Contacts of the helix formed by residues 957 - 964 (chain A) in PDB entry 2RD0
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 THR 957 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A PHE* 6.0 4.5 - - + -
918A ASN* 5.1 9.0 + - - +
955A VAL* 3.0 16.9 + - + +
956A LEU* 1.3 78.0 - - - +
958A GLN* 1.3 69.3 + - - +
959A ASP* 3.4 21.5 + - - -
960A PHE* 2.9 42.4 + - + +
961A LEU* 3.4 10.8 + - - +
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Residues in contact with GLN 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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872A PHE* 5.8 6.0 - - + -
874A SER* 5.8 0.7 - - - +
956A LEU 4.9 1.5 + - - +
957A THR* 1.3 78.4 - - - +
959A ASP* 1.3 59.4 + - - +
961A LEU* 3.0 23.0 + - + +
962A ILE* 2.8 47.6 + - + +
970A GLU* 5.7 2.6 + - - -
971A CYS* 6.2 2.2 - - - -
1047A HIS 5.8 1.6 + - - -
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Residues in contact with ASP 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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857A ILE* 4.6 5.4 - - + +
861A GLN* 3.2 23.6 - - - +
872A PHE* 3.2 44.9 - - - +
874A SER* 4.1 6.3 + - - +
877A LEU* 4.0 19.7 - - + +
918A ASN* 4.7 3.8 + - - +
957A THR* 3.4 18.1 + - - +
958A GLN* 1.3 77.8 + - - +
960A PHE* 1.3 63.7 + - + +
962A ILE* 3.7 10.2 + - - +
963A VAL* 3.2 28.5 + - - +
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Residues in contact with PHE 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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857A ILE* 3.6 36.1 - - + -
877A LEU* 4.8 4.7 - - + -
897A PHE* 3.7 25.5 - + + -
901A CYS* 4.7 2.7 - - - -
918A ASN* 4.8 5.8 - - - -
921A ILE* 4.1 19.3 - - + -
929A LEU* 3.9 17.5 - - + -
954A PHE* 4.5 8.3 - + - -
955A VAL 4.7 0.9 - - - -
956A LEU* 4.1 21.8 - - + -
957A THR* 2.9 56.7 + - + +
958A GLN 3.2 0.2 - - - -
959A ASP* 1.3 75.2 - - + +
961A LEU* 1.3 66.5 + - + +
963A VAL* 3.5 8.9 + - - +
964A ILE* 3.2 26.7 + - + +
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Residues in contact with LEU 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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956A LEU* 4.4 23.3 - - + +
957A THR 3.4 10.8 - - - +
958A GLN* 3.0 35.8 + - + +
960A PHE* 1.3 76.4 - - - +
962A ILE* 1.3 65.6 + - - +
964A ILE* 3.1 29.5 + - + +
971A CYS* 3.7 32.4 - - + +
972A THR* 5.3 9.6 - - - +
977A PHE* 3.6 33.9 - - + -
1047A HIS* 5.7 4.9 - - + -
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Residues in contact with ILE 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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874A SER* 3.4 43.1 - - - +
878A HIS* 3.5 25.0 - - + +
958A GLN* 2.8 30.6 + - + +
959A ASP* 3.9 5.2 - - - +
961A LEU* 1.3 77.2 - - - +
963A VAL* 1.3 62.2 + - - +
964A ILE 3.1 1.6 + - - -
965A SER* 3.2 23.2 - - - -
966A LYS* 3.3 21.9 + - + +
967A GLY 5.4 5.4 - - - +
971A CYS* 4.4 13.9 - - - -
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Residues in contact with VAL 963 (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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877A LEU* 3.2 36.8 - - + +
878A HIS* 4.0 11.2 - - + -
881A LEU* 3.6 22.2 - - + -
894A ILE* 3.1 28.5 - - + +
897A PHE* 3.6 33.2 - - + -
959A ASP 3.2 17.4 + - - +
960A PHE 3.7 8.1 - - - +
961A LEU 3.3 0.6 - - - -
962A ILE* 1.3 75.8 - - - +
964A ILE* 1.3 52.8 + - - +
965A SER* 2.6 14.9 + - - -
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Residues in contact with ILE 964 (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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894A ILE* 4.6 4.7 - - + -
897A PHE* 5.0 8.3 - - + -
898A THR* 4.1 21.3 - - + +
901A CYS* 6.0 3.1 - - - -
956A LEU* 6.3 1.6 - - + -
960A PHE* 3.2 18.2 - - + +
961A LEU* 3.1 17.7 + - + +
962A ILE 3.1 1.5 - - - -
963A VAL* 1.3 71.8 - - - +
965A SER* 1.3 69.0 + - - +
971A CYS* 5.1 2.6 - - - +
974A THR* 4.6 5.2 + - - +
976A GLU* 3.6 43.3 - - + +
977A PHE* 4.3 18.8 - - + +
979A ARG* 4.2 3.6 - - - +
980A PHE* 4.1 31.9 - - + -
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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