Contacts of the helix formed by residues 31 - 40 (chain A) in PDB entry 1CEC
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 GLU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 1.3 74.6 - - - +
32A LYS* 1.3 56.9 + - - +
34A ILE* 3.3 2.3 + - - +
35A GLU* 2.9 28.6 + - - +
77A TRP* 3.7 47.7 + - + +
80A LYS* 2.7 36.9 + - - -
81A TYR* 2.8 28.2 + - + +
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Residues in contact with LYS 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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30A THR* 2.9 12.3 + - - +
31A GLU* 1.3 79.1 - - - +
33A ASP* 1.3 53.4 + - - +
35A GLU* 3.2 39.2 + - - +
36A THR* 2.8 41.6 + - - +
327A ARG* 3.5 30.1 - - - +
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Residues in contact with ASP 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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27A THR 5.0 0.2 - - - +
28A PHE 3.4 4.9 - - - +
29A ILE* 3.3 17.3 - - + -
30A THR* 2.8 37.3 + - - +
32A LYS* 1.3 75.4 - - - +
34A ILE* 1.3 59.0 + - - +
36A THR* 3.0 2.9 + - - -
37A ILE* 2.8 38.1 + - + +
315A TYR* 2.7 41.8 + - + +
316A LYS* 3.4 9.4 + - - -
327A ARG* 3.2 23.1 + - - +
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Residues in contact with ILE 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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10A LEU* 4.5 7.2 - - + -
29A ILE* 4.9 5.2 - - + -
30A THR 3.6 2.9 + - - +
31A GLU 3.3 7.0 + - - +
33A ASP* 1.3 77.0 - - - +
35A GLU* 1.3 58.2 + - - +
37A ILE* 3.4 9.5 + - + +
38A ALA* 2.8 28.8 + - - +
45A VAL* 4.1 25.1 - - + -
74A CYS* 4.4 16.8 - - - -
77A TRP* 3.8 46.4 - - + +
78A CYS* 4.2 5.4 - - - +
81A TYR* 3.7 19.5 - - + -
83A LEU* 3.6 18.1 - - + +
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Residues in contact with GLU 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 GLU* 2.9 16.7 + - - +
32A LYS* 3.2 43.3 + - - +
34A ILE* 1.3 78.8 - - - +
36A THR* 1.3 51.9 + - - +
38A ALA* 3.2 5.1 + - - +
39A GLU* 2.7 40.0 + - + +
81A TYR* 3.5 39.2 + - + +
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Residues in contact with THR 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 LYS* 2.8 28.6 + - - +
33A ASP 3.2 10.1 - - - -
35A GLU* 1.3 76.1 - - - +
37A ILE* 1.3 58.1 + - - +
39A GLU* 2.6 42.2 + - - +
40A ALA* 2.9 11.6 + - - +
315A TYR* 4.1 11.7 - - + +
323A TYR* 3.7 31.4 - - + -
327A ARG* 3.5 26.6 - - + +
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Residues in contact with ILE 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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8A ILE* 3.8 18.4 - - + -
10A LEU* 3.8 29.8 - - + -
33A ASP* 2.8 23.5 + - + +
34A ILE* 3.6 7.2 - - + +
36A THR* 1.3 72.7 - - - +
38A ALA* 1.3 68.2 + - - +
40A ALA* 3.2 10.1 + - - -
41A GLY 3.3 7.8 + - - -
42A PHE* 3.3 41.2 + - + -
44A HIS 4.8 0.4 - - - +
45A VAL* 3.9 17.9 - - + -
83A LEU* 4.1 7.6 - - + -
315A TYR* 3.8 30.1 - - + -
323A TYR* 5.0 2.5 - - + -
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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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34A ILE 2.8 18.8 + - - +
35A GLU 3.4 4.3 - - - +
37A ILE* 1.3 76.3 - - - +
39A GLU* 1.3 64.0 + - - +
41A GLY* 3.1 15.2 + - - -
42A PHE 4.3 1.3 - - - +
81A TYR* 3.6 35.7 - - + +
83A LEU* 4.0 19.7 - - + -
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Residues in contact with GLU 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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35A GLU* 2.7 20.0 + - + +
36A THR* 2.6 40.5 + - - +
38A ALA* 1.3 74.3 - - - +
40A ALA* 1.3 77.1 + - - +
41A GLY* 3.1 2.0 + - - -
323A TYR* 4.2 2.4 + - - -
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Residues in contact with ALA 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 THR 2.9 6.1 + - - +
37A ILE 3.2 6.9 + - - +
39A GLU* 1.3 89.2 + - - +
41A GLY* 1.3 57.4 + - - +
42A PHE* 3.6 13.7 - - + -
323A TYR* 3.1 28.3 - - - +
332A GLN* 6.3 0.2 - - - +
335A VAL* 3.9 11.9 - - + +
336A ASN* 5.4 3.5 + - - -
339A ALA* 3.5 16.5 - - - +
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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