Contacts of the helix formed by residues 871 - 883 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A ILE* 5.5 1.8 - - + -
436A PRO* 4.3 26.5 - - + -
466A VAL* 3.4 31.5 - - + +
869A PRO* 3.9 15.9 - - + -
870A ALA* 1.3 77.1 - - + +
872A GLY* 1.3 62.9 + - - +
874A PRO* 3.3 19.4 - - - +
875A ASN* 4.2 10.2 + - - -
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Residues in contact with GLY 872 (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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466A VAL* 3.5 22.7 - - - +
467A CYS* 5.2 0.4 - - - -
840A LEU* 3.9 15.9 - - - -
869A PRO* 2.8 14.3 + - - +
871A VAL* 1.3 82.6 - - - +
873A GLU* 1.3 65.3 + - - +
875A ASN* 3.3 7.4 + - - +
876A ILE* 3.3 20.3 + - - +
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Residues in contact with GLU 873 (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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840A LEU* 4.4 1.2 - - - +
867A ARG* 3.0 30.8 + - + -
869A PRO 3.9 1.8 + - - +
870A ALA* 2.9 13.9 + - - +
872A GLY* 1.3 75.4 - - - +
874A PRO* 1.4 69.4 - - + +
876A ILE* 3.0 5.9 + - - +
877A GLN* 3.0 34.8 + - + +
887A GLN* 5.9 0.2 + - - -
892A PHE* 3.3 58.9 + - + +
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Residues in contact with PRO 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A ALA 3.5 6.7 - - - +
871A VAL* 3.3 21.8 - - - +
873A GLU* 1.4 93.4 - - + +
875A ASN* 1.3 61.1 + - - +
877A GLN* 3.2 10.9 + - + +
878A GLN* 2.7 30.6 + - - +
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Residues in contact with ASN 875 (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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466A VAL* 2.8 28.3 + - - +
467A CYS* 3.4 17.9 - - + +
468A ASP* 3.7 21.7 + - - +
871A VAL 4.2 8.1 + - - -
872A GLY 3.3 8.0 + - - +
873A GLU 3.2 0.8 - - - -
874A PRO* 1.3 75.0 - - - +
876A ILE* 1.3 71.7 + - - +
878A GLN* 3.0 7.9 + - - +
879A TYR* 3.0 30.2 + - + -
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Residues in contact with ILE 876 (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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467A CYS* 3.9 22.4 - - + -
469A TRP* 3.8 28.3 - - + -
840A LEU* 5.0 6.1 - - + -
843A ILE* 4.6 15.5 - - + -
848A LEU* 4.0 17.7 - - + -
865A LEU* 4.5 8.1 - - + -
872A GLY 3.3 13.7 + - - +
873A GLU 3.0 5.6 + - - +
875A ASN* 1.3 74.6 - - - +
877A GLN* 1.3 57.8 + - - +
879A TYR* 2.8 8.1 + - - +
880A ALA* 2.7 33.3 + - - +
890A ILE* 4.3 18.2 - - + -
892A PHE* 4.0 23.3 - - + -
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Residues in contact with GLN 877 (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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873A GLU* 3.0 31.3 + - + +
874A PRO* 3.2 11.7 - - + +
876A ILE* 1.3 74.6 - - - +
878A GLN* 1.3 61.9 + - - +
880A ALA* 3.4 7.9 + - - +
881A GLN* 3.0 29.8 + - - +
887A GLN* 3.8 39.1 + - - +
890A ILE* 3.8 32.6 + - - +
892A PHE* 3.9 18.0 - - + -
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Residues in contact with GLN 878 (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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874A PRO 2.7 15.9 + - - +
875A ASN* 3.2 14.1 - - - +
876A ILE 2.9 0.6 + - - -
877A GLN* 1.3 71.1 - - - +
879A TYR* 1.3 73.5 + - + +
881A GLN* 2.9 31.2 + - - +
882A ASN* 3.1 44.4 + - - +
677B GLU* 5.3 0.6 - - - +
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Residues in contact with TYR 879 (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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467A CYS 3.4 21.3 - - - -
468A ASP* 4.1 2.5 + - - -
469A TRP* 3.0 61.3 + + + -
470A THR* 3.6 10.6 + - - -
848A LEU* 4.2 14.1 - - + -
875A ASN* 3.0 31.9 + - + -
876A ILE* 2.8 8.7 + - - +
878A GLN* 1.3 85.8 - - + +
880A ALA* 1.3 61.9 + - - +
882A ASN* 3.3 15.9 + - + +
883A MET* 3.0 38.0 + - + +
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Residues in contact with ALA 880 (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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848A LEU* 4.5 8.4 - - + +
852A ALA* 6.3 0.4 - - - -
876A ILE* 2.7 22.6 + - + +
877A GLN* 3.5 9.9 - - - +
879A TYR* 1.3 72.9 - - - +
881A GLN* 1.3 60.1 + - - +
883A MET* 3.4 7.0 + - - +
884A GLY 3.4 5.2 + - - -
885A LEU* 2.9 39.6 + - + +
890A ILE* 3.6 31.0 - - + -
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Residues in contact with GLN 881 (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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877A GLN* 3.0 16.1 + - - +
878A GLN* 2.9 22.0 + - - +
880A ALA* 1.3 78.3 - - - +
882A ASN* 1.3 55.6 + - - +
884A GLY* 3.0 16.8 + - - -
885A LEU 3.4 17.6 + - - +
887A GLN* 5.1 15.3 + - - +
676B ALA* 4.1 1.5 - - - +
677B GLU* 2.6 79.3 + - + +
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Residues in contact with ASN 882 (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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878A GLN* 3.1 37.8 + - - +
879A TYR* 3.3 18.3 + - + +
881A GLN* 1.3 72.8 - - - +
883A MET* 1.3 61.5 + - + +
884A GLY* 3.1 6.5 + - - -
671B GLN* 5.4 5.9 + - - -
677B GLU* 4.1 15.2 - - - +
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Residues in contact with MET 883 (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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469A TRP* 5.5 0.4 - - + -
845A PRO* 3.7 28.9 - - + +
848A LEU* 4.2 18.2 - - + -
849A GLN* 3.8 47.0 + - + +
852A ALA* 4.1 18.4 - - + -
856A LYS* 3.1 24.6 + - - -
879A TYR* 3.0 29.8 + - + +
880A ALA* 3.8 6.5 - - - +
881A GLN 3.2 0.4 - - - -
882A ASN* 1.3 77.1 - - + +
884A GLY* 1.3 57.0 + - - +
885A LEU* 3.7 1.6 - - + -
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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