Contacts of the helix formed by residues 870 - 884 (chain A) in PDB entry 2Y6O
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 LYS 870 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A ALA* 5.4 8.0 - - + +
807A VAL* 4.8 2.7 - - + -
865A ARG 5.1 3.0 + - - -
866A SER* 4.9 15.1 + - - +
868A ARG 4.4 10.3 + - - +
869A PRO* 1.3 78.0 - - - +
871A PHE* 1.3 65.8 + - - +
872A GLY 3.2 5.4 - - - +
873A GLN* 2.9 34.2 + - + +
874A ILE* 3.0 13.1 + - - +
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Residues in contact with PHE 871 (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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731A GLY* 4.3 8.7 - - - +
734A MET* 3.5 41.5 - - + -
735A LYS* 3.6 23.6 - - + +
738A SER* 3.6 24.2 - - - +
803A SER* 3.7 11.7 - - - -
806A ASP* 3.7 26.5 - - + -
807A VAL* 3.5 25.0 - - + +
810A TYR* 3.7 27.6 - + + -
870A LYS* 1.3 74.9 - - - +
872A GLY* 1.3 62.3 + - - +
874A ILE* 3.2 15.0 + - + +
875A VAL* 3.0 28.4 + - - +
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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
----------------------------------------------------------
735A LYS* 3.8 35.0 + - - +
870A LYS* 3.2 4.2 - - - +
871A PHE* 1.3 77.2 - - - +
873A GLN* 1.3 58.3 + - - +
875A VAL* 3.5 2.6 + - - +
876A ASN* 3.0 28.4 + - - +
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Residues in contact with GLN 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A ARG 4.7 0.3 - - - +
869A PRO* 3.4 8.5 - - + +
870A LYS* 2.9 43.8 + - + +
872A GLY* 1.3 74.5 - - - +
874A ILE* 1.3 60.2 + - - +
876A ASN* 3.6 6.4 - - - +
877A MET* 2.8 49.8 + - + +
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Residues in contact with ILE 874 (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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731A GLY* 5.1 1.1 - - - -
807A VAL* 4.0 15.5 - - + -
810A TYR* 3.5 36.8 - - + +
856A LEU* 4.3 14.9 - - + +
860A CYS* 3.9 20.6 - - - -
869A PRO* 4.0 16.4 - - + -
870A LYS 3.0 15.4 + - - +
871A PHE* 3.5 31.6 - - + +
873A GLN* 1.3 76.9 - - - +
875A VAL* 1.3 65.9 + - + +
877A MET* 3.2 9.0 + - - +
878A LEU* 3.0 30.0 + - + +
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Residues in contact with VAL 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ARG* 3.8 39.0 - - - +
731A GLY* 3.4 37.2 - - - +
732A SER* 3.6 8.5 - - - +
735A LYS* 4.6 11.0 - - + +
871A PHE 3.0 21.0 + - - +
872A GLY* 3.9 4.9 - - - +
874A ILE* 1.3 74.4 - - - +
876A ASN* 1.3 59.2 + - - +
878A LEU* 3.2 7.9 + - + +
879A ASP* 2.8 31.4 + - - +
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Residues in contact with ASN 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A GLY 3.0 19.1 + - - +
873A GLN* 3.6 7.3 + - - +
875A VAL* 1.3 78.3 - - - +
877A MET* 1.3 61.2 + - - +
879A ASP* 3.3 10.7 + - - +
880A LYS* 3.0 72.3 + - - +
883A ARG* 5.3 3.1 + - - -
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Residues in contact with MET 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A LEU* 3.6 37.2 - - + -
859A ASP* 4.7 9.0 - - - +
869A PRO* 3.9 17.9 - - + -
873A GLN* 2.8 43.3 + - + +
874A ILE 3.7 4.9 - - - +
876A ASN* 1.3 78.3 - - - +
878A LEU* 1.3 61.3 + - - +
880A LYS* 3.2 11.5 + - + +
881A LEU* 3.0 30.7 + - + +
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Residues in contact with LEU 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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724A VAL* 4.1 13.6 - - + +
727A LEU* 3.8 4.3 - - + +
728A ARG* 3.7 35.2 - - + +
731A GLY* 5.6 0.9 - - - -
810A TYR* 3.3 27.4 - - - +
814A MET* 4.8 3.8 - - + -
853A LEU* 3.9 24.2 - - + -
856A LEU* 3.8 20.6 - - + -
874A ILE* 3.0 28.1 + - + +
875A VAL* 3.7 5.6 - - - +
877A MET* 1.3 73.2 - - - +
879A ASP* 1.3 66.3 + - - +
881A LEU* 3.2 7.8 + - + +
882A ILE* 2.9 30.0 + - - +
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Residues in contact with ASP 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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728A ARG* 2.7 47.2 + - - +
875A VAL* 2.8 23.8 + - - +
876A ASN* 3.5 10.3 - - - +
878A LEU* 1.3 76.0 - - - +
880A LYS* 1.3 57.3 + - - +
882A ILE* 3.3 9.1 + - - +
883A ARG* 2.9 44.1 + - - +
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Residues in contact with LYS 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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876A ASN* 3.0 48.7 + - - +
877A MET* 3.6 12.1 - - + +
878A LEU 3.2 0.2 - - - -
879A ASP* 1.3 75.2 - - - +
881A LEU* 1.3 61.9 + - + +
883A ARG* 4.2 22.9 - - - +
884A ASN* 2.9 44.4 + - - +
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Residues in contact with LEU 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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724A VAL* 5.1 4.0 - - + -
852A ALA* 3.9 27.6 - - + +
853A LEU* 3.8 28.9 - - + -
856A LEU* 5.3 4.0 - - + -
877A MET* 3.0 21.8 + - + +
878A LEU* 3.6 14.8 - - + +
880A LYS* 1.3 78.9 - - + +
882A ILE* 1.3 60.2 + - - +
884A ASN 3.2 20.1 - - - +
885A PRO* 3.4 7.6 - - - +
887A SER* 3.1 28.3 + - - +
888A LEU* 4.2 21.4 - - + +
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Residues in contact with ILE 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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721A ILE* 4.6 25.2 - - + +
724A VAL* 3.7 27.6 - - + +
725A GLY* 4.7 7.9 - - - +
728A ARG* 4.2 27.1 - - + -
878A LEU 2.9 21.3 + - - +
879A ASP* 3.7 8.5 - - - +
881A LEU* 1.3 76.1 - - - +
883A ARG* 1.3 61.8 + - - +
884A ASN 3.5 0.2 + - - -
885A PRO* 3.6 13.0 - - - +
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Residues in contact with ARG 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ASN* 5.3 3.6 + - - -
879A ASP* 2.9 34.3 + - - +
880A LYS* 3.9 27.9 - - - +
882A ILE* 1.3 77.4 - - - +
884A ASN* 1.3 75.8 + - - +
885A PRO* 3.3 7.8 - - - +
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Residues in contact with ASN 884 (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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880A LYS* 2.9 31.0 + - - +
881A LEU 3.2 3.1 - - - -
883A ARG* 1.3 100.0 - - - +
885A PRO* 1.3 56.8 - - - +
886A ASN* 3.1 4.0 - - + -
887A SER* 2.5 41.9 + - - +
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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