Contacts of the helix formed by residues 1001 - 1013 (chain C) in PDB entry 5Y3R
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 PHE1001 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942C LEU* 5.4 5.4 - - + -
948C MET* 4.7 22.7 - - + -
952C GLY* 6.1 5.2 - - - -
994C TRP* 5.0 4.7 - - - -
995C PHE* 4.5 4.9 - - + -
998C ASN* 4.8 5.6 - - + -
999C LYS* 3.3 37.4 + - + -
1000C LYS* 1.3 73.0 - - - +
1002C GLU* 1.3 102.3 + - + +
1003C SER 2.8 3.9 - - - +
1004C GLN* 2.6 31.4 + - - +
1005C ASP* 2.9 21.4 - - - +
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Residues in contact with GLU1002 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C LEU* 3.6 20.9 - - - +
959C TYR* 5.2 8.3 - - + -
963C LYS* 4.1 7.4 - - - +
991C LEU* 3.5 8.3 - - - +
994C TRP* 2.9 36.9 + - - -
995C PHE* 3.1 27.4 - - + +
1001C PHE* 1.3 111.5 - - + +
1003C SER* 1.3 53.7 + - - +
1005C ASP* 3.0 15.7 - - + +
1006C THR* 2.7 38.6 + - - -
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Residues in contact with SER1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995C PHE* 3.1 26.5 - - - -
1000C LYS* 3.0 50.4 + - - +
1001C PHE 2.8 1.0 - - - +
1002C GLU* 1.3 72.5 - - - +
1004C GLN* 1.3 55.2 + - - -
1005C ASP 2.6 15.0 + - - -
1007C VAL* 2.8 31.5 + - - +
1054C VAL* 4.1 13.8 - - - +
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Residues in contact with GLN1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956C PRO* 6.0 2.9 - - + -
1000C LYS 4.8 1.1 - - - +
1001C PHE* 2.6 23.1 + - - +
1003C SER* 1.3 73.1 - - - +
1005C ASP* 1.3 64.4 + - - +
1007C VAL* 4.0 10.1 - - - +
1008C ALA* 3.7 16.5 + - - +
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Residues in contact with ASP1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956C PRO* 4.8 23.5 - - - +
959C TYR* 4.8 10.1 - - + -
960C GLN* 5.7 5.3 - - - +
963C LYS* 3.2 25.9 - - + +
1001C PHE* 2.9 23.4 - - - +
1002C GLU* 3.0 19.5 + - - +
1003C SER 2.6 6.1 + - - -
1004C GLN* 1.3 87.8 - - - +
1006C THR* 1.3 59.7 + - - +
1007C VAL 3.1 1.3 - - - -
1008C ALA* 2.9 11.7 + - - +
1009C LEU 2.8 21.1 + - - -
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Residues in contact with THR1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963C LYS* 2.2 37.3 + - - +
991C LEU* 3.2 8.4 - - + +
992C ILE* 4.2 12.3 - - + -
995C PHE* 3.1 26.1 - - + -
1002C GLU 2.7 14.6 + - - -
1005C ASP* 1.3 68.0 - - - +
1007C VAL* 1.3 66.5 + - - +
1009C LEU* 2.8 43.4 + - + +
1010C LEU* 2.9 19.6 + - + +
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Residues in contact with VAL1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C SER* 2.8 27.6 + - - +
1004C GLN* 4.0 9.9 - - - +
1006C THR* 1.3 78.0 - - - +
1008C ALA* 1.3 67.3 + - - +
1010C LEU* 2.9 25.3 - - + +
1011C GLU* 2.9 28.2 - - - +
1053C PRO* 6.5 0.2 - - + -
1054C VAL* 3.7 36.9 - - + +
1062C ARG* 5.3 12.6 - - - +
3725C ARG* 6.3 0.2 - - - +
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Residues in contact with ALA1008 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960C GLN* 4.8 21.3 - - + +
1004C GLN* 3.7 12.0 + - - +
1005C ASP* 2.9 16.7 + - - +
1007C VAL* 1.3 76.1 - - - +
1009C LEU* 1.3 65.0 + - - +
1011C GLU* 2.8 29.2 + - - +
1012C ALA* 3.9 2.4 + - - +
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Residues in contact with LEU1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963C LYS* 3.5 40.6 - - + +
964C ARG* 4.6 2.6 - - - +
966C PHE* 5.7 2.2 - - + -
967C PRO* 4.0 27.6 - - + -
988C VAL* 6.0 5.8 - - + -
991C LEU* 4.5 7.0 - - + -
992C ILE* 5.6 1.8 - - + -
1005C ASP 2.8 6.1 + - - -
1006C THR* 2.8 39.4 + - + +
1008C ALA* 1.3 79.4 - - - +
1010C LEU* 1.3 63.4 + - + +
1011C GLU 2.9 0.5 + - - -
1012C ALA* 3.9 2.6 + - - +
1013C ILE* 3.0 22.1 + - + +
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Residues in contact with LEU1010 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006C THR* 2.9 23.9 + - + +
1007C VAL* 2.9 29.2 - - + +
1009C LEU* 1.3 75.3 - - + +
1011C GLU* 1.3 85.2 + - - +
1013C ILE* 2.7 25.8 + - - +
1014C LEU 3.1 2.4 + - - -
1028C PHE* 3.1 32.9 - - + -
1031C ARG* 6.3 2.5 - - + -
1032C CYS* 5.4 3.8 - - - -
1035C GLU* 4.8 15.9 - - - +
1054C VAL* 5.5 4.9 - - + -
1059C LEU* 6.3 4.9 - - + -
1062C ARG* 5.7 5.6 - - - +
1063C LEU* 5.9 3.1 - - + -
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Residues in contact with GLU1011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C VAL* 2.9 46.3 + - + +
1008C ALA* 2.8 23.9 + - - +
1010C LEU* 1.3 85.6 - - - +
1012C ALA* 1.3 53.3 + - - +
1014C LEU* 2.3 49.5 + - + +
1062C ARG* 4.6 11.6 + - - -
1066C LEU* 4.6 16.8 - - - +
3725C ARG* 4.4 16.7 + - - +
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Residues in contact with ALA1012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964C ARG* 5.6 9.9 - - - -
1008C ALA 3.9 3.5 + - - +
1009C LEU 3.9 1.5 + - - +
1011C GLU* 1.3 78.2 - - - +
1013C ILE* 1.3 58.8 + - + +
1014C LEU* 2.8 13.9 - - + +
1015C ASP* 2.3 38.9 + - + +
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Residues in contact with ILE1013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964C ARG* 6.0 2.5 - - - -
967C PRO* 4.1 28.9 - - + -
1009C LEU* 3.0 27.8 - - + +
1010C LEU* 2.7 16.9 + - - +
1011C GLU 2.7 0.8 + - - -
1012C ALA* 1.3 80.0 - - + +
1014C LEU* 1.3 64.4 + - - +
1015C ASP 3.0 4.3 - - - -
1024C THR* 3.8 28.9 - - + +
1025C LEU* 3.0 14.6 - - - +
1027C ASP* 5.3 2.0 - - + -
1028C PHE* 3.3 40.5 - - + +
1078C ALA* 5.8 0.3 - - - +
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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