Contacts of the helix formed by residues 897 - 904 (chain D) in PDB entry 4AY6
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 897 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800D THR* 5.5 0.9 - - - +
801D THR* 3.7 28.5 - - + -
808D ALA* 3.5 20.6 - - + +
809D THR* 5.1 3.8 - - + -
896D ALA* 1.4 88.6 - - + +
898D LYS* 1.3 68.8 + - - +
899D GLU 3.0 2.3 + - - -
900D GLU* 3.1 22.6 + - + +
901D HIS 2.8 17.7 + - - -
1200D 12V 4.8 0.2 - - - +
1390H VAL* 4.3 28.0 - - + -
1392H VAL* 4.8 3.4 - - + -
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Residues in contact with LYS 898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D HIS* 3.5 33.4 + - + +
698D HIS* 5.3 1.5 + - - -
701D MET* 5.1 3.6 - - + -
702D PHE* 3.8 21.1 - - + -
808D ALA 3.6 1.8 + - - -
809D THR* 3.6 23.1 + - - +
897D PRO* 1.3 70.2 - - - +
899D GLU* 1.3 58.0 + - - +
901D HIS* 3.0 3.2 + - + +
902D VAL* 2.8 38.6 + - + +
921D THR* 3.4 19.6 - - - +
925D ASP* 3.7 12.8 + - - -
1200D 12V 2.7 61.2 + - - +
1392H VAL* 4.9 6.4 - - + +
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Residues in contact with GLU 899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D PHE* 3.8 20.5 - - + -
704D HIS* 3.0 35.6 + - + +
705D LEU* 5.5 0.3 - - - +
800D THR* 3.9 14.5 + - - +
807D ALA 3.2 27.6 - - - +
808D ALA* 3.1 11.2 + - - +
809D THR 4.8 0.2 - - - -
810D GLY 4.6 0.9 - - - +
814D PRO* 4.4 4.7 - - + -
818D ILE* 3.8 9.3 - - - +
897D PRO 3.0 0.2 + - - -
898D LYS* 1.3 78.0 - - - +
900D GLU* 1.3 71.9 + - - +
902D VAL* 3.5 1.6 + - - +
903D ARG* 2.7 56.3 + - - +
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Residues in contact with GLU 900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D GLY 4.1 7.0 - - - +
798D LEU* 3.9 21.5 - - - +
800D THR* 4.9 6.1 + - - +
808D ALA* 4.5 1.2 + - - +
825D TYR* 2.9 41.1 + - - +
896D ALA* 3.5 18.0 - - + +
897D PRO* 3.1 27.2 + - + +
899D GLU* 1.3 81.5 + - - +
901D HIS* 1.3 64.3 + - - +
903D ARG* 3.2 24.2 + - - +
904D ARG* 3.0 26.0 + - - +
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Residues in contact with HIS 901 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837D PHE* 3.7 34.0 - + + -
896D ALA* 3.9 1.8 - - - +
897D PRO 2.8 9.8 + - - +
898D LYS* 3.2 9.4 - - + +
900D GLU* 1.3 79.0 - - - +
902D VAL* 1.3 70.5 + - + +
904D ARG* 3.5 27.2 + - - +
905D GLY* 3.9 3.8 + - - -
922D THR* 4.6 6.0 - - + +
925D ASP* 3.4 24.9 + - + +
1200D 12V 3.2 75.1 + + + +
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Residues in contact with VAL 902 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D HIS* 4.8 0.4 - - + -
702D PHE* 3.7 31.2 - - + -
705D LEU* 3.8 21.3 - - + +
898D LYS* 2.8 26.8 + - + +
899D GLU 4.0 3.1 - - - +
901D HIS* 1.3 83.4 - - + +
903D ARG* 1.3 63.4 + - - +
905D GLY* 3.2 13.3 + - - -
925D ASP* 3.7 39.7 - - - +
928D TRP* 4.2 13.0 - - + -
929D ALA* 3.8 11.3 - - - +
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Residues in contact with ARG 903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704D HIS* 4.9 1.1 - - - -
705D LEU* 4.1 20.6 - - + +
727D ASN* 4.3 8.3 - - - +
797D GLY* 3.0 39.8 + - - -
800D THR* 3.9 8.7 + - - +
818D ILE* 3.5 22.8 - - - +
820D THR* 3.4 40.0 + - - +
825D TYR* 4.5 3.0 + - - -
899D GLU* 2.7 54.8 + - - +
900D GLU* 3.2 17.9 + - - +
902D VAL* 1.3 77.0 - - - +
904D ARG* 1.3 60.8 + - - +
905D GLY 3.2 1.0 + - - -
906D GLN* 3.2 34.7 + - - +
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Residues in contact with ARG 904 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820D THR* 4.2 11.2 - - + -
825D TYR* 3.6 55.0 - - + +
837D PHE* 4.8 7.5 - - + -
864D TRP* 3.4 29.2 - - + -
866D LEU* 3.3 30.5 - - - +
893D SER* 4.2 6.2 - - - -
894D PRO* 3.3 19.8 + - - +
896D ALA* 3.5 17.2 - - - +
900D GLU* 3.0 21.2 + - + +
901D HIS* 3.5 17.1 + - - +
903D ARG* 1.3 73.1 - - - +
905D GLY* 1.3 62.4 + - - +
906D GLN 3.0 2.4 + - - -
907D LEU* 3.3 12.5 + - + +
1200D 12V 3.3 24.5 + - - -
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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
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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