Contacts of the helix formed by residues 28 - 46 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ARG 2.9 26.2 + - - -
17B TYR 3.3 7.3 + - - -
18B TYR* 3.7 13.6 - - - +
19B ARG* 4.2 10.8 - - - +
26B HIS* 3.4 2.6 + - - -
27B VAL* 1.3 75.3 - - - +
29B ALA* 1.3 71.1 + - - +
30B GLU* 3.0 12.8 + - - +
31B GLY 3.0 8.7 + - - -
32B GLN* 3.0 14.0 + - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER* 1.3 75.3 + - - +
30B GLU* 1.3 61.9 + - + +
32B GLN* 3.5 4.5 - - - +
33B ALA* 2.8 34.9 + - - +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 3.5 31.2 - - + +
16B ARG* 4.2 20.2 - - + +
28B SER* 3.0 8.2 + - - +
29B ALA* 1.3 87.6 - - + +
31B GLY* 1.3 67.9 + - - +
33B ALA* 3.5 14.6 - - - +
34B TYR 3.1 14.0 + - - -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.2 43.5 + - - +
27B VAL* 4.4 3.6 - - - -
28B SER* 3.0 12.1 + - - -
30B GLU* 1.3 74.4 - - - +
32B GLN* 1.3 66.2 + - - +
34B TYR* 2.9 21.1 + - - +
35B ARG* 3.2 8.6 + - - +
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.6 25.5 - - + +
28B SER 3.0 15.4 + - - +
29B ALA* 3.5 5.2 - - - +
31B GLY* 1.3 68.9 - - - +
33B ALA* 1.3 67.4 + - - +
34B TYR 2.8 1.4 + - - -
35B ARG* 2.9 27.4 + - - +
36B ASP* 2.8 35.0 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA 2.8 22.7 + - - +
30B GLU* 3.5 24.0 - - - +
31B GLY 3.3 0.2 - - - -
32B GLN* 1.3 72.3 - - - +
34B TYR* 1.3 60.5 + - - +
36B ASP* 3.4 9.9 + - - +
37B ASN* 2.7 35.1 + - - +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.4 8.0 - - - +
9B PRO* 2.6 41.0 + - + +
10B TRP 3.6 5.6 - - - -
11B PRO* 3.4 37.2 - - + +
12B PRO* 3.8 7.6 - - + -
17B TYR* 3.7 25.8 - + + -
30B GLU 3.1 8.7 + - - +
31B GLY 2.9 12.1 + - - +
32B GLN 2.8 0.4 + - - -
33B ALA* 1.3 77.9 - - - +
35B ARG* 1.3 71.5 + - - +
36B ASP 2.7 2.8 + - - -
37B ASN* 2.9 20.1 + - + +
38B VAL* 3.0 29.0 - - + +
77B ALA 4.5 9.9 - - - -
78B ALA* 5.3 3.9 + - - -
81B ALA* 4.4 11.4 - - + -
110B LEU* 4.5 5.4 - - - +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.9 6.1 - - - +
27B VAL* 3.4 36.1 - - - +
31B GLY 3.2 10.5 + - - -
32B GLN* 2.9 27.4 + - - +
34B TYR* 1.3 76.3 - - - +
36B ASP* 1.3 70.4 + - - +
38B VAL* 3.1 10.1 - - - +
39B ALA* 2.9 20.8 + - - +
80B ASP* 2.6 43.7 + - - +
81B ALA* 4.4 10.3 - - - +
84B LYS* 3.0 50.2 - - + +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 2.8 35.8 + - - +
33B ALA* 3.6 10.5 - - - +
34B TYR 2.7 3.8 + - - -
35B ARG* 1.3 70.2 - - - +
37B ASN* 1.3 57.9 - - - +
38B VAL 2.2 20.3 + - - -
39B ALA* 2.8 17.3 + - - +
40B ARG* 3.0 23.4 + - + +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 5.2 6.2 - - + +
33B ALA* 2.7 30.6 + - - +
34B TYR* 2.9 13.2 + - + +
36B ASP* 1.3 74.1 - - - +
