Contacts of the helix formed by residues 34 - 43 (chain A) in PDB entry 2ICP
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 ALA 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA* 4.1 0.4 - - - -
33A ILE* 1.3 76.9 - - - +
35A PRO* 1.3 75.1 - - + +
36A SER* 4.2 11.2 - - - +
37A THR* 3.0 10.3 + - - +
38A ALA* 3.0 20.1 + - - +
5001A MG 3.2 15.9 - - - -
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Residues in contact with PRO 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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24A LEU* 3.9 15.6 - - + +
25A ARG* 5.0 16.4 - - + +
28A ALA* 4.0 15.7 - - + -
33A ILE 3.8 2.4 - - - +
34A ALA* 1.3 87.8 - - + +
36A SER* 1.3 56.5 + - - +
38A ALA* 3.2 4.0 + - - +
39A SER* 2.9 32.1 + - - -
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Residues in contact with SER 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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34A ALA* 4.2 9.9 - - - +
35A PRO* 1.3 80.2 - - - +
37A THR* 1.3 59.5 + - - +
39A SER* 3.5 7.8 + - - -
40A ARG* 3.0 56.6 + - - +
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Residues in contact with THR 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 ILE* 4.2 7.0 - - + -
34A ALA* 3.0 15.3 + - - +
36A SER* 1.3 75.9 + - - +
38A ALA* 1.3 66.1 + - - +
40A ARG* 3.1 26.6 + - - +
41A LEU* 3.0 21.7 + - - +
46A ALA* 5.0 4.0 - - + +
52A MSE 3.6 25.1 - - + -
5001A MG 3.1 24.9 - - - -
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Residues in contact with ALA 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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24A LEU* 3.4 20.0 - - + -
27A PHE* 4.1 10.1 - - + -
28A ALA* 3.7 24.5 - - + -
33A ILE* 3.7 15.7 - - + +
34A ALA 3.0 6.0 + - - +
35A PRO 3.4 9.2 - - - +
37A THR* 1.3 77.1 - - - +
39A SER* 1.3 56.4 + - - +
41A LEU* 3.1 6.8 + - - +
42A LEU* 2.9 31.9 + - - +
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Residues in contact with SER 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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24A LEU* 3.9 19.4 - - - +
35A PRO 2.9 17.6 + - - -
36A SER* 3.7 8.4 - - - -
38A ALA* 1.3 77.0 - - - +
40A ARG* 1.3 57.4 + - - +
42A LEU* 3.3 5.2 + - - +
43A THR* 2.9 39.8 + - - +
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Residues in contact with ARG 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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36A SER* 3.0 46.4 + - - +
37A THR* 3.1 32.3 + - - +
38A ALA 3.3 0.2 - - - -
39A SER* 1.3 77.1 - - - +
41A LEU* 1.3 59.6 + - - +
43A THR* 3.7 6.1 - - - -
44A GLY 3.3 1.4 + - - -
45A LYS* 2.9 44.6 + - + -
46A ALA* 2.9 25.2 + - + +
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Residues in contact with LEU 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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10A GLY* 3.8 10.4 + - - -
13A ILE* 4.0 24.0 - - + -
27A PHE* 4.3 19.5 - - + -
31A MSE 4.6 5.6 - - + -
33A ILE* 4.9 1.1 - - + -
37A THR 3.0 12.9 + - - +
38A ALA 3.3 7.9 - - - +
40A ARG* 1.3 78.0 - - - +
42A LEU* 1.3 63.0 + - - +
44A GLY* 3.2 12.3 + - - -
46A ALA* 3.7 22.9 - - + +
47A ALA 4.3 2.2 - - - +
48A LEU* 4.2 28.0 - - + -
52A MSE 3.5 34.5 - - + -
56A LEU* 4.7 4.5 - - + -
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Residues in contact with LEU 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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10A GLY* 3.3 31.6 - - - +
11A ASP* 4.2 2.6 + - - +
13A ILE* 3.7 22.2 - - + -
14A GLN* 3.5 28.3 - - + +
17A LEU* 4.4 8.1 - - + -
24A LEU* 3.7 31.0 - - + -
27A PHE* 3.4 25.1 - - + -
38A ALA 2.9 16.7 + - - +
39A SER* 3.8 5.2 - - - +
41A LEU* 1.3 81.9 - - + +
43A THR* 1.3 61.6 + - + +
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Residues in contact with THR 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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10A GLY* 5.6 0.2 - - - -
39A SER* 2.9 24.9 + - - +
40A ARG* 3.4 4.5 + - - -
42A LEU* 1.3 79.0 - - + +
44A GLY* 1.3 59.0 + - - +
45A LYS* 3.2 45.1 + - + +
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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