Contacts of the helix formed by residues 897 - 904 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B THR* 5.4 0.9 - - - +
801B THR* 3.6 28.7 - - + -
808B ALA* 3.6 21.1 - - + +
809B THR* 5.1 4.0 - - + -
896B ALA* 1.3 89.3 - - + +
898B LYS* 1.3 68.9 + - - +
899B GLU 3.3 0.9 - - - -
900B GLU* 3.0 24.5 + - + +
901B HIS 2.8 17.7 + - - -
1200B 12V 4.8 0.2 - - - +
1390F VAL* 4.4 27.5 - - + -
1392F VAL* 4.9 2.9 - - + -
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Residues in contact with LYS 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B HIS* 3.4 37.5 + - + +
698B HIS* 5.2 2.2 + - - -
701B MET* 5.0 2.9 - - + -
702B PHE* 3.7 22.4 - - + -
808B ALA 3.7 1.6 + - - -
809B THR* 3.6 23.2 - - - +
896B ALA 3.6 1.4 + - - -
897B PRO* 1.3 72.1 - - - +
899B GLU* 1.3 58.5 + - - +
901B HIS* 3.0 2.8 + - + +
902B VAL* 2.8 38.1 + - + +
921B THR* 3.4 20.0 - - - +
925B ASP* 3.7 12.4 + - - -
1200B 12V 2.7 58.1 + - - +
1392F VAL* 4.8 5.2 - - + +
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Residues in contact with GLU 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B PHE* 3.9 20.1 - - + -
704B HIS* 3.0 37.0 + - + +
705B LEU* 5.4 0.5 - - - +
800B THR* 3.9 15.1 + - - +
807B ALA 3.3 26.9 - - - +
808B ALA* 3.1 10.8 + - - +
810B GLY 4.6 1.1 - - - +
814B PRO* 4.3 4.5 - - + -
818B ILE* 3.9 8.3 - - - +
897B PRO 3.0 1.4 + - - -
898B LYS* 1.3 77.5 - - - +
900B GLU* 1.3 70.9 + - - +
902B VAL* 3.4 1.6 + - - +
903B ARG* 2.8 62.4 + - - +
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Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B GLY 3.9 7.8 - - - +
798B LEU* 4.0 21.4 - - - +
800B THR* 4.8 7.0 + - - +
808B ALA* 4.5 1.0 + - - +
825B TYR* 2.9 39.7 + - - +
896B ALA* 3.6 17.5 - - + +
897B PRO* 3.0 28.5 + - + +
899B GLU* 1.3 75.5 + - - +
901B HIS* 1.3 66.8 + - - +
903B ARG* 3.3 26.7 + - - +
904B ARG* 3.0 25.9 + - - +
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Residues in contact with HIS 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B PHE* 3.7 36.0 - + + -
896B ALA* 3.8 3.0 - - - +
897B PRO 2.8 9.4 + - - +
898B LYS* 3.2 9.0 - - + +
900B GLU* 1.3 78.0 - - - +
902B VAL* 1.3 69.1 + - + +
904B ARG* 3.4 28.5 + - - +
905B GLY* 3.8 3.3 + - - -
922B THR* 4.6 5.8 - - + +
925B ASP* 3.4 24.7 + - + +
1200B 12V 3.3 75.7 + + + +
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Residues in contact with VAL 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B HIS* 4.8 0.4 - - + -
702B PHE* 3.6 31.0 - - + -
705B LEU* 3.9 19.3 - - + -
898B LYS* 2.8 27.3 + - + +
899B GLU 3.9 3.1 - - - +
901B HIS* 1.3 84.2 - - + +
903B ARG* 1.3 64.3 + - - +
905B GLY* 3.1 15.4 + - - -
925B ASP* 3.6 37.3 - - - +
928B TRP* 4.2 13.0 - - + -
929B ALA* 3.8 10.3 - - - +
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Residues in contact with ARG 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B HIS* 4.9 0.9 - - - -
705B LEU* 4.1 21.7 - - + +
727B ASN* 4.3 8.3 - - - +
797B GLY* 3.1 39.2 + - - -
800B THR* 4.0 8.7 + - - +
818B ILE* 3.6 23.6 - - - +
820B THR* 3.4 37.4 + - - +
825B TYR* 4.5 2.4 + - - -
899B GLU* 2.8 53.8 + - - +
900B GLU* 3.4 18.2 + - - +
902B VAL* 1.3 73.8 - - - +
904B ARG* 1.3 58.5 + - - +
905B GLY 3.0 9.0 + - - -
906B GLN* 3.1 39.0 + - - +
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Residues in contact with ARG 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B THR* 4.2 12.6 - - + -
825B TYR* 3.7 54.8 - - + +
837B PHE* 4.7 7.5 - - + -
864B TRP* 3.5 30.6 - - + -
866B LEU* 3.2 34.6 - - - +
893B SER* 4.2 5.8 - - - -
894B PRO* 3.3 19.8 + - - +
896B ALA* 3.5 17.6 - - - +
900B GLU* 3.0 23.1 + - - +
901B HIS* 3.4 18.9 + - - +
903B ARG* 1.3 73.6 - - - +
905B GLY* 1.3 64.1 + - - +
906B GLN 3.1 1.0 + - - -
907B LEU* 3.4 12.9 + - + +
1200B 12V 3.4 20.8 + - - -
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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
------------------------------------------------------------
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