Contacts of the helix formed by residues 25 - 38 (chain B) in PDB entry 2QJ3
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 GLY 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU 3.7 1.2 + - - -
24B PRO* 1.3 70.4 - - - +
26B ALA* 1.3 59.2 + - - +
27B ALA* 3.3 3.7 - - - +
28B ASP* 3.2 27.0 - - - +
29B GLN* 3.5 28.6 + - - +
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Residues in contact with ALA 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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20B TRP 3.4 25.4 - - - +
21B LEU* 4.4 4.9 - - - +
23B LEU* 3.7 15.7 + - + +
24B PRO 2.9 5.4 + - - +
25B GLY* 1.3 78.1 - - - +
27B ALA* 1.3 59.9 + - - +
28B ASP 3.3 0.2 - - - -
29B GLN* 3.9 3.9 - - - +
30B ILE* 3.1 34.3 + - - +
69B LEU* 3.7 25.7 - - + +
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Residues in contact with ALA 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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21B LEU* 4.4 21.4 + - + +
23B LEU 4.7 1.1 + - - +
25B GLY* 3.3 2.2 - - - +
26B ALA* 1.3 80.9 - - - +
28B ASP* 1.3 63.2 + - - +
30B ILE* 3.5 3.4 + - - +
31B ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 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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25B GLY* 3.2 27.3 + - - +
26B ALA 3.3 0.2 - - - -
27B ALA* 1.3 80.8 - - - +
29B GLN* 1.3 60.8 + - + +
31B ALA* 3.7 6.6 + - - +
32B ALA* 3.1 26.7 + - - +
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Residues in contact with GLN 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 GLY 3.5 18.8 + - - +
26B ALA* 4.1 6.0 - - - +
27B ALA 3.4 0.4 - - - -
28B ASP* 1.3 76.9 - - + +
30B ILE* 1.3 59.1 + - - +
32B ALA* 3.3 5.5 + - + +
33B TRP* 3.1 61.6 + - + +
69B LEU* 4.2 8.6 - - + +
72B GLN* 2.7 42.7 + - - -
76B ARG* 5.3 2.8 - - - +
106B ALA* 4.8 2.6 - - - +
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Residues in contact with ILE 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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17B LEU* 3.9 22.7 - - + -
21B LEU* 3.5 26.5 - - + -
26B ALA 3.1 15.0 + - - +
27B ALA 4.0 3.6 - - - +
29B GLN* 1.3 76.3 - - - +
31B ALA* 1.3 61.1 + - - +
33B TRP* 3.6 23.8 + - + +
34B SER* 2.7 33.8 + - - +
41B LEU* 4.1 9.1 - - + +
42B ALA* 3.9 35.4 - - + +
65B ALA* 5.3 2.9 - - + -
69B LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.9 + - - +
28B ASP* 3.7 8.5 - - - +
30B ILE* 1.3 77.0 - - - +
32B ALA* 1.3 63.3 + - - +
34B SER* 3.2 7.5 + - - -
35B LYS* 3.1 25.2 + - - +
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Residues in contact with ALA 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 ASP 3.1 16.0 + - - +
29B GLN* 3.5 9.4 - - - +
30B ILE 3.2 0.2 - - - -
31B ALA* 1.3 80.0 - - - +
33B TRP* 1.3 68.5 + - + +
35B LYS* 3.5 6.1 + - - +
36B ALA* 3.3 21.1 + - - +
107B ASP* 6.3 0.7 - - + -
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Residues in contact with TRP 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 GLN* 3.1 45.6 + - + +
30B ILE* 4.1 20.0 - - + +
32B ALA* 1.3 79.6 - - + +
34B SER* 1.3 63.1 + - - +
36B ALA* 3.6 6.5 + - + +
37B ALA* 3.1 27.2 + - - +
41B LEU* 4.1 9.0 - - + +
65B ALA* 3.9 27.1 - - + -
68B LEU* 4.7 12.3 - - + -
69B LEU* 4.1 24.0 - - + -
72B GLN* 4.8 1.6 - - - -
106B ALA* 4.2 15.5 - - + -
107B ASP* 3.4 37.6 - - + +
110B VAL* 3.7 39.5 - - + +
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Residues in contact with SER 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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30B ILE* 2.7 23.7 + - - +
31B ALA* 3.2 8.4 + - - -
33B TRP* 1.3 74.9 - - - +
35B LYS* 1.3 58.7 - - - +
37B ALA* 3.2 1.0 + - - -
38B ASP* 2.9 28.4 + - - -
39B LEU 2.8 33.1 + - - +
40B ASP* 4.0 9.1 - - - -
41B LEU* 3.2 20.7 + - - +
42B ALA 4.5 0.5 + - - -
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Residues in contact with LYS 35 (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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31B ALA 3.1 15.6 + - - +
32B ALA* 3.7 6.7 - - - +
34B SER* 1.3 77.3 - - - +
36B ALA* 1.3 59.8 + - - +
37B ALA 3.5 0.2 + - - -
38B ASP* 3.9 12.5 - - - +
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Residues in contact with ALA 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 ALA 3.3 13.0 + - - +
33B TRP* 3.9 7.0 - - - +
34B SER 3.3 0.6 - - - -
35B LYS* 1.3 78.7 - - - +
37B ALA* 1.3 59.5 + - + +
38B ASP* 3.6 2.7 + - - +
111B ALA* 5.2 15.3 - - + -
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Residues in contact with ALA 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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33B TRP 3.1 18.9 + - - +
34B SER 3.2 1.5 + - - +
36B ALA* 1.3 79.6 - - + +
38B ASP* 1.3 71.3 + - - +
39B LEU* 3.3 18.2 + - + +
41B LEU* 5.6 2.9 - - + -
61B PRO* 5.8 0.7 - - + -
110B VAL* 5.2 3.4 - - + +
111B ALA* 5.6 4.5 - - - +
114B ALA* 3.9 29.0 - - + +
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Residues in contact with ASP 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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34B SER 2.9 8.6 + - - -
35B LYS 3.9 10.6 + - - +
36B ALA 3.6 2.6 - - - +
37B ALA* 1.3 79.5 - - - +
39B LEU* 1.3 65.4 + - - +
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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