Contacts of the helix formed by residues 937 - 951 (chain A) in PDB entry 3NYX
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 GLY 937 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935A ASP* 3.8 4.6 + - - -
936A CYS* 1.3 76.5 - - - +
938A PRO* 1.3 76.2 - - - +
939A GLN 3.2 2.7 - - - -
940A HIS* 3.1 9.0 + - - -
941A ARG* 3.0 26.2 + - - +
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Residues in contact with PRO 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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937A GLY* 1.3 83.1 - - - +
939A GLN* 1.3 72.1 + - - +
941A ARG* 3.5 29.6 + - - +
942A SER* 2.7 35.5 + - - -
967A GLU* 4.9 2.1 - - - +
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Residues in contact with GLN 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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937A GLY 3.2 0.4 - - - -
938A PRO* 1.3 95.7 + - - +
940A HIS* 1.3 69.6 + - + +
941A ARG 3.2 0.2 - - - -
942A SER* 3.3 10.3 + - - +
943A GLY* 3.0 20.4 + - - -
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Residues in contact with HIS 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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2A DTT 3.6 19.0 + - - -
936A CYS* 2.6 35.0 - - + +
937A GLY* 3.1 5.6 + - - +
939A GLN* 1.3 79.6 - - + +
941A ARG* 1.3 61.7 + - - +
943A GLY* 3.2 4.2 + - - -
944A TRP* 3.1 22.5 + - - +
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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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2A DTT 3.8 8.2 - - - -
934A ALA* 3.1 46.3 + - + +
935A ASP* 4.1 5.5 + - - +
936A CYS 4.4 2.6 - - - +
937A GLY* 3.0 14.1 + - - +
938A PRO* 3.5 32.7 - - - +
939A GLN 3.2 0.2 - - - -
940A HIS* 1.3 76.9 - - - +
942A SER* 1.3 61.2 + - - +
944A TRP* 3.2 6.6 + - - +
945A LYS* 3.1 19.9 + - - +
967A GLU* 3.1 39.8 + - - +
969A GLN* 4.7 13.6 + - - +
972A LYS* 3.5 42.0 - - - +
973A SER 4.5 2.5 - - - +
974A LEU* 4.2 8.6 - - + +
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Residues in contact with SER 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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938A PRO 2.7 20.3 + - - -
939A GLN* 3.3 13.5 + - - -
941A ARG* 1.3 73.7 - - - +
943A GLY* 1.3 59.2 + - - +
945A LYS* 3.1 12.3 + - - +
946A GLN* 2.8 46.7 + - - -
967A GLU* 4.5 10.3 + - - -
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Residues in contact with GLY 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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939A GLN 3.0 13.9 + - - -
940A HIS* 3.2 5.3 + - - -
942A SER* 1.3 76.8 - - - +
944A TRP* 1.3 56.2 - - - +
946A GLN* 3.7 13.9 + - - +
947A GLU* 3.2 27.7 + - - +
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Residues in contact with TRP 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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1A TZ1 5.5 4.8 - + - -
2A DTT 3.2 70.5 - - + +
932A LEU* 3.4 39.0 - - + -
933A LYS 3.5 19.3 - - - -
934A ALA* 3.7 13.5 - - + -
940A HIS 3.1 10.9 + - - +
941A ARG* 3.5 8.3 - - - +
942A SER 3.1 0.2 - - - -
943A GLY* 1.3 76.3 - - - +
945A LYS* 1.3 60.4 + - - +
947A GLU* 3.3 17.8 + - + +
948A ILE* 2.9 50.0 + - + +
974A LEU* 3.7 15.3 - - + -
1043A GLY 5.9 1.3 + - - -
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Residues in contact with LYS 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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941A ARG 3.1 12.0 + - - +
942A SER* 3.1 12.3 + - - +
944A TRP* 1.3 72.5 - - - +
946A GLN* 1.3 59.3 + - + +
947A GLU 3.1 0.3 + - - -
948A ILE* 3.3 0.5 + - - +
949A ASP* 2.7 56.5 + - - +
965A CYS* 2.8 43.6 + - - +
966A CYS* 4.5 7.6 - - - +
967A GLU* 4.1 22.7 - - - +
974A LEU* 4.1 14.7 - - + +
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Residues in contact with GLN 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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942A SER* 2.8 38.0 + - - +
943A GLY* 3.9 13.1 - - - +
945A LYS* 1.3 76.6 - - + +
947A GLU* 1.3 61.6 + - - +
949A ASP* 3.3 10.4 + - - +
950A ILE* 3.2 30.0 + - + +
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Residues in contact with GLU 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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943A GLY 3.2 16.9 + - - +
944A TRP* 3.5 18.6 + - + +
945A LYS 3.1 0.8 - - - -
946A GLN* 1.3 74.5 - - - +
948A ILE* 1.3 66.1 + - - +
950A ILE* 3.2 29.2 + - + +
951A LEU* 3.9 6.6 + - - +
1019A TYR* 5.2 1.0 + - - -
1045A ALA 4.8 3.8 - - - +
1046A LYS* 3.7 30.4 + - - +
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Residues in contact with ILE 948 (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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1A TZ1 4.6 13.5 - - + -
932A LEU* 4.2 16.8 - - + -
944A TRP* 2.9 55.6 + - + +
945A LYS 3.7 2.2 - - - +
947A GLU* 1.3 73.5 - - - +
949A ASP* 1.3 64.7 + - - +
951A LEU* 2.9 38.0 + - + +
952A ARG* 4.1 2.1 + - - +
962A TYR* 5.7 1.6 - - + +
965A CYS* 3.8 24.9 - - + -
974A LEU* 4.1 17.0 - - + -
976A LEU* 4.0 21.1 - - + -
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Residues in contact with ASP 949 (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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945A LYS* 2.7 50.5 + - - +
946A GLN* 3.4 10.6 - - - +
947A GLU 3.3 0.4 - - - -
948A ILE* 1.3 72.0 - - - +
950A ILE* 1.3 61.8 + - - +
952A ARG* 3.1 51.5 + - - +
953A THR* 4.3 2.3 + - - +
965A CYS* 3.3 30.2 + - - +
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Residues in contact with ILE 950 (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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946A GLN* 3.2 21.4 + - + +
947A GLU* 3.5 21.1 - - + +
948A ILE 3.0 1.4 + - - -
949A ASP* 1.3 76.9 - - + +
951A LEU* 1.3 57.7 + - - +
953A THR* 2.6 46.5 + - + +
954A LEU* 4.8 1.2 - - - +
1019A TYR* 3.3 23.2 + - + +
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Residues in contact with LEU 951 (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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1A TZ1 4.3 16.2 - - + -
947A GLU 4.3 4.5 - - - +
948A ILE* 2.9 30.9 + - + +
950A ILE* 1.3 77.7 - - - +
952A ARG* 1.3 54.0 + - - +
954A LEU* 3.1 43.5 + - + +
962A TYR* 4.2 25.9 + - + +
1019A TYR* 3.9 28.0 - - + +
1042A PHE* 4.1 36.3 - - + +
1045A ALA* 4.5 4.9 - - + -
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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