Contacts of the helix formed by residues 38 - 45 (chain A) in PDB entry 1ICZ
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 LYS 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 5.6 0.9 - - - +
34A GLU* 2.7 45.1 + - + +
35A PHE* 3.7 19.1 - - - +
36A MET 4.6 0.7 - - - +
37A ASP* 1.3 71.4 + - - +
39A LYS* 1.3 62.2 + - - +
40A LEU 3.3 0.2 - - - -
41A PRO* 3.3 21.7 - - - +
42A GLY 3.8 1.0 + - - -
207A MET* 3.6 30.9 - - - +
221A LEU* 5.3 1.8 - - + -
241A TRP* 3.0 23.9 + - + -
245A THR* 3.8 6.2 + - - +
246A GLU* 2.8 47.8 + - + +
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Residues in contact with LYS 39 (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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36A MET 3.9 4.2 + - - +
37A ASP 2.9 5.3 + - - +
38A LYS* 1.3 78.8 - - - +
40A LEU* 1.3 62.0 + - - +
42A GLY* 3.5 2.3 + - - -
43A ILE* 3.1 48.4 + - + +
168A MET* 5.6 6.7 - - + -
199A ILE* 5.1 2.2 - - - +
202A ASP 4.1 3.8 + - - -
203A ASP* 2.7 51.4 + - - +
204A LEU* 4.6 0.6 - - - +
221A LEU* 3.2 51.4 + - + +
223A THR* 4.0 12.3 - - + +
241A TRP* 3.3 28.4 - - + +
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Residues in contact with LEU 40 (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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37A ASP* 2.8 19.8 + - - +
39A LYS* 1.3 72.6 - - - +
41A PRO* 1.4 57.9 - - + +
42A GLY 3.2 0.2 + - - -
43A ILE* 4.2 4.7 - - - -
44A ILE* 2.8 51.1 + - + +
69A GLN* 4.1 2.7 - - + +
72A SER* 3.9 25.8 - - - +
137A ASP* 5.5 0.2 - - - +
139A ILE* 4.5 21.5 - - + -
141A MET* 3.5 31.2 - - + -
166A ALA* 4.4 9.6 - - + -
168A MET* 4.1 7.5 - - + +
224A MET* 3.7 27.4 - - + -
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Residues in contact with PRO 41 (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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20A ARG* 3.8 15.3 - - - +
37A ASP* 3.2 16.6 - - - +
38A LYS* 3.3 20.2 - - - +
40A LEU* 1.4 84.0 - - + +
42A GLY* 1.3 61.7 + - - +
44A ILE* 3.9 8.7 - - + -
45A GLY* 3.1 17.8 + - - -
72A SER* 3.6 32.8 - - - +
76A ALA* 3.6 19.7 - - + +
246A GLU* 6.0 5.8 - - - +
247A THR* 5.8 2.7 - - - +
248A CYS* 4.8 12.6 - - + +
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Residues in contact with GLY 42 (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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38A LYS 3.8 2.2 + - - -
39A LYS 3.5 5.3 + - - -
40A LEU 3.2 0.6 - - - -
41A PRO* 1.3 84.8 - - - +
43A ILE* 1.3 62.9 + - - +
45A GLY 3.1 10.0 + - - -
46A ARG* 3.2 14.3 + - - +
240A LEU 4.5 2.2 - - - +
241A TRP* 4.0 22.0 - - - -
244A LEU 5.5 4.0 - - - -
247A THR* 5.7 3.7 + - - -
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Residues in contact with ILE 43 (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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39A LYS* 3.1 27.7 + - + +
40A LEU* 3.7 5.8 - - - +
42A GLY* 1.3 71.0 - - - -
44A ILE* 1.3 59.5 + - + +
46A ARG* 3.0 22.7 + - - +
47A ILE* 3.0 20.7 + - - +
168A MET* 6.2 0.2 - - - -
203A ASP* 3.9 12.1 - - - +
223A THR* 3.8 17.0 - - + -
224A MET* 3.6 44.4 - - + -
239A LEU* 3.9 20.1 - - + +
240A LEU 4.3 12.1 - - - +
241A TRP* 3.7 22.0 - - + -
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Residues in contact with ILE 44 (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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40A LEU* 2.8 45.4 + - + +
41A PRO* 3.8 5.8 - - + +
43A ILE* 1.3 73.9 - - + +
45A GLY* 1.3 57.0 + - - +
46A ARG 3.3 0.7 - - - -
47A ILE* 3.1 29.5 - - + +
56A ILE* 4.5 7.4 - - + -
72A SER 3.5 25.4 - - - +
73A LYS* 5.1 2.5 - - + -
76A ALA* 4.8 0.9 - - + -
77A GLN* 2.9 49.2 + - + +
137A ASP* 4.3 15.5 - - - +
139A ILE* 5.8 2.5 - - + -
162A LEU* 4.2 13.7 - - + -
224A MET* 4.4 9.6 - - + -
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Residues in contact with GLY 45 (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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41A PRO 3.1 11.2 + - - -
42A GLY 3.1 11.9 + - - -
44A ILE* 1.3 74.1 - - - +
46A ARG* 1.3 59.1 + - - +
47A ILE 4.8 1.8 - - - -
76A ALA 3.2 30.6 - - - +
77A GLN* 4.1 3.6 - - - -
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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