38B VAL* 1.3 57.8 + - + +
40B ARG* 2.9 39.1 + - - +
41B ILE* 2.9 27.1 + - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.0 28.9 - - + -
9B PRO* 5.0 5.4 - - + -
34B TYR* 3.0 52.9 - - + +
35B ARG* 3.1 8.1 - - - +
36B ASP 2.2 15.2 + - - -
37B ASN* 1.3 69.8 - - + +
39B ALA* 1.3 55.5 + - - +
40B ARG 2.7 5.0 + - - -
41B ILE* 2.6 30.3 + - - +
42B ILE* 2.8 12.3 + - + +
81B ALA* 3.7 23.1 - - + +
82B LEU* 5.0 3.6 - - + -
85B ALA* 4.8 3.1 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG 2.9 10.8 + - - +
36B ASP* 2.8 8.0 + - - +
38B VAL* 1.3 76.2 - - - +
40B ARG* 1.3 55.3 + - + +
42B ILE* 3.6 4.8 - - - +
43B LYS* 2.9 30.3 + - - +
84B LYS 4.8 3.4 - - - +
85B ALA* 3.7 34.7 - - - +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP* 3.0 18.1 + - + +
37B ASN* 2.9 47.3 + - - +
38B VAL 2.7 0.6 + - - -
39B ALA* 1.3 75.5 - - + +
41B ILE* 1.3 57.7 + - - +
43B LYS* 3.6 2.5 - - - +
44B ASN* 2.6 44.8 + - - +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.8 7.9 - - + -
7B THR 4.6 12.6 - - - +
8B LEU* 4.5 11.9 - - + -
9B PRO* 3.9 33.0 - - + -
37B ASN 2.9 23.8 - - - +
38B VAL* 2.6 15.0 + - - +
40B ARG* 1.3 75.8 - - + +
42B ILE* 1.3 55.4 + - - +
44B ASN* 4.1 5.6 - - - +
45B ALA* 2.7 43.0 + - + +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.5 17.3 - - + -
8B LEU* 5.8 1.1 - - + -
38B VAL* 2.8 16.6 + - + +
39B ALA* 3.6 12.1 - - - +
41B ILE* 1.3 72.9 - - + +
43B LYS* 1.3 55.1 + - - +
45B ALA* 3.1 4.0 - - - +
46B MET 2.2 31.9 + - - -
47B LEU* 2.7 43.4 + - + +
48B ASP* 3.9 16.4 - - + +
82B LEU* 4.7 8.7 - - + -
85B ALA* 3.1 39.5 - - + +
87B PHE* 4.3 18.4 - - + -
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ALA 2.9 16.0 + - - +
40B ARG* 4.2 2.9 - - - +
42B ILE* 1.3 80.2 - - + +
44B ASN* 1.3 61.8 + - - +
46B MET* 3.1 25.7 - - - +
48B ASP* 4.3 18.2 - - + +
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 2.6 28.6 + - - +
41B ILE* 3.4 6.8 - - - +
43B LYS* 1.3 70.9 - - - +
45B ALA* 1.3 64.6 + - - +
46B MET* 2.8 18.1 + - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.7 3.8 - - + -
41B ILE* 2.7 26.2 + - + +
44B ASN* 1.3 72.6 - - - +
46B MET* 1.3 68.4 + - - +
47B LEU* 3.3 27.6 + - + +
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Residues in contact with MET 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ILE 2.2 19.8 + - - -
43B LYS* 3.1 18.8 - - - +
44B ASN 2.8 11.5 - - - +
45B ALA* 1.3 78.4 - - - +
47B LEU* 1.3 54.6 + - - +
48B ASP* 3.3 15.9 + - - +
49B ILE* 4.3 6.8 - - - +
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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
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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