Contacts of the helix formed by residues 37 - 43 (chain A) in PDB entry 5C6E
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 PRO 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PHE 3.5 13.5 - - - +
34A LEU 3.7 11.0 - - - +
35A GLY 3.4 9.2 - - - +
36A PHE* 1.4 86.3 - - - +
38A THR* 1.3 63.3 + - + +
39A THR 3.1 0.4 - - - -
40A LYS* 3.1 21.7 + - - +
321A DOD 2.8 25.4 + - - +
323A DOD 3.9 5.4 - - - +
327A DOD 4.4 3.8 - - - +
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Residues in contact with THR 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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36A PHE* 3.2 0.9 + - - +
37A PRO* 1.3 77.8 - - + +
39A THR* 1.3 60.9 + - - +
41A THR* 3.1 31.7 + - - +
42A TYR* 4.6 2.7 - - - -
97A ASN* 5.6 0.7 - - - -
316A DOD 2.8 25.9 + - - +
321A DOD 4.3 3.8 - - - -
323A DOD 2.8 22.1 + - - +
351A DOD 4.5 3.4 - - - -
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Residues in contact with THR 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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32A MET* 3.6 40.1 + - + +
33A PHE* 3.8 9.6 - - - -
36A PHE* 2.8 20.3 + - + +
38A THR* 1.3 74.9 - - - +
40A LYS* 1.3 60.6 + - - +
41A THR 3.1 6.4 + - - -
42A TYR* 3.3 27.6 + - - +
43A PHE* 3.9 9.4 - - - -
97A ASN* 3.5 27.4 - - + +
100A LEU* 4.0 17.0 - - + -
201A HEM 4.1 4.0 - - + +
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Residues in contact with LYS 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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33A PHE* 3.7 42.8 - - + +
37A PRO* 3.1 20.5 + - - +
39A THR* 1.3 72.1 + - - +
41A THR* 1.3 53.3 + - - +
42A TYR 3.1 5.8 - - - -
43A PHE* 3.0 17.3 + - - +
48A LEU* 3.7 22.6 - - + +
305A DOD 2.6 29.9 + - - +
306A DOD 2.6 27.1 + - - +
321A DOD 3.8 17.3 - - - +
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Residues in contact with THR 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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38A THR* 3.1 22.6 + - - +
40A LYS* 1.3 76.8 - - - +
42A TYR* 1.3 73.8 + - - +
43A PHE 3.3 0.2 - - - -
44A PRO* 3.5 13.9 - - - +
306A DOD 4.2 4.5 - - - -
321A DOD 4.1 14.6 - - - +
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Residues in contact with TYR 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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39A THR* 3.4 20.0 - - - +
40A LYS 3.1 0.8 - - - -
41A THR* 1.3 88.9 - - - +
43A PHE* 1.3 69.4 + - + +
44A PRO* 3.2 9.1 - - - +
45A HIS* 4.0 3.8 - - - -
91A LEU* 4.2 9.4 - - + -
92A ARG 4.2 4.5 - - - -
93A VAL* 3.9 29.6 - - + -
94A ASP* 3.2 24.1 + - - +
97A ASN* 3.2 24.7 + - - -
201A HEM 3.2 34.1 - - + +
318A DOD 3.2 14.0 + - - -
340A DOD 3.0 25.5 + - - -
351A DOD 4.0 9.8 + - - -
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Residues in contact with PHE 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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29A LEU* 4.8 1.1 - - + -
32A MET* 4.8 2.0 - - + -
33A PHE* 3.6 34.1 - + - -
39A THR 3.9 7.6 - - - -
40A LYS 3.0 11.4 + - - +
42A TYR* 1.3 86.6 - - + +
44A PRO* 1.3 63.1 - - - +
45A HIS* 3.1 7.6 - + - -
46A PHE* 3.2 46.1 + + + +
48A LEU* 4.2 9.7 - - + +
58A HIS* 4.0 21.1 - + - -
201A HEM 3.5 59.7 - + + -
202A CYN 4.0 11.7 - - - -
306A DOD 3.6 0.9 + - - -
343A DOD 3.3 11.6 + - - -
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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