Contacts of the helix formed by residues 41 - 53 (chain A) in PDB entry 1X3C
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 ILE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.1 11.3 - - - +
40A THR* 1.3 85.0 - - + +
42A GLN* 1.3 68.1 + - - +
43A GLN* 3.8 18.4 - - + +
44A ASN* 3.4 29.7 + - + +
45A LEU* 3.2 16.3 + - - +
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Residues in contact with GLN 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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28A TYR* 3.5 39.9 - - + +
40A THR 3.7 3.2 + - - -
41A ILE* 1.3 74.8 - - + +
43A GLN* 1.3 94.0 + - - +
45A LEU* 3.2 23.2 + - + +
46A ILE* 3.3 26.8 + - + +
57A LEU* 6.0 2.9 - - + +
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Residues in contact with GLN 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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41A ILE* 3.1 13.2 - - + +
42A GLN* 1.3 85.5 + - - +
44A ASN* 1.3 63.5 + - - +
45A LEU 2.7 4.9 + - - -
46A ILE* 2.6 43.0 + - - +
47A LEU* 2.9 38.4 - - + +
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Residues in contact with ASN 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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39A PHE* 3.1 37.8 - - + -
41A ILE* 3.4 36.4 + - + +
43A GLN* 1.3 86.8 - - - +
45A LEU* 1.3 58.0 + - - +
46A ILE 3.4 0.2 - - - -
47A LEU* 3.2 20.1 - - - +
48A HIS 3.9 4.3 + - - -
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Residues in contact with LEU 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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28A TYR* 3.3 48.0 - - + -
29A ARG 5.0 1.1 - - - +
30A CYS* 4.8 9.2 - - + +
38A ALA* 5.0 0.7 - - - -
39A PHE* 3.8 27.4 - - + +
41A ILE 3.2 11.1 + - - +
42A GLN* 3.2 14.8 - - + +
43A GLN 2.7 1.6 + - - -
44A ASN* 1.3 79.9 - - - +
46A ILE* 1.3 64.0 + - - +
48A HIS* 3.3 18.3 - - + +
49A TYR* 3.6 21.7 - - + -
57A LEU* 3.8 24.7 - - + -
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Residues in contact with ILE 46 (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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42A GLN* 3.3 43.5 + - - +
43A GLN* 2.6 29.2 + - - +
45A LEU* 1.3 67.9 - - - +
47A LEU* 1.3 84.1 + - + +
49A TYR* 2.9 21.8 + - - +
50A GLN* 3.4 19.1 + - + +
56A ASP* 5.6 4.0 - - + +
57A LEU* 3.3 28.5 - - + +
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Residues in contact with LEU 47 (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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43A GLN* 2.9 44.9 - - + +
44A ASN* 3.2 25.8 - - - +
46A ILE* 1.3 88.1 - - + +
48A HIS* 1.3 49.2 + - - +
50A GLN* 2.5 39.4 + - - +
51A ALA* 2.5 24.5 + - + +
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Residues in contact with HIS 48 (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 CYS* 3.3 6.2 - - + +
35A CYS* 4.0 1.6 - - - -
37A ALA* 3.0 30.4 - - + +
39A PHE* 3.1 41.0 - + + -
44A ASN 3.9 3.4 + - - +
45A LEU* 3.3 14.3 + - + +
46A ILE 3.1 0.2 + - - -
47A LEU* 1.3 78.1 - - - +
49A TYR* 1.3 79.6 + + - +
51A ALA* 4.4 5.8 - - - -
52A VAL* 2.8 55.1 + - + +
53A HIS* 4.0 0.2 + - - -
201A ZN 2.3 33.4 - - - -
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Residues in contact with TYR 49 (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 CYS* 3.1 16.8 - - - -
31A VAL* 3.1 42.2 + - + +
32A HIS* 3.1 35.7 - + - -
45A LEU* 3.6 22.4 - - + -
46A ILE 2.9 8.9 + - - +
48A HIS* 1.3 90.3 - + - +
50A GLN* 1.3 52.0 + - - +
53A HIS* 3.0 15.8 + + - +
54A LYS 2.8 10.6 + - - -
55A SER* 2.8 46.1 + - - +
56A ASP 4.9 0.7 - - - -
57A LEU* 4.0 32.3 - - + +
58A PRO* 4.8 12.2 - - + +
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Residues in contact with GLN 50 (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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46A ILE* 4.1 23.7 - - + +
47A LEU* 2.5 23.5 + - - +
49A TYR* 1.3 73.4 - - - +
51A ALA* 1.3 55.8 - - - -
54A LYS* 3.2 27.8 - - - +
55A SER* 3.0 28.0 - - - +
56A ASP* 2.9 24.3 - - - +
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Residues in contact with ALA 51 (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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47A LEU* 2.5 23.0 + - + +
48A HIS* 4.0 6.5 - - - +
50A GLN* 1.3 76.5 - - - +
52A VAL* 1.3 62.6 + - + +
54A LYS* 4.0 10.5 - - - +
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Residues in contact with VAL 52 (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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35A CYS* 4.6 5.6 - - - -
48A HIS* 2.8 40.3 + - + +
51A ALA* 1.3 84.0 - - + +
53A HIS* 1.3 83.6 + - + +
54A LYS* 3.4 14.8 + - - -
201A ZN 4.4 1.8 - - - -
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Residues in contact with HIS 53 (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 HIS* 3.2 40.7 + + + +
35A CYS* 3.9 6.7 - - + -
49A TYR* 3.1 19.8 + + - +
52A VAL* 1.3 96.6 - - + +
54A LYS* 1.3 74.1 + - - +
55A SER* 2.8 18.8 + - - +
201A ZN 2.3 34.6 - - - -
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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