Contacts of the helix formed by residues 871 - 883 (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 VAL 871 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B ILE* 5.5 2.0 - - + -
436B PRO* 4.3 26.5 - - + -
466B VAL* 3.6 28.6 - - + +
869B PRO* 3.7 17.5 - - + -
870B ALA* 1.3 78.2 - - + +
872B GLY* 1.3 62.7 + - - +
874B PRO* 3.4 19.0 - - - +
875B ASN* 4.2 10.4 + - - -
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Residues in contact with GLY 872 (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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466B VAL* 3.4 23.4 - - - +
467B CYS* 5.2 0.7 - - - -
840B LEU* 3.9 15.5 - - - -
869B PRO* 2.8 14.1 + - - -
871B VAL* 1.3 82.1 - - - +
873B GLU* 1.3 65.1 + - - +
875B ASN* 3.3 7.8 + - - +
876B ILE* 3.3 20.0 + - - +
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Residues in contact with GLU 873 (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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840B LEU* 4.4 1.6 - - - +
867B ARG* 3.0 31.3 + - + -
869B PRO 3.9 2.0 + - - -
870B ALA* 3.0 15.6 + - - +
872B GLY* 1.3 74.3 - - - +
874B PRO* 1.4 70.2 - - + +
876B ILE* 3.0 6.8 + - - +
877B GLN* 3.0 32.2 + - + +
892B PHE* 3.3 59.3 + - + +
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Residues in contact with PRO 874 (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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870B ALA 3.4 9.4 - - - +
871B VAL* 3.4 17.3 - - - +
873B GLU* 1.4 93.4 - - + +
875B ASN* 1.3 55.0 + - - +
877B GLN* 3.1 11.8 + - + +
878B GLN* 2.7 36.5 + - - +
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Residues in contact with ASN 875 (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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466B VAL* 2.7 29.4 + - - +
467B CYS* 3.2 24.7 + - + +
468B ASP* 3.6 13.2 - - - +
871B VAL 4.2 7.4 + - - -
872B GLY 3.3 8.4 + - - +
874B PRO* 1.3 80.2 - - - +
876B ILE* 1.3 64.4 + - - +
878B GLN* 3.1 8.8 + - - +
879B TYR* 3.0 33.5 + - + -
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Residues in contact with ILE 876 (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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467B CYS* 3.8 23.6 - - + -
469B TRP* 3.7 30.3 - - + -
840B LEU* 5.1 6.7 - - + -
843B ILE* 4.6 13.2 - - + -
848B LEU* 4.1 16.6 - - + -
865B LEU* 4.4 8.3 - - + -
872B GLY 3.3 12.1 + - - +
873B GLU 3.0 6.7 + - - +
875B ASN* 1.3 75.9 - - - +
877B GLN* 1.3 56.6 + - - +
878B GLN 3.1 0.3 + - - -
879B TYR* 3.1 2.9 + - - +
880B ALA* 2.7 35.2 + - - +
890B ILE* 4.3 17.7 - - + -
892B PHE* 4.0 23.3 - - + -
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Residues in contact with GLN 877 (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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873B GLU* 3.0 30.6 + - + +
874B PRO* 3.2 12.6 - - + +
876B ILE* 1.3 74.1 - - - +
878B GLN* 1.3 65.1 - - - +
880B ALA* 3.5 7.4 + - - +
881B GLN* 3.0 27.2 + - - +
885B LEU 5.3 0.3 - - - +
887B GLN* 3.7 43.6 + - - +
890B ILE* 3.9 23.7 + - - +
892B PHE* 3.9 22.3 - - - -
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Residues in contact with GLN 878 (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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874B PRO 2.7 15.6 + - - +
875B ASN* 3.1 13.9 - - - +
876B ILE 3.1 0.2 + - - -
877B GLN* 1.3 70.1 - - - +
879B TYR* 1.3 64.5 + - + +
881B GLN* 2.7 43.5 + - - +
882B ASN* 3.1 42.0 + - - +
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Residues in contact with TYR 879 (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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467B CYS 3.4 21.8 - - - -
468B ASP* 3.9 2.5 + - - -
469B TRP* 2.8 62.5 + + + -
470B THR* 3.5 9.8 + - - -
848B LEU* 4.1 15.9 - - + -
875B ASN* 3.0 35.9 + - + +
876B ILE* 4.0 2.5 - - - +
878B GLN* 1.3 82.5 - - + +
880B ALA* 1.3 62.0 + - - +
882B ASN* 3.2 16.7 + - + +
883B MET* 3.0 34.5 + - + +
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Residues in contact with ALA 880 (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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848B LEU* 4.4 8.7 - - + +
852B ALA* 6.2 0.4 - - - -
876B ILE* 2.7 24.0 + - + +
877B GLN* 3.6 8.3 - - - +
879B TYR* 1.3 73.5 - - - +
881B GLN* 1.3 60.0 + - - +
883B MET* 3.2 13.7 + - - +
884B GLY 3.3 0.9 + - - -
885B LEU* 3.0 37.9 + - + +
890B ILE* 3.7 29.8 - - + -
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Residues in contact with GLN 881 (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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877B GLN* 3.0 16.0 + - - +
878B GLN* 2.7 33.1 + - - +
880B ALA* 1.3 73.4 - - - +
882B ASN* 1.3 58.4 + - - +
884B GLY* 3.0 18.4 + - - -
885B LEU 3.5 18.4 + - - +
886B PRO* 5.4 1.3 - - + -
887B GLN* 5.1 15.5 + - - +
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Residues in contact with ASN 882 (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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878B GLN* 3.1 35.0 + - - +
879B TYR* 3.2 18.6 + - + +
881B GLN* 1.3 76.8 - - - +
883B MET* 1.3 60.7 + - + +
884B GLY* 3.0 6.4 + - - -
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Residues in contact with MET 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B TRP* 5.5 0.7 - - + -
845B PRO* 3.7 29.6 - - + +
848B LEU* 4.2 15.9 - - + -
849B GLN* 3.7 48.1 + - + +
852B ALA* 4.1 17.7 - - + -
856B LYS* 3.0 24.4 + - - -
879B TYR* 3.0 28.2 + - + +
880B ALA* 3.2 7.8 + - - +
882B ASN* 1.3 77.4 - - + +
884B GLY* 1.3 56.9 + - - +
885B LEU* 4.8 0.9 - - - -
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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