Contacts of the helix formed by residues 954 - 965 (chain A) in PDB entry 5I4E
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 SER 954 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950A GLU* 3.1 32.5 - - - +
951A THR* 2.4 32.3 + - - -
952A GLY 3.1 2.1 - - - -
953A ASP* 1.3 79.8 - - - +
955A ILE* 1.3 59.6 + - - +
956A THR 3.4 0.4 - - - -
957A ALA* 3.3 6.7 + - - +
958A VAL* 2.9 33.9 + - - +
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Residues in contact with ILE 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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950A GLU* 3.0 33.7 - - + +
951A THR 4.2 7.2 - - - +
952A GLY* 5.6 2.0 - - - -
953A ASP 4.4 1.8 - - - +
954A SER* 1.3 79.2 - - - +
956A THR* 1.3 55.4 + - - +
958A VAL* 3.3 5.4 + - + +
959A GLN* 2.8 53.8 + - - +
1020A ALA* 3.2 37.7 - - + +
1022A THR* 4.2 16.6 - - + -
1024A LYS* 4.0 11.2 - - - -
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Residues in contact with THR 956 (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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953A ASP* 4.7 12.7 + - - -
954A SER 3.4 1.4 - - - +
955A ILE* 1.3 76.4 - - - +
957A ALA* 1.4 56.4 + - - +
959A GLN* 3.5 13.6 + - + +
960A ALA* 3.1 27.0 + - - +
1024A LYS* 4.4 15.4 + - - +
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Residues in contact with ALA 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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953A ASP 4.0 14.8 + - - +
954A SER* 3.3 11.5 + - - +
955A ILE 3.3 0.4 - - - -
956A THR* 1.4 76.7 - - - +
958A VAL* 1.4 60.9 + - + +
960A ALA* 3.3 8.8 + - - +
961A LYS* 3.1 33.4 + - + +
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Residues in contact with VAL 958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A GLU* 3.5 25.8 - - - +
954A SER* 2.9 21.0 + - - +
955A ILE* 3.3 8.3 + - + +
957A ALA* 1.4 75.1 - - + +
959A GLN* 1.4 57.0 + - - +
961A LYS* 3.0 25.4 + - + +
962A LEU* 2.9 36.5 + - + +
1016A VAL* 5.4 6.7 - - + -
1020A ALA* 4.9 15.3 - - + -
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Residues in contact with GLN 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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955A ILE* 2.8 39.4 + - + +
956A THR* 3.7 14.7 - - + +
957A ALA 3.4 0.2 - - - -
958A VAL* 1.4 71.4 - - - +
960A ALA* 1.3 59.1 + - - +
962A LEU* 3.8 12.8 + - + +
963A LYS* 3.6 27.3 + - - +
1017A LYS* 5.3 5.2 - - + +
1020A ALA* 4.1 9.8 - - + +
1021A GLU* 2.9 44.0 + - - +
1024A LYS* 2.8 28.0 + - - +
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Residues in contact with ALA 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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956A THR 3.1 13.3 + - - +
957A ALA* 3.4 13.0 - - - +
958A VAL 3.2 0.4 - - - -
959A GLN* 1.3 74.6 - - - +
961A LYS* 1.4 62.1 + - + +
962A LEU 3.4 0.7 - - - -
963A LYS* 3.5 22.7 - - - +
964A ASN* 3.3 20.6 - - - +
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Residues in contact with LYS 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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957A ALA* 3.1 21.5 + - + +
958A VAL* 3.0 27.6 + - - +
960A ALA* 1.4 75.0 - - + +
962A LEU* 1.3 61.1 + - - +
963A LYS 3.3 0.7 - - - -
964A ASN* 3.9 8.9 + - - +
965A LEU* 3.4 31.8 + - + +
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Residues in contact with LEU 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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942A LYS* 5.9 3.1 - - - +
958A VAL* 2.9 21.6 + - + +
959A GLN* 3.9 12.8 - - + +
960A ALA 3.4 0.2 - - - -
961A LYS* 1.3 74.7 - - - +
963A LYS* 1.4 62.3 + - - +
964A ASN 3.6 0.2 - - - -
965A LEU* 3.5 20.7 + - + +
966A GLU* 3.8 16.7 + - - +
1013A TRP* 4.1 31.6 - - + +
1016A VAL* 3.9 28.7 - - + +
1017A LYS* 4.0 40.2 - - + +
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Residues in contact with LYS 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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959A GLN* 3.6 17.5 + - - +
960A ALA* 3.5 20.6 + - - +
961A LYS 3.3 0.6 - - - -
962A LEU* 1.4 75.7 - - + +
964A ASN* 1.4 60.3 + - - +
965A LEU 3.1 1.6 - - - -
966A GLU* 3.1 33.2 + - - +
967A ALA 4.5 0.2 + - - -
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Residues in contact with ASN 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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960A ALA 3.3 16.3 + - - +
961A LYS* 3.9 10.3 + - - +
963A LYS* 1.4 72.7 - - - +
965A LEU* 1.3 62.4 + - + +
966A GLU 3.1 5.4 - - - -
967A ALA* 3.2 28.8 + - - +
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Residues in contact with LEU 965 (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 TRP* 5.5 3.8 - - + -
942A LYS* 2.8 34.3 - - + +
961A LYS* 3.4 21.2 + - + +
962A LEU* 3.5 16.8 - - + +
963A LYS 3.1 0.4 - - - -
964A ASN* 1.3 82.8 - - + +
966A GLU* 1.4 47.6 + - - +
967A ALA 3.2 1.6 - - - -
968A PHE* 2.8 33.8 - - - +
1013A TRP* 3.1 27.3 - - + -
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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