Contacts of the helix formed by residues 25 - 34 (chain F) in PDB entry 2ZHX
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 LEU 25 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ARG* 3.8 47.6 - - + +
171E ASP* 4.7 15.3 - - + +
174E THR* 6.0 4.9 - - + -
23F LEU* 5.5 4.7 - - + -
24F MET* 1.3 78.7 - - - +
26F PRO* 1.3 78.8 - - + +
27F GLU* 3.1 8.5 - - + +
28F GLU* 2.9 21.8 + - + +
29F VAL* 3.4 9.3 + - - +
40F ASP* 3.2 20.2 - - - +
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Residues in contact with PRO 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 1.3 87.4 - - + +
27F GLU* 1.3 64.4 + - - +
28F GLU 2.8 1.6 + - - -
29F VAL* 3.2 1.0 + - + +
30F GLU* 3.0 27.7 + - - +
36F LYS* 4.0 18.2 - - + -
37F PRO* 3.4 45.4 - - + +
38F GLU 4.8 3.8 - - - +
39F SER* 4.6 3.1 - - - +
40F ASP* 3.4 21.9 - - - +
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E ARG* 4.5 17.9 - - - +
25F LEU* 4.7 7.6 - - + -
26F PRO* 1.3 82.0 - - - +
28F GLU* 1.3 66.7 + - + +
30F GLU* 4.1 11.5 - - - +
31F GLU* 4.0 15.6 + - - +
36F LYS* 5.1 2.3 - - - +
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E GLY* 4.3 3.3 - - - -
170E ARG* 3.0 50.7 + - + +
171E ASP 4.8 0.5 + - - -
190E PRO* 4.7 10.9 - - - +
195E LEU* 5.3 1.0 - - - +
196E SER* 5.6 2.3 - - - -
24F MET* 3.3 41.5 - - + +
25F LEU* 2.9 31.8 + - + +
27F GLU* 1.3 79.8 - - + +
29F VAL* 1.3 66.3 + - - +
31F GLU* 3.8 16.2 + - - +
32F VAL* 4.0 10.4 - - - +
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU* 4.3 17.0 - - + -
24F MET* 4.3 13.0 - - + -
25F LEU 3.8 12.1 - - - +
26F PRO* 3.2 4.2 + - + +
28F GLU* 1.3 74.6 - - - +
30F GLU* 1.3 68.3 + - - +
31F GLU 3.2 0.2 - - - -
32F VAL* 2.9 15.6 + - - +
33F ILE* 3.0 17.7 + - + +
37F PRO* 4.5 6.3 - - + -
41F ILE* 4.1 26.7 - - + -
43F VAL* 5.0 0.2 - - + -
58F LEU* 3.7 15.9 - - + -
68F TRP* 3.4 34.8 - - + -
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Residues in contact with GLU 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PRO 3.0 15.8 + - - +
27F GLU* 4.1 10.2 - - - +
29F VAL* 1.3 77.0 - - - +
31F GLU* 1.3 60.9 + - - +
34F GLY* 2.8 33.4 + - - -
35F ASN 4.1 14.6 - - - +
36F LYS* 3.4 49.7 + - + +
37F PRO* 4.5 1.2 - - - +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E PRO* 6.1 0.2 - - - +
199E ARG* 3.4 49.3 + - - +
27F GLU 4.0 9.4 + - - +
28F GLU* 3.8 13.2 + - - +
29F VAL 3.1 1.0 + - - -
30F GLU* 1.3 81.0 - - - +
32F VAL* 1.3 62.0 + - + +
34F GLY* 4.6 1.9 + - - -
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU* 3.4 44.9 - - + +
196E SER* 5.1 1.3 - - - -
199E ARG* 3.6 31.6 - - + +
28F GLU 4.0 14.1 - - - +
29F VAL 2.9 5.4 + - - +
31F GLU* 1.3 78.2 - - + +
33F ILE* 1.3 61.5 + - + +
34F GLY 3.5 0.2 - - - -
79F ASN* 3.7 25.5 + - - +
81F ILE* 3.3 15.2 - - + +
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Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU* 4.5 9.6 - - + -
29F VAL* 3.0 15.9 + - + +
32F VAL* 1.3 80.8 - - - +
34F GLY* 1.3 60.0 + - - +
35F ASN* 4.3 10.0 - - - +
58F LEU* 3.6 30.7 - - + -
68F TRP* 3.8 21.5 - - + -
69F ALA* 4.1 7.4 - - + -
71F VAL* 4.0 20.0 - - + -
81F ILE* 3.7 25.3 - - + +
83F MET* 3.7 28.7 - - - -
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Residues in contact with GLY 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLU* 2.8 18.0 + - - -
31F GLU 4.5 1.5 - - - -
32F VAL 3.5 1.2 - - - -
33F ILE* 1.3 78.2 - - - +
35F ASN* 1.3 74.1 + - - +
36F LYS 4.3 0.7 - - - -
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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