Contacts of the helix formed by residues 27 - 38 (chain A) in PDB entry 1IZC
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 ASN 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TYR* 2.6 32.8 + - + +
26A GLY* 1.3 68.6 - - - -
28A LEU* 1.3 60.0 + - - +
29A ARG* 3.2 13.3 + - - +
30A GLN* 2.9 36.9 + - + +
31A ALA* 3.1 19.9 + - - +
97A LEU* 4.3 0.4 - - - -
163A LEU* 6.0 1.1 - - + +
164A PHE* 5.4 2.6 - - - -
176A ASN* 3.8 2.5 + - - +
177A HIS* 3.3 37.2 + - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 3.0 8.3 + - - -
27A ASN* 1.3 70.5 - - - +
29A ARG* 1.3 65.6 + - - +
31A ALA* 4.1 0.4 - - + -
32A LEU* 2.9 38.2 + - + +
43A LEU* 3.7 29.8 - - + -
66A PHE* 5.9 0.2 - - + -
97A LEU* 3.7 18.3 - - + +
99A ILE* 3.9 25.1 - - + -
119A ALA* 3.6 38.1 - - + +
120A GLY* 3.7 16.4 - - - -
177A HIS 3.5 1.6 + - - +
179A CYS* 3.8 13.7 - - + -
181A ILE* 4.8 0.9 - - + -
251A PHE* 4.8 4.5 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.2 9.4 - - - +
28A LEU* 1.3 78.4 - - - +
30A GLN* 1.3 61.6 + - - +
32A LEU* 3.5 4.2 + - - +
33A LYS* 3.2 57.2 + - - +
140A TYR* 3.8 8.1 + - - -
175A ASN 2.8 28.7 + - - -
176A ASN* 3.4 27.3 + - - +
177A HIS 3.3 6.9 + - - +
178A VAL 2.8 27.7 + - - -
179A CYS* 3.4 7.9 - - - -
203A HIS* 3.3 39.7 + - - -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 4.0 10.5 - - + -
27A ASN* 2.9 33.1 + - - +
29A ARG* 1.3 73.9 - - - +
31A ALA* 1.3 60.8 + - - +
33A LYS* 3.1 25.2 + - - +
34A ASP* 2.8 67.0 + - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.6 34.8 + - + -
27A ASN 3.1 14.2 + - - +
28A LEU* 3.1 7.8 + - - +
30A GLN* 1.3 76.3 - - - +
32A LEU* 1.3 58.3 + - - +
34A ASP* 3.3 2.4 + - - +
35A ALA* 3.0 28.1 + - - +
41A LYS* 5.2 0.3 - - - +
43A LEU* 3.9 20.0 - - + +
97A LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 2.9 39.3 + - + +
29A ARG* 3.8 4.3 - - - +
31A ALA* 1.3 75.0 - - - +
33A LYS* 1.3 64.8 + - - +
35A ALA* 3.2 5.2 + - - +
36A MET* 3.0 37.2 + - + +
43A LEU* 4.6 4.5 - - + -
179A CYS* 4.0 13.9 - - + -
203A HIS* 3.6 20.9 - - + +
249A PRO* 4.3 11.0 - - + -
251A PHE* 3.6 38.8 - - + -
269A ARG* 4.5 10.2 - - + +
270A ALA* 4.5 11.9 - - + -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.2 45.2 + - - +
30A GLN* 3.1 31.9 + - - +
32A LEU* 1.3 76.8 - - - +
34A ASP* 1.3 59.8 + - - +
36A MET* 3.2 22.3 + - + +
37A ALA* 3.0 27.9 + - - +
203A HIS* 6.2 0.2 - - - -
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 2.6 40.5 + - - +
30A GLN* 2.8 39.6 + - - +
31A ALA 3.7 1.6 - - - +
33A LYS* 1.3 79.3 - - - +
35A ALA* 1.3 56.9 + - - +
37A ALA* 3.3 6.8 + - - +
38A ASP* 2.9 30.1 + - - +
41A LYS* 4.2 20.2 + - + +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 3.0 16.8 + - - +
32A LEU* 3.7 4.7 - - - +
34A ASP* 1.3 73.9 - - - +
36A MET* 1.3 66.3 + - - +
38A ASP 3.1 24.3 - - - -
39A PRO* 3.1 10.2 - - - +
41A LYS* 3.6 25.5 - - - +
42A THR* 4.0 7.2 - - - -
43A LEU* 3.8 12.3 - - + -
269A ARG* 3.4 17.9 - - + -
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.0 34.5 + - + +
33A LYS* 3.3 32.1 - - + +
35A ALA* 1.3 78.7 - - - +
37A ALA* 1.3 62.2 + - - +
38A ASP 3.5 0.2 + - - -
39A PRO* 4.0 9.7 - - - +
203A HIS 5.6 0.2 - - - +
247A GLY* 3.9 15.9 - - - +
249A PRO* 3.8 38.6 - - + -
269A ARG* 4.1 13.4 + - + +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS 3.0 15.9 + - - +
34A ASP* 3.7 9.0 - - - +
36A MET* 1.3 78.6 - - - +
38A ASP* 1.3 59.7 + - + +
39A PRO* 3.9 4.2 - - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP 2.9 10.7 + - - +
35A ALA 3.1 7.4 - - - +
37A ALA* 1.3 80.3 - - + +
39A PRO* 1.3 60.1 - - - +
40A SER* 2.8 31.2 + - - -
41A LYS* 2.8 46.3 + - + +
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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