Contacts of the helix formed by residues 40 - 51 (chain B) in PDB entry 4ZCU
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 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLN* 3.0 28.7 + - - +
58A ASP* 3.2 29.0 - - - +
34B ASN* 5.2 5.2 + - - -
36B ASP* 5.5 1.9 - - - +
38B VAL* 4.0 5.0 - - + +
39B VAL* 1.3 77.1 - - - +
41B ILE* 1.3 65.5 + - - +
42B GLY 3.4 0.3 + - - -
43B GLU* 2.9 49.7 + - - +
44B LEU* 3.0 18.0 + - - +
64B PHE* 3.5 9.2 - - - -
73B GLY 4.7 2.2 - - - +
74B LYS* 5.2 3.1 - - + +
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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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41A ILE* 4.5 7.0 - - + -
45A GLN* 4.2 17.9 - - - +
57A GLN* 3.8 26.9 - - + +
61A GLU* 3.5 24.9 - - + +
40B ASP* 1.3 72.4 - - - +
42B GLY* 1.3 60.5 + - - +
44B LEU* 3.2 11.2 + - + +
45B GLN* 2.9 54.3 + - + +
60B GLU* 4.9 3.4 - - + +
61B GLU* 3.8 23.8 - - + +
64B PHE* 3.4 25.6 - - + -
73B GLY 5.2 0.6 + - - -
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Residues in contact with GLY 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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57A GLN* 3.3 16.4 + - - -
40B ASP* 3.3 0.6 - - - -
41B ILE* 1.3 85.8 - - - +
43B GLU* 1.3 56.6 + - - +
45B GLN* 3.3 10.4 + - - +
46B GLU* 2.9 37.4 + - - +
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Residues in contact with GLU 43 (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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31B LEU* 3.6 20.0 - - - +
32B ASP* 4.0 0.2 - - - -
33B ARG* 3.8 21.9 - - + +
34B ASN* 2.7 29.1 + - - +
38B VAL 3.0 9.2 - - - +
39B VAL* 3.2 7.4 - - + +
40B ASP* 2.9 37.6 + - - +
42B GLY* 1.3 74.7 - - - +
44B LEU* 1.3 58.8 + - - +
46B GLU* 5.1 2.0 - - - -
47B GLY* 2.9 27.8 + - - +
1001B CA 2.4 30.6 - - - -
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Residues in contact with LEU 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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31B LEU* 3.8 24.5 - - + -
39B VAL* 3.8 11.4 - - + +
40B ASP 3.0 12.9 + - - +
41B ILE* 3.5 15.7 - - + +
43B GLU* 1.3 75.4 - - - +
45B GLN* 1.3 60.5 + - - +
48B LEU* 2.9 57.1 + - + +
60B GLU* 3.7 31.2 - - + +
63B ILE* 4.7 14.8 - - + -
64B PHE* 3.8 22.2 - - + -
75B LEU* 5.1 4.3 - - + -
80B PHE* 5.2 5.8 - - + -
153B PHE* 6.4 0.2 - - + -
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Residues in contact with GLN 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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41A ILE* 4.1 20.0 - - - +
45A GLN* 5.5 7.2 + - - +
41B ILE* 2.9 43.0 + - + +
42B GLY* 3.7 9.1 - - - +
44B LEU* 1.3 77.4 - - - +
46B GLU* 1.3 69.8 + - + +
48B LEU* 3.3 2.6 + - - +
49B ARG* 2.9 28.3 + - - +
57B GLN* 4.8 7.1 + - - +
60B GLU* 3.3 32.9 + - - +
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Residues in contact with GLU 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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33B ARG* 6.0 6.5 - - - -
42B GLY* 2.9 20.2 + - - +
43B GLU* 4.8 1.8 - - - +
45B GLN* 1.3 87.1 - - + +
47B GLY* 1.3 57.5 + - - +
49B ARG* 3.9 25.6 + - - +
50B ASN* 2.9 47.8 + - - +
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Residues in contact with GLY 47 (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 ALA 5.6 1.8 - - - -
31B LEU* 3.8 19.5 - - - -
43B GLU 2.9 22.5 + - - -
46B GLU* 1.3 77.3 - - - +
48B LEU* 1.3 60.8 + - - +
50B ASN* 3.2 5.6 + - - +
51B LEU* 3.0 29.5 + - - +
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Residues in contact with LEU 48 (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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31B LEU* 4.1 10.0 - - + +
44B LEU* 2.9 46.3 + - + +
45B GLN 3.8 2.9 - - - +
47B GLY* 1.3 76.1 - - - +
49B ARG* 1.3 59.0 + - - +
51B LEU* 3.5 5.2 + - + -
52B GLY 3.2 3.6 + - - -
53B ILE* 2.9 54.8 + - + +
55B LEU* 3.9 17.5 - - + -
60B GLU* 3.8 29.8 - - + +
63B ILE* 5.2 4.5 - - + -
153B PHE* 4.0 30.1 - - + -
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Residues in contact with ARG 49 (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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45B GLN 2.9 16.1 + - - +
46B GLU* 3.9 23.3 + - - +
48B LEU* 1.3 77.1 - - - +
50B ASN* 1.3 72.9 + - - +
52B GLY* 3.3 12.5 + - - -
53B ILE 4.6 5.4 - - - +
54B PRO* 5.8 4.2 - - - +
55B LEU 5.0 11.9 + - - +
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Residues in contact with ASN 50 (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 ARG* 5.9 3.4 - - - +
46B GLU* 2.9 32.6 + - - +
47B GLY* 3.8 4.9 - - - +
49B ARG* 1.3 86.5 - - - +
51B LEU* 1.3 64.2 + - + +
52B GLY 3.3 0.4 + - - -
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Residues in contact with LEU 51 (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 LEU* 4.7 14.6 - - + -
30B ALA* 4.4 23.1 - - + +
31B LEU* 3.8 22.0 - - + -
47B GLY* 3.0 21.7 + - - +
48B LEU* 4.0 3.1 - - + +
49B ARG 3.2 0.2 - - - -
50B ASN* 1.3 82.0 - - + +
52B GLY* 1.3 61.2 + - - +
53B ILE* 3.5 25.4 - - + +
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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