Contacts of the helix formed by residues 758 - 762 (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 PHE 758 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757N PRO* 1.3 73.0 - - - +
759N PRO* 1.3 60.5 - - - +
760N ASP* 2.9 11.9 - - - -
761N HIS* 2.8 40.5 + + + +
1024N ALA* 3.4 15.6 - - + +
1027N ILE* 3.0 50.0 - - + -
1028N GLU* 4.0 7.6 - - - -
1031N LEU* 3.3 31.9 - - + -
1043N ASP 3.7 4.7 - - - -
1044N ALA* 2.8 45.3 + - + -
1045N SER 4.3 7.6 - - - -
1046N PRO 4.9 0.9 - - - -
1048N THR* 5.3 1.3 - - - -
1050N ILE* 4.9 13.7 - - + -
1055N ILE* 4.7 5.6 - - + -
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Residues in contact with PRO 759 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813M PHE* 3.7 13.9 - - + -
749N LEU* 4.6 13.0 - - + -
753N ALA* 5.3 1.1 - - + +
756N ILE* 2.9 37.9 - - + +
757N PRO 3.2 2.6 - - - +
758N PHE* 1.3 82.8 - - - +
760N ASP* 1.3 60.1 + - + +
761N HIS 2.9 6.3 + - - -
762N ASN* 3.3 10.6 + - - +
767N ASN* 2.9 45.2 + - - +
1044N ALA 4.5 0.4 - - - +
1046N PRO* 4.3 28.0 - - + -
1047N PHE* 6.4 0.7 - - + -
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Residues in contact with ASP 760 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807M GLY* 3.0 24.9 - - - -
808M LEU* 3.1 17.2 + - - +
813M PHE* 4.1 13.0 - - + -
728N ARG* 2.7 30.9 + - - -
758N PHE* 3.3 11.8 - - - -
759N PRO* 1.3 73.6 - - + +
761N HIS* 1.3 74.2 + - - -
762N ASN 3.7 1.6 - - - -
1046N PRO 2.9 27.1 - - - +
1047N PHE* 3.7 23.7 - - + -
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Residues in contact with HIS 761 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804M TYR* 2.6 37.6 + - - +
805M LEU 3.1 22.8 + - - -
806M ARG 3.2 20.2 - - - -
807M GLY* 3.3 5.6 + - - -
728N ARG* 3.7 10.3 + - - -
758N PHE* 2.8 26.0 + + + +
760N ASP* 1.3 105.3 + - - +
762N ASN* 1.3 63.5 + - - +
1023N VAL* 3.4 25.5 + - - +
1024N ALA* 4.0 13.0 - - + +
1027N ILE* 4.0 15.3 - - + +
1050N ILE 5.6 4.5 + - - -
1052N VAL* 5.8 0.9 - - + -
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Residues in contact with ASN 762 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804M TYR* 3.3 13.8 - - - -
808M LEU* 5.6 1.6 - - - +
813M PHE* 5.9 0.7 - - - -
816M HIS* 4.7 1.7 - - - -
756N ILE* 4.3 1.2 - - - +
759N PRO* 3.3 13.7 + - - +
760N ASP 5.0 0.5 - - - -
761N HIS* 1.3 80.7 + - - +
763N GLN* 1.3 66.9 + - - +
764N SER* 3.2 4.0 + - - -
766N ARG* 4.2 8.2 - - + +
767N ASN* 3.4 30.6 + - - +
984N HIS* 3.1 28.5 + - - +
1021N MET 4.1 2.0 - - - -
1022N THR* 2.8 42.7 + - - -
1024N ALA* 3.2 15.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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