - - +
27C VAL* 4.1 31.8 - - - +
31C GLY 3.6 13.5 - - - +
32C GLN* 2.6 39.4 + - - +
34C TYR* 1.3 74.7 - - - +
36C ASP* 1.3 55.1 + - - +
38C VAL* 2.9 11.9 + - - +
39C ALA* 2.4 39.1 + - + +
80C ASP* 2.9 34.4 + - - +
81C ALA* 4.3 10.1 - - - +
84C LYS* 3.7 31.8 - - + +
85C ALA* 5.1 1.6 - - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 2.3 43.6 + - - +
33C ALA* 3.4 14.6 - - - +
35C ARG* 1.3 67.6 - - - +
37C ASN* 1.3 57.3 + - - +
39C ALA* 2.7 28.9 + - - +
40C ARG* 2.9 34.0 + - - +
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Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 5.3 10.8 - - + +
33C ALA 3.1 9.0 + - - +
34C TYR* 2.7 21.8 + - + +
36C ASP* 1.3 75.5 - - - +
38C VAL* 1.3 63.7 + - - +
40C ARG* 3.2 35.7 - - - +
41C ILE* 3.3 8.7 + - - +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 6.4 0.9 - - + -
8C LEU* 5.7 7.6 - - + -
9C PRO* 5.2 8.0 - - + +
34C TYR* 2.6 64.1 + - + +
35C ARG 3.0 5.4 - - - +
37C ASN* 1.3 71.6 - - - +
39C ALA* 1.3 55.2 + - - +
41C ILE* 2.7 29.8 + - + +
42C ILE* 3.3 25.4 + - + +
81C ALA* 3.6 24.7 - - + -
82C LEU* 4.1 13.7 - - + +
85C ALA* 4.6 1.3 - - + -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 2.4 28.1 + - + +
36C ASP* 2.7 17.4 + - - +
38C VAL* 1.3 67.0 - - - +
40C ARG* 1.3 54.8 + - - +
42C ILE* 3.3 2.8 + - - +
43C LYS* 2.9 31.2 + - - +
85C ALA* 3.8 29.8 - - + +
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA 4.6 2.2 + - - -
36C ASP* 2.9 32.7 + - - +
37C ASN* 3.2 36.5 - - - +
38C VAL 2.8 0.2 + - - -
39C ALA* 1.3 75.1 - - + +
41C ILE* 1.3 55.7 + - - +
42C ILE 3.2 0.7 - - - -
43C LYS* 4.9 2.9 - - - -
44C ASN* 2.6 48.0 - - - +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 5.9 0.4 - - + -
7C THR 4.9 12.1 - - - +
9C PRO* 5.7 6.5 - - + -
37C ASN 3.3 9.7 + - - +
38C VAL* 2.7 14.4 + - + +
40C ARG* 1.3 77.3 - - - +
42C ILE* 1.3 65.4 + - + +
44C ASN* 4.3 2.0 - - - +
45C ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.6 41.3 - - + -
38C VAL* 3.3 26.0 + - + +
39C ALA* 3.5 7.2 - - - +
41C ILE* 1.3 86.4 - - + +
43C LYS* 1.3 55.0 + - - +
44C ASN 3.1 3.4 - - - -
45C ALA* 3.0 4.4 + - + -
46C MET 2.6 30.7 + - - -
47C LEU* 2.8 42.4 + - + +
48C ASP* 4.1 1.3 - - - +
82C LEU* 4.5 7.0 - - + -
85C ALA* 4.2 26.5 - - + +
87C PHE* 4.4 7.2 - - + -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 2.9 20.0 + - + +
40C ARG* 4.9 2.2 - - - -
42C ILE* 1.3 73.5 - - - +
44C ASN* 1.3 59.6 + - - +
46C MET* 3.6 19.3 - - - +
48C ASP* 3.7 28.6 - - + +
85C ALA 6.2 0.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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