Contacts of the helix formed by residues 20 - 33 (chain B) in PDB entry 2GPY
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 ASP 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ARG* 1.3 72.7 - - - +
21B GLN* 1.3 86.0 + - - +
22B TYR* 3.3 25.7 + - - +
23B ILE* 2.9 26.4 + - + +
24B GLU* 3.0 10.2 + - - +
74B GLN* 4.9 6.6 - - - +
101B LEU* 3.6 17.5 - - - +
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Residues in contact with GLN 21 (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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19B ARG 3.5 3.7 + - - -
20B ASP* 1.3 81.0 + - - +
22B TYR* 1.3 61.4 + - + +
24B GLU* 3.3 11.8 + - - +
25B GLN* 2.9 29.3 + - - +
28B ARG* 4.9 1.9 + - - -
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Residues in contact with TYR 22 (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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20B ASP* 2.9 18.8 + - - +
21B GLN* 1.3 85.1 - - + +
23B ILE* 1.3 56.7 + - - +
25B GLN* 3.4 11.3 + - + +
26B MSE 3.0 35.5 + - + +
96B LYS* 4.4 1.4 + - - +
97B HIS* 2.9 40.5 - + - -
100B ALA* 3.3 30.6 - - + +
101B LEU* 4.0 25.1 - - + -
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Residues in contact with ILE 23 (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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19B ARG* 3.7 18.6 - - + -
20B ASP* 3.3 30.1 - - + +
22B TYR* 1.3 73.0 - - - +
24B GLU* 1.3 63.6 + - - +
26B MSE 3.0 14.2 + - - +
27B GLU* 3.0 26.4 + - - +
67B TYR* 3.6 23.8 - - + -
70B ILE* 3.6 22.2 - - + -
71B ARG* 3.7 15.9 - - + +
74B GLN* 3.6 26.7 - - - +
101B LEU* 4.0 12.6 - - + -
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Residues in contact with GLU 24 (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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18B ALA* 3.9 8.5 - - - +
19B ARG* 3.3 56.9 + - + +
20B ASP 3.0 13.2 + - - +
21B GLN* 3.6 11.7 - - - +
23B ILE* 1.3 76.0 - - - +
25B GLN* 1.3 56.5 + - - +
27B GLU* 3.3 12.3 + - - +
28B ARG* 3.1 48.1 + - - +
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Residues in contact with GLN 25 (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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21B GLN 2.9 16.8 + - - +
22B TYR* 3.4 13.7 - - + +
24B GLU* 1.3 74.0 - - - +
26B MSE 1.3 60.2 + - + +
28B ARG* 2.6 37.7 + - - +
29B GLU* 3.0 36.9 + - + +
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Residues in contact with MSE 26 (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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22B TYR* 3.0 41.1 + - + +
23B ILE* 3.0 21.5 + - - +
25B GLN* 1.3 74.6 - - + +
27B GLU* 1.3 59.7 + - - +
29B GLU* 3.4 8.5 + - - +
30B ALA* 2.9 30.5 + - - +
37B ILE* 4.5 1.7 - - - +
65B ILE* 3.5 33.8 - - + +
67B TYR* 3.6 36.6 - - + +
70B ILE* 3.9 19.5 - - + -
97B HIS* 3.7 27.1 - - + +
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Residues in contact with GLU 27 (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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19B ARG* 2.9 45.8 + - - +
23B ILE* 3.0 19.3 + - - +
24B GLU* 3.5 13.7 - - - +
25B GLN 3.3 0.2 - - - -
26B MSE 1.3 76.6 - - - +
28B ARG* 1.3 63.0 + - + +
30B ALA* 3.4 3.6 + - - +
31B HIS* 3.1 22.0 + - - +
37B ILE* 3.9 14.2 - - + +
40B LEU* 4.8 6.8 - - - +
67B TYR* 2.6 39.9 + - + +
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Residues in contact with ARG 28 (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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21B GLN 4.9 1.8 + - - -
24B GLU* 3.1 33.4 + - - +
25B GLN* 2.6 42.2 + - - +
27B GLU* 1.3 78.2 - - + +
29B GLU* 1.3 56.7 + - - +
31B HIS* 3.3 9.1 + - - +
32B GLU* 2.8 32.4 + - - +
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Residues in contact with GLU 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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25B GLN* 3.0 24.6 + - - +
26B MSE 3.5 7.1 - - - +
27B GLU 3.2 0.2 - - - -
28B ARG* 1.3 75.1 - - - +
30B ALA* 1.3 59.0 + - - +
32B GLU* 3.6 19.5 - - - +
33B GLN* 2.9 45.9 + - + +
35B VAL* 5.6 2.1 - - - +
65B ILE* 3.8 11.6 - - - +
93B GLU* 2.2 31.0 - - - +
97B HIS* 3.7 2.9 + - - -
309B ZN 2.4 27.4 - - - -
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Residues in contact with ALA 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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26B MSE 2.9 17.1 + - - +
27B GLU 3.6 5.6 - - - +
29B GLU* 1.3 75.1 - - - +
31B HIS* 1.3 53.9 + - - +
34B GLN* 2.7 30.1 + - - -
35B VAL* 2.8 39.9 + - + +
37B ILE* 3.8 25.8 - - + -
65B ILE* 4.5 10.3 - - + -
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Residues in contact with HIS 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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27B GLU 3.1 10.8 + - - +
28B ARG* 3.6 10.7 + - - +
29B GLU 3.2 0.2 - - - -
30B ALA* 1.3 76.2 - - - +
32B GLU* 1.3 70.7 + - - +
34B GLN* 2.8 36.6 + - - +
37B ILE* 5.3 3.0 - - + +
303B ZN 2.2 35.7 - - - -
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Residues in contact with GLU 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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28B ARG 2.8 20.7 + - - +
29B GLU* 3.2 23.7 - - - +
31B HIS* 1.3 81.1 - - - +
33B GLN* 1.3 90.1 + - + +
34B GLN* 3.9 3.3 + - - +
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Residues in contact with GLN 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 GLU* 2.9 32.1 + - + +
30B ALA 3.5 0.2 - - - -
32B GLU* 1.3 106.8 - - - +
34B GLN* 1.3 69.2 + - - +
35B VAL* 3.4 17.9 + - + +
89B ARG* 4.0 22.0 + - - +
90B ARG* 5.7 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