Contacts of the helix formed by residues 937 - 947 (chain A) in PDB entry 4YOZ
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 ILE 937 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A LEU* 3.7 28.0 - - + -
838A ARG* 3.7 10.5 - - - +
884A LEU* 3.2 41.1 - - + +
933A PHE* 3.0 33.4 + - + +
935A ASN 3.4 0.8 - - - -
936A THR* 1.3 92.3 - - - +
938A TYR* 1.3 68.5 + - - +
939A VAL 3.4 1.6 + - - -
940A GLY* 3.5 11.2 + - - -
941A ARG* 3.5 17.6 + - + +
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Residues in contact with TYR 938 (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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823A CYS* 3.3 15.8 - - - -
827A THR* 3.6 17.9 - - + +
834A LEU* 4.5 7.6 - - + -
843A LEU* 4.3 13.7 - - + -
846A CYS* 3.7 33.4 - - + -
847A ALA* 3.3 21.8 - - - +
850A ILE* 3.9 16.2 - - + -
933A PHE* 3.2 23.9 + + + +
934A TYR* 3.5 36.1 - + - +
937A ILE* 1.3 82.9 - - - +
939A VAL* 1.3 62.7 + - - +
941A ARG* 3.3 3.8 + - - -
942A VAL* 3.0 53.0 + - + +
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Residues in contact with VAL 939 (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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850A ILE* 4.8 4.0 - - + -
934A TYR* 2.9 62.3 + - + +
935A ASN* 4.1 12.3 - - - +
937A ILE 3.4 0.4 - - - -
938A TYR* 1.3 74.6 - - - +
940A GLY* 1.3 60.5 + - - +
941A ARG 3.1 0.2 + - - -
943A LYS* 2.8 56.2 + - + +
22B LEU* 4.0 19.5 - - + +
23B TYR* 4.1 22.7 - - + +
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Residues in contact with GLY 940 (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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935A ASN 4.9 2.2 + - - -
936A THR 5.7 0.6 - - - -
937A ILE 3.5 7.5 + - - -
938A TYR 3.4 0.6 - - - -
939A VAL* 1.3 80.5 - - - +
941A ARG* 1.3 63.5 + - - +
943A LYS* 4.4 15.1 + - - +
944A SER* 5.3 0.9 + - - -
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Residues in contact with ARG 941 (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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826A PHE* 4.4 10.4 - - - -
830A HIS 4.2 3.4 + - - -
831A CYS* 3.4 34.4 - - - +
833A ASP* 2.9 42.6 + - - -
834A LEU* 3.9 25.2 - - + +
937A ILE* 3.5 15.4 + - + +
938A TYR 3.3 6.0 + - - +
939A VAL 3.1 0.6 - - - -
940A GLY* 1.3 80.3 - - - +
942A VAL* 1.3 66.4 + - + +
943A LYS 3.6 0.4 + - - -
944A SER* 4.8 6.6 + - - -
945A PHE 5.4 0.2 + - - -
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Residues in contact with VAL 942 (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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823A CYS* 3.6 30.3 - - - -
826A PHE* 3.8 25.8 - - + -
827A THR* 3.7 15.0 - - + -
831A CYS* 4.9 0.9 - - - -
834A LEU* 4.6 3.4 - - + -
850A ILE* 4.7 2.7 - - + -
938A TYR* 3.0 47.1 + - + +
941A ARG* 1.3 82.4 - - + +
943A LYS* 1.3 60.5 + - - +
944A SER 3.2 2.9 - - - -
945A PHE* 3.1 6.6 + - + -
946A ALA* 2.9 27.9 + - + +
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Residues in contact with LYS 943 (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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850A ILE* 4.6 2.0 - - - -
939A VAL* 2.8 37.1 + - + +
940A GLY* 4.5 13.0 - - - +
941A ARG 3.6 1.0 - - - -
942A VAL* 1.3 78.1 - - - +
944A SER* 1.3 62.7 + - - +
946A ALA* 4.2 6.5 - - - -
947A LEU* 2.8 55.2 + - + +
22B LEU* 4.2 14.4 - - + -
23B TYR* 6.1 1.1 - - - +
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Residues in contact with SER 944 (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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826A PHE* 6.4 0.2 - - - -
940A GLY 5.3 0.2 + - - -
941A ARG 4.8 6.2 + - - -
942A VAL 3.2 1.0 - - - -
943A LYS* 1.3 86.9 - - - +
945A PHE* 1.3 61.7 + - - +
947A LEU* 4.2 6.1 - - - +
948A LYS* 3.7 15.1 + - - +
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Residues in contact with PHE 945 (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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822A THR* 3.4 34.8 - - + -
823A CYS* 3.5 33.2 - - + -
826A PHE* 3.3 58.7 - + + -
851A MET* 4.7 2.7 - - + -
941A ARG 5.4 0.2 + - - -
942A VAL* 3.1 5.1 + - + +
944A SER* 1.3 75.6 - - - +
946A ALA* 1.3 69.6 + - - +
948A LYS* 3.1 19.7 - - + +
949A TYR* 3.3 28.5 - + - -
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Residues in contact with ALA 946 (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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850A ILE* 3.9 22.7 - - + -
851A MET* 3.3 33.0 - - + -
854A VAL* 4.3 10.6 - - + +
942A VAL* 2.9 17.5 + - + +
943A LYS* 3.8 3.4 - - - +
945A PHE* 1.3 73.7 - - + +
947A LEU* 1.3 51.8 + - - +
948A LYS 2.3 18.6 + - - -
949A TYR* 2.6 25.3 + - - +
22B LEU* 4.7 0.9 - - + -
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Residues in contact with LEU 947 (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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854A VAL* 4.7 8.5 - - + -
943A LYS* 2.8 49.3 + - + +
944A SER* 4.2 6.5 - - - +
946A ALA* 1.3 70.1 - - - +
948A LYS* 1.3 55.7 + - - +
949A TYR 3.1 11.3 + - - +
22B LEU* 3.9 24.9 - - + -
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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