Contacts of the helix formed by residues 695 - 701 (chain A) in PDB entry 5KMO
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 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A TRP 4.2 0.9 - - - +
694A MET* 1.3 90.8 - - + +
696A PRO* 1.4 73.2 - - + +
697A GLU* 2.9 28.3 - - - +
698A SER* 3.0 36.2 + - - +
699A ILE* 3.3 9.4 + - - +
704A PHE* 6.1 0.7 - - + -
708A SER* 3.5 28.7 - - - +
711A TRP* 3.5 28.0 - - + -
712A SER* 4.7 2.0 - - - +
740A ILE* 4.4 1.1 - - - -
771A ARG* 3.8 1.1 - - - +
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Residues in contact with PRO 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A PRO* 1.4 85.4 - - + +
697A GLU* 1.3 52.5 + - + +
699A ILE* 3.3 4.1 + - + +
700A LEU* 2.8 49.0 + - + +
711A TRP* 3.7 27.1 - - + -
740A ILE* 3.4 31.6 - - + +
741A THR* 4.5 3.6 - - + -
766A ARG* 3.6 38.8 - - + +
771A ARG* 4.5 4.5 - - - +
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Residues in contact with GLU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A PRO* 2.9 19.7 - - + +
696A PRO* 1.3 73.1 - - + +
698A SER* 1.3 56.5 + - - +
701A TYR* 3.2 43.0 + - + +
703A LYS* 3.2 31.6 + - + +
705A THR* 4.4 7.3 + - - -
708A SER* 3.9 12.2 - - - -
766A ARG 4.8 2.0 - - - +
768A PRO* 3.5 34.2 - - + +
771A ARG* 2.7 37.8 + - - +
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Residues in contact with SER 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A MET* 3.7 26.1 - - - +
695A PRO* 3.0 34.8 + - - +
697A GLU* 1.3 78.3 - - - +
699A ILE* 1.4 59.6 + - - +
702A ARG* 3.2 24.5 + - - +
703A LYS 2.8 23.8 + - - +
704A PHE* 4.0 13.7 - - - -
708A SER* 3.9 5.5 - - - -
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Residues in contact with ILE 699 (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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691A ILE* 3.8 33.4 - - + +
694A MET* 3.8 24.9 - - + +
695A PRO 3.3 1.5 + - - +
696A PRO 3.3 6.3 + - - +
698A SER* 1.4 80.1 - - - +
700A LEU* 1.3 60.4 + - + +
702A ARG* 4.6 10.7 + - - +
737A ILE* 3.6 27.1 - - + -
740A ILE* 3.7 34.5 - - + -
741A THR* 3.5 22.0 - - + -
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A PRO* 2.8 33.5 + - + +
699A ILE* 1.3 79.3 - - + +
701A TYR* 1.3 91.9 + - + +
702A ARG* 3.7 6.5 + - - +
741A THR* 3.7 28.7 - - + +
766A ARG* 4.4 11.9 - - - +
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Residues in contact with TYR 701 (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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697A GLU* 3.2 34.6 + - + +
700A LEU* 1.3 102.6 - - + +
702A ARG* 1.4 70.6 + - - +
703A LYS* 3.5 36.4 + - + +
766A ARG* 5.7 1.0 + - - -
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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