Contacts of the helix formed by residues 689 - 700 (chain A) in PDB entry 6A69
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 GLU 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687A ARG* 3.1 11.6 - - - +
688A PRO* 1.3 100.2 - - + +
690A VAL* 1.3 53.5 + - - +
691A PRO* 3.5 1.6 - - - -
692A ASP* 3.2 11.1 + - - +
693A ALA* 2.9 32.5 + - - +
834A ASN* 4.2 11.8 - - - +
836A THR* 3.8 20.0 - - + -
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Residues in contact with VAL 690 (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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480A LEU* 3.6 42.4 - - + +
686A VAL* 3.7 20.0 - - + -
687A ARG* 3.6 15.7 - - + +
689A GLU* 1.3 75.6 - - - +
691A PRO* 1.3 64.7 - - + +
693A ALA* 2.9 22.1 + - - -
694A ILE* 2.9 38.0 + - + +
722A CYS* 4.0 7.2 - - - -
834A ASN* 4.7 9.4 - - - +
835A PHE* 4.8 5.8 - - + -
836A THR* 5.3 1.1 - - + -
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Residues in contact with PRO 691 (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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686A VAL* 4.4 6.1 - - + -
687A ARG 3.7 10.5 - - - +
688A PRO* 4.0 8.1 - - + +
689A GLU 3.7 3.1 - - - -
690A VAL* 1.3 92.9 - - + +
692A ASP* 1.3 60.2 + - - +
694A ILE* 4.4 1.1 - - + -
695A LYS* 3.7 24.6 + - - +
721A LYS 5.0 6.3 - - - +
722A CYS* 3.8 24.3 - - - +
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Residues in contact with ASP 692 (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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688A PRO 5.5 1.3 - - - +
689A GLU* 3.2 12.2 + - - +
690A VAL 3.2 0.4 - - - -
691A PRO* 1.3 82.1 - - - +
693A ALA* 1.3 59.5 + - - +
695A LYS* 3.3 8.9 + - - +
696A LYS* 2.9 45.8 + - - +
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Residues in contact with ALA 693 (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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689A GLU 2.9 16.3 + - - +
690A VAL* 2.9 11.1 + - - +
692A ASP* 1.3 77.7 - - - +
694A ILE* 1.3 57.7 + - - +
696A LYS* 3.3 8.9 + - - +
697A CYS* 2.9 29.9 + - - +
835A PHE* 4.5 9.6 - - + -
836A THR* 4.0 20.9 - - + -
839A VAL* 4.0 19.4 - - + +
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Residues in contact with ILE 694 (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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480A LEU* 4.1 10.8 - - + -
690A VAL* 2.9 37.2 + - + +
691A PRO 5.0 0.4 - - - +
693A ALA* 1.3 75.3 - - - +
695A LYS* 1.3 58.0 + - - +
697A CYS* 3.8 5.2 - - - +
698A GLN* 2.8 40.2 + - + +
704A VAL* 4.4 16.5 - - + +
722A CYS* 3.9 27.4 - - + +
723A GLY 4.8 10.8 - - - +
724A ILE* 4.3 26.7 - - + +
835A PHE* 3.8 20.4 - - + -
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Residues in contact with LYS 695 (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 PRO 3.7 15.7 + - - +
692A ASP* 3.3 13.3 + - - +
693A ALA 3.2 0.4 - - - -
694A ILE* 1.3 78.8 - - - +
696A LYS* 1.3 57.8 + - - +
698A GLN* 3.2 7.0 + - + +
699A ARG* 3.0 51.8 + - - +
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Residues in contact with LYS 696 (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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692A ASP* 2.9 34.8 + - - +
693A ALA* 3.7 7.4 - - - +
695A LYS* 1.3 77.6 - - - +
697A CYS* 1.3 61.4 + - - +
699A ARG* 3.9 18.6 + - - +
700A ALA* 3.8 15.1 + - - +
839A VAL* 4.6 12.6 - - + -
843A MET* 6.1 0.4 - - + -
909A GLU* 4.9 20.5 + - + +
912A LEU* 4.1 36.3 - - + +
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Residues in contact with CYS 697 (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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472A ILE* 4.4 12.6 - - - -
693A ALA 2.9 17.7 + - - +
694A ILE* 3.8 6.1 - - - +
696A LYS* 1.3 76.3 - - - +
698A GLN* 1.3 56.0 + - - +
700A ALA* 2.8 32.9 + - - +
702A ILE* 3.6 41.5 + - - +
704A VAL* 4.6 9.9 - - + -
835A PHE* 5.1 3.4 - - + -
839A VAL* 4.2 19.2 - - + +
842A VAL* 5.5 5.4 - - - -
912A LEU* 6.0 2.2 - - - -
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Residues in contact with GLN 698 (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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694A ILE* 2.8 32.3 + - + +
695A LYS* 3.2 8.7 + - + +
697A CYS* 1.3 73.0 - - - +
699A ARG* 1.3 62.7 + - - +
700A ALA 3.4 0.5 + - - -
701A GLY* 3.5 10.8 + - - -
702A ILE 3.7 16.1 + - - +
703A THR* 4.5 13.3 - - - +
704A VAL* 4.5 10.7 + - - +
723A GLY 5.6 3.5 - - - +
724A ILE* 5.5 6.0 - - - +
763A ARG* 5.1 7.9 + - - +
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Residues in contact with ARG 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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695A LYS* 3.0 41.1 + - - +
696A LYS* 4.2 18.3 - - - +
697A CYS 3.2 0.4 - - - -
698A GLN* 1.3 77.7 - - - +
700A ALA* 1.3 57.0 + - - +
701A GLY 3.2 5.0 + - - -
912A LEU 5.1 5.8 + - - +
913A LEU* 4.5 30.5 - - - +
914A ARG 5.1 1.9 - - - +
915A LYS* 4.8 13.0 - - - +
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Residues in contact with ALA 700 (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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696A LYS 3.8 10.0 + - - +
697A CYS* 2.8 14.2 + - - +
699A ARG* 1.3 77.3 - - - +
701A GLY* 1.3 53.8 + - - +
702A ILE* 3.2 22.7 + - + +
846A ARG* 3.7 17.7 + - - +
912A LEU* 4.1 25.4 - - + +
914A ARG 4.2 10.1 - - - +
915A LYS* 5.1 0.9 - - - -
916A PRO* 3.3 19.9 - - - +
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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