Contacts of the helix formed by residues 31 - 36 (chain A) in PDB entry 3HUU
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A SER* 3.2 16.2 + - - +
30A SER* 1.3 77.4 + - - +
32A PRO* 1.3 65.0 - - + -
33A GLU* 3.3 20.4 - - - +
34A ILE* 2.7 31.7 + - + +
35A ARG 2.9 9.4 + - - -
64A GLU* 4.2 18.0 - - + +
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Residues in contact with PRO 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 SER 3.6 0.8 - - - -
31A ALA* 1.3 87.0 - - + -
33A GLU* 1.3 63.8 + - - +
35A ARG* 3.6 22.2 - - - +
36A GLN* 2.8 61.5 + - - +
64A GLU* 4.9 5.6 - - - +
239B PHE* 5.1 4.7 - - + +
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Residues in contact with GLU 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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31A ALA* 3.6 15.0 - - - +
32A PRO* 1.3 90.7 - - - +
34A ILE* 1.3 78.7 + - + +
36A GLN 4.5 0.2 - - - -
37A ASN* 4.3 1.2 + - - +
210A MET* 3.8 28.7 - - + +
239B PHE* 3.9 35.5 - - + -
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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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27A GLN* 5.6 0.9 - - + +
28A LYS* 3.7 34.5 - - + +
29A SER* 3.4 35.2 - - - +
31A ALA* 2.7 18.4 + - + +
33A GLU* 1.3 88.7 - - + +
35A ARG* 1.3 58.9 + - - +
36A GLN 3.2 1.3 - - - -
37A ASN* 3.1 11.0 + - - +
40A ASN* 2.7 36.2 + - - +
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Residues in contact with ARG 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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27A GLN* 4.0 22.2 - - - +
29A SER 4.3 0.2 + - - -
30A SER* 2.6 30.9 + - - +
31A ALA 2.9 12.8 + - - +
32A PRO* 3.6 22.9 - - - +
34A ILE* 1.3 75.2 - - - +
36A GLN* 1.3 67.2 + - - +
37A ASN 3.4 6.1 + - - +
40A ASN* 3.9 12.8 - - + +
41A SER* 5.3 0.9 + - - -
60A MET* 5.3 7.0 - - + -
64A GLU* 5.9 1.4 + - - -
41B SER* 2.9 46.7 + - - +
42B ASP* 2.5 36.5 + - - +
45B ASN* 3.4 35.8 + - - +
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Residues in contact with GLN 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 PRO* 2.8 38.3 + - - +
35A ARG* 1.3 73.0 - - - +
37A ASN* 1.3 63.9 + - - +
38A PRO* 3.2 8.5 - - - +
210A MET* 3.7 13.9 - - + +
240A LEU* 5.0 2.3 - - - +
36B GLN 4.8 8.1 - - - +
38B PRO* 3.9 21.8 - - + +
41B SER* 4.0 7.4 - - - +
42B ASP* 2.9 36.9 + - - +
238B SER* 3.5 18.5 - - - +
239B PHE* 2.9 34.2 + - + +
240B LEU* 4.4 2.8 + - + +
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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