Contacts of the helix formed by residues 951 - 962 (chain A) in PDB entry 5A7R
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 951 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A TYR* 3.2 35.7 + - - -
878A ASP* 5.6 2.0 - - - -
935A TYR* 3.6 3.4 - - - -
948A PRO* 4.5 13.5 + - + +
950A ILE* 1.3 84.9 - - - +
952A LEU* 1.3 66.5 + - - +
953A TYR 3.5 1.1 - - - +
954A PRO* 3.5 23.9 - - + +
955A PHE* 3.2 20.6 + - - +
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Residues in contact with LEU 952 (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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832A TYR* 5.7 1.2 + - - -
836A PHE* 4.3 9.4 - - + -
878A ASP* 5.7 3.1 - - - +
880A ARG* 5.8 1.8 - - + -
881A LEU* 3.8 44.6 - - + +
884A LEU* 4.6 3.8 - - + -
932A LEU* 3.9 22.2 - - + -
935A TYR* 3.5 49.4 + - + -
951A LYS* 1.3 74.8 - - - +
953A TYR* 1.3 79.8 + - + +
955A PHE* 3.3 4.3 + - - +
956A ILE* 3.0 39.9 + - + +
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Residues in contact with TYR 953 (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 ARG* 2.7 65.6 + - + -
883A ALA* 4.2 3.5 - - - +
884A LEU* 4.2 22.1 + - + +
887A ILE* 6.1 0.3 - - - +
910A ASP* 3.5 38.4 - - + -
911A ILE* 4.1 14.4 - - - +
914A MET* 3.6 33.1 - - + +
951A LYS* 4.5 0.6 - - - +
952A LEU* 1.3 87.5 - - + +
954A PRO* 1.4 74.6 - - + +
956A ILE* 3.2 4.7 + - + +
957A TYR* 3.0 38.2 + + + -
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Residues in contact with PRO 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A ILE* 4.3 12.3 - - + -
951A LYS* 3.5 31.6 - - + +
953A TYR* 1.4 93.0 - - + +
955A PHE* 1.3 61.4 + - - +
957A TYR* 3.4 11.5 + - + +
958A HIS* 3.0 26.2 + - - +
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Residues in contact with PHE 955 (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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931A LEU* 3.8 11.4 - - + -
934A ARG* 3.8 8.1 - - + -
935A TYR* 3.5 54.1 - + + -
938A GLU* 3.4 44.6 - - + -
939A GLU* 4.1 12.1 - - + -
950A ILE* 3.7 16.0 - - + +
951A LYS 3.2 12.2 + - - +
952A LEU 3.3 8.3 - - - +
954A PRO* 1.3 81.2 - - - +
956A ILE* 1.3 66.2 + - + +
958A HIS* 3.7 8.6 - + - +
959A ALA* 2.9 44.4 + - + +
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Residues in contact with ILE 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A LEU* 3.7 29.8 - - + -
914A MET* 3.8 27.6 - - + -
917A PHE* 4.7 1.3 - - + -
918A LEU* 4.3 10.3 - - + -
928A VAL* 5.5 3.1 - - + -
931A LEU* 4.2 31.6 - - + +
932A LEU* 4.6 5.4 - - + -
952A LEU* 3.0 38.0 + - + +
953A TYR* 3.6 7.2 - - + +
955A PHE* 1.3 81.6 - - + +
957A TYR* 1.3 68.0 + - - +
959A ALA* 3.3 3.6 + - - +
960A VAL* 3.1 25.8 + - + +
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Residues in contact with TYR 957 (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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910A ASP* 4.4 1.9 + - - -
913A SER* 3.3 15.4 - - - -
914A MET* 3.2 45.4 + - + +
917A PHE* 3.7 47.6 - + + -
953A TYR* 3.0 33.3 + + + +
954A PRO* 3.9 9.2 - - + +
956A ILE* 1.3 76.8 - - - +
958A HIS* 1.3 57.5 + - - +
960A VAL* 4.0 1.0 - - - +
961A GLU* 2.9 47.8 + - - +
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Residues in contact with HIS 958 (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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950A ILE* 6.1 1.8 - - + -
954A PRO 3.0 17.3 + - - +
955A PHE* 3.7 10.8 - + - +
957A TYR* 1.3 78.4 - - - +
959A ALA* 1.3 56.0 + - - +
961A GLU* 3.8 5.1 - - - -
962A SER* 2.8 61.5 + - - -
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Residues in contact with ALA 959 (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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931A LEU* 3.9 19.7 - - + -
934A ARG* 3.8 29.6 + - - +
955A PHE* 2.9 29.4 + - + +
956A ILE 3.8 4.0 - - - +
958A HIS* 1.3 83.1 - - + +
960A VAL* 1.3 62.6 + - - +
962A SER* 4.1 4.1 - - - -
963A CYS* 3.6 19.2 + - - +
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Residues in contact with VAL 960 (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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917A PHE* 3.6 28.0 - - + -
921A ARG* 3.7 29.5 + - - +
923A LEU* 4.1 18.4 - - + -
931A LEU* 3.7 29.4 - - + -
956A ILE* 3.1 18.4 + - + +
959A ALA* 1.3 76.8 - - - +
961A GLU* 1.3 65.1 + - - +
962A SER 3.3 0.3 + - - -
963A CYS* 3.4 18.5 + - - +
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Residues in contact with GLU 961 (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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917A PHE* 4.0 19.0 - - + -
921A ARG* 4.0 23.3 + - - +
957A TYR* 2.9 31.9 + - - +
958A HIS* 4.2 4.1 - - - +
960A VAL* 1.3 77.8 - - - +
962A SER* 1.3 59.7 + - - +
963A CYS 3.4 3.3 + - - +
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Residues in contact with SER 962 (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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958A HIS* 2.8 51.7 + - - -
959A ALA* 4.1 6.1 - - - -
960A VAL 3.2 0.2 - - - -
961A GLU* 1.3 76.9 - - - +
963A CYS* 1.3 62.8 + - - +
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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