Contacts of the helix formed by residues 1013 - 1017 (chain N) in PDB entry 3HOU
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 ASN1013 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525M GLN* 4.5 6.3 - - - +
526M ASP* 2.5 35.1 + - - -
827N ILE* 4.1 2.1 - - - +
829N CYS* 3.9 6.7 - - - -
834N ASN* 3.3 34.4 + - - +
835N GLN* 4.0 7.3 - - - +
836N GLU 5.2 0.4 - - - +
837N ASP* 5.5 2.2 - - - +
838N SER 4.9 0.4 + - - -
1012N ILE* 1.3 76.1 - - - +
1014N PRO* 1.3 71.5 - - - +
1015N HIS* 2.7 48.0 + - + +
1016N ALA* 2.9 22.1 + - + +
1017N ILE* 5.1 1.4 - - - +
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Residues in contact with PRO1014 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662M PHE* 3.7 23.6 - - + +
663M SER 3.8 11.9 - - - -
664M THR* 3.4 30.3 - - + +
746M MET* 4.1 2.7 - - - -
827N ILE* 3.4 6.2 - - + -
828N ALA* 3.6 28.5 - - - +
829N CYS* 3.5 23.6 - - - +
1012N ILE 3.7 1.3 - - - +
1013N ASN* 1.3 84.0 - - - +
1015N HIS* 1.3 63.8 + - + +
1016N ALA 3.1 1.6 + - - -
1017N ILE* 3.3 16.6 + - - +
1018N PRO* 3.3 9.9 - - - +
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Residues in contact with HIS1015 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525M GLN* 3.3 46.2 - - + +
526M ASP* 3.4 22.8 + - - -
529M CYS* 3.3 28.4 - - + +
662M PHE* 4.7 1.6 - + - -
746M MET* 3.1 20.9 - - - -
751M SER* 2.9 29.2 + - - -
752M LYS* 3.4 25.4 - - + +
829N CYS* 4.5 4.1 - - - -
1013N ASN* 2.7 29.5 + - - +
1014N PRO* 1.3 71.9 - - + +
1016N ALA* 1.3 55.3 + - - +
1017N ILE 3.1 6.2 + - - -
1018N PRO* 3.4 5.8 - - - +
1019N SER* 4.6 3.3 + - - -
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Residues in contact with ALA1016 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837N ASP* 4.4 22.0 - - - +
986N GLN* 3.3 24.3 + - + +
1012N ILE* 6.4 1.3 - - + -
1013N ASN* 2.9 22.4 + - + +
1015N HIS* 1.3 70.9 - - - +
1017N ILE* 1.3 58.7 + - + +
1020N ARG* 2.8 39.6 - - - +
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Residues in contact with ILE1017 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664M THR* 4.4 19.3 - - + +
743M VAL* 5.3 2.9 - - + -
761M MET* 5.1 11.6 - - + +
827N ILE* 4.8 7.2 - - + -
986N GLN* 3.6 24.9 - - - +
1012N ILE* 5.8 3.1 - - + -
1013N ASN 5.1 1.3 - - - +
1014N PRO* 3.4 12.6 - - + +
1015N HIS 3.1 0.4 + - - -
1016N ALA* 1.3 78.6 - - - +
1018N PRO* 1.3 80.9 - - + +
1019N SER 3.4 1.8 - - - -
1020N ARG* 3.0 3.3 + - - +
1021N MET* 2.8 23.4 + - - -
1022N THR* 4.2 14.3 + - + +
1025N HIS* 4.8 7.6 - - + +
1026N LEU* 4.1 43.1 - - + -
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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