Contacts of the helix formed by residues 793 - 798 (chain M) 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 SER 793 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694M THR* 5.9 3.7 - - - +
774M ARG* 3.5 0.5 + - - -
791M ASP* 2.7 25.0 + - - -
792M TYR* 1.3 83.2 - - - +
794M PRO* 1.3 73.4 - - - +
795M GLU* 3.1 24.7 + - - +
796M SER* 3.3 7.4 + - - -
797M LYS 3.2 14.7 + - - -
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Residues in contact with PRO 794 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687M LYS* 4.3 12.6 - - + -
690M VAL* 3.8 32.5 - - + -
722M LEU* 3.3 29.6 - - + -
774M ARG* 3.8 11.7 - - - +
792M TYR 4.5 0.7 - - - +
793M SER* 1.3 82.8 - - - +
795M GLU* 1.3 71.9 + - - +
796M SER 2.6 18.0 + - - -
797M LYS 3.2 5.4 + - - -
798M GLY 3.3 0.2 + - - -
799M PHE* 3.1 35.2 + - + -
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Residues in contact with GLU 795 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687M LYS* 2.8 42.6 - - - +
787M PHE* 2.8 23.2 - - - -
793M SER* 3.1 24.2 + - - +
794M PRO* 1.3 96.5 - - - +
796M SER* 1.3 56.6 + - - +
798M GLY 5.0 0.2 - - - -
799M PHE* 4.7 9.4 - - + -
801M GLU* 6.5 0.2 - - + -
811M GLN* 5.5 1.6 - - - +
815M PHE* 4.9 4.5 - - - -
731N VAL* 3.5 36.5 - - + +
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Residues in contact with SER 796 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782M ARG* 5.8 0.2 - - - -
783M THR* 2.4 45.7 + - - +
787M PHE* 3.3 20.9 - - - +
791M ASP* 3.2 47.1 + - - +
793M SER* 3.6 4.3 - - - -
794M PRO 2.6 9.5 + - - -
795M GLU* 1.3 77.0 - - - +
797M LYS* 1.3 59.4 + - - +
798M GLY 3.2 2.2 + - - -
815M PHE* 3.6 4.5 - - - -
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Residues in contact with LYS 797 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715M GLU* 4.2 8.6 + - - -
767M GLN* 3.1 5.2 + - - -
774M ARG* 2.9 61.8 + - + +
775M ILE* 2.6 55.4 + - - +
776M ALA* 4.5 4.8 - - - +
777M PHE* 3.7 37.8 - - + +
791M ASP 4.1 5.6 - - - +
792M TYR* 3.3 26.6 - - - +
793M SER 3.2 1.0 + - - +
794M PRO 3.2 2.4 + - - +
796M SER* 1.3 77.6 - - - +
798M GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 798 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767M GLN* 3.4 7.8 - - - -
768M GLN* 2.7 36.0 + - - +
775M ILE* 3.9 7.6 - - - -
794M PRO 3.3 1.0 + - - -
796M SER 3.2 4.6 - - - -
797M LYS* 1.3 80.9 - - - +
799M PHE* 1.3 60.2 + - - +
800M VAL* 3.6 2.2 + - - -
815M PHE* 3.5 26.0 - - - -
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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