Contacts of the helix formed by residues 26 - 34 (chain A) in PDB entry 1IW1
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 SER 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS 3.4 6.6 + - - -
23A ALA 3.1 17.9 + - - -
24A GLU 3.4 0.2 - - - -
25A HIS* 1.3 78.5 - - - +
27A THR* 1.3 66.8 + - - +
28A PHE 4.4 0.9 - - - -
29A MET* 3.3 12.6 + - - +
30A SER* 2.9 17.7 + - - -
205A HIS* 3.8 20.2 - - - -
208A PHE* 3.1 32.9 - - - +
209A ALA* 5.3 0.7 - - - -
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Residues in contact with THR 27 (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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25A HIS 3.4 3.2 + - - -
26A SER* 1.3 70.5 - - - +
28A PHE* 1.3 58.7 + - - +
30A SER* 3.7 5.1 - - - -
31A ASP* 2.9 49.2 + - - +
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Residues in contact with PHE 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 SER* 3.2 1.2 - - - -
27A THR* 1.3 78.9 - - - +
29A MET* 1.3 62.4 + - - +
31A ASP* 4.7 3.4 - - - -
32A LEU* 2.9 40.6 + - + +
37A LEU* 3.6 24.8 - - + +
41A GLU* 3.7 37.5 - - + -
45A LEU* 4.2 13.0 - - + -
208A PHE* 3.4 41.1 - + + +
211A LEU* 3.8 43.5 - - + -
212A GLY* 3.9 16.9 - - - +
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Residues in contact with MET 29 (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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24A GLU 3.9 9.0 - - - +
26A SER* 3.2 19.7 + - - +
28A PHE* 1.3 79.1 - - + +
30A SER* 1.3 65.6 + - - +
32A LEU* 3.2 13.1 + - + -
33A LEU* 2.9 50.5 + - + +
45A LEU* 3.9 19.7 - - + -
143A ILE* 4.1 20.2 - - + -
208A PHE* 3.4 37.7 - - + -
901A HEM 3.6 24.5 - - + -
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Residues in contact with SER 30 (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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24A GLU 4.6 3.7 + - - -
25A HIS* 4.4 12.6 - - - -
26A SER 2.9 17.8 + - - -
27A THR* 3.7 7.2 - - - -
29A MET* 1.3 78.9 - - - +
31A ASP* 1.3 64.8 + - - +
33A LEU* 3.4 4.9 + - - +
34A LYS* 3.1 48.2 + - - +
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Residues in contact with ASP 31 (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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27A THR* 2.9 37.4 + - - +
28A PHE* 3.8 4.6 - - - +
30A SER* 1.3 78.5 + - - +
32A LEU* 1.3 62.9 + - - +
34A LYS* 3.5 7.1 + - - +
35A GLY 3.4 3.3 + - - -
36A ARG* 2.9 63.0 + - + +
37A LEU* 3.7 23.6 + - + +
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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
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28A PHE* 2.9 25.3 + - + +
29A MET* 3.2 29.6 + - + +
31A ASP* 1.3 77.5 - - - +
33A LEU* 1.3 62.3 + - + +
35A GLY 3.4 1.6 + - - -
37A LEU* 3.7 17.7 - - + +
38A GLY 4.0 15.0 - - - +
41A GLU* 4.5 1.3 - - + -
42A PHE* 4.1 16.6 - - + +
45A LEU* 4.3 15.3 - - + -
143A ILE* 5.1 2.5 - - + -
147A MET* 3.9 23.0 - - + +
150A HIS* 4.6 0.7 - - - -
151A TYR* 2.7 49.8 + - + -
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Residues in contact with LEU 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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24A GLU 5.6 0.9 - - - +
29A MET* 2.9 39.8 + - + +
30A SER* 4.1 4.0 - - - +
32A LEU* 1.3 76.4 - - + +
34A LYS* 1.3 56.4 + - - +
35A GLY 3.2 0.9 - - - -
142A VAL* 4.9 2.7 - - + -
143A ILE* 3.9 34.5 - - + +
146A MET* 3.7 26.8 - - + +
147A MET* 4.0 9.4 - - + -
150A HIS* 3.0 22.4 + - - -
901A HEM 3.8 36.8 - - + -
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Residues in contact with LYS 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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30A SER* 3.1 37.0 + - - +
31A ASP* 3.6 9.2 - - - +
32A LEU 3.3 0.2 - - - -
33A LEU* 1.3 76.6 - - - +
35A GLY* 1.3 58.0 + - - +
36A ARG* 3.2 55.1 - - + +
150A HIS* 3.5 15.0 - - - -
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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