Contacts of the helix formed by residues 1023 - 1029 (chain A) in PDB entry 4EJX
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 VAL1023 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLY 4.3 2.2 - - - -
271A ASN* 3.4 22.2 - - - +
272A GLU* 3.6 19.3 - - + +
299A PRO* 3.7 13.5 - - + -
974A LEU* 4.0 15.7 - - + +
976A THR* 3.3 24.0 - - + -
1021A CYS* 3.4 12.1 + - - -
1022A HIS* 1.3 75.6 - - - +
1024A THR* 1.3 75.2 + - - +
1026A HIS* 2.8 32.9 + - + +
1027A ILE* 2.8 19.4 + - - -
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Residues in contact with THR1024 (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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167A PRO* 3.2 32.7 - - + +
209A PHE* 3.9 24.7 - - + -
269A MET* 5.9 0.3 - - - -
270A GLY* 2.9 26.5 + - - -
271A ASN* 3.5 21.6 - - - +
1022A HIS 3.9 0.6 + - - -
1023A VAL* 1.3 74.7 - - - +
1025A ASP* 1.3 66.7 + - - +
1027A ILE* 2.8 12.4 + - - +
1028A HIS* 3.0 29.7 + - + +
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Residues in contact with ASP1025 (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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209A PHE* 5.5 6.2 - - - -
271A ASN* 3.4 23.2 + - - +
272A GLU* 3.7 15.1 - - - +
748A PHE* 4.6 5.0 - - - -
935A GLU* 5.0 6.6 - - - +
1024A THR* 1.3 82.6 - - - +
1026A HIS* 1.3 50.9 + - - +
1028A HIS* 3.1 9.4 + - - +
1029A ALA* 2.7 40.5 + - - +
1107A CU 3.1 23.6 - - - -
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Residues in contact with HIS1026 (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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272A GLU* 2.7 40.2 + - + -
903A VAL* 4.1 4.5 - - + +
940A HIS* 3.3 23.6 + + - -
972A ILE* 3.2 26.9 + - - +
974A LEU* 3.6 15.2 + - + -
975A HIS* 3.6 8.6 + + - -
1021A CYS* 4.3 2.9 - - - -
1023A VAL* 2.8 27.4 + - + +
1025A ASP* 1.3 73.4 - - - +
1027A ILE* 1.3 59.8 + - - +
1029A ALA* 3.0 14.7 + - - +
1031A MET* 3.1 28.8 + - + +
1106A CU 3.3 25.9 - - - -
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Residues in contact with ILE1027 (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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165A ASP* 5.8 1.3 - - - +
166A ALA* 4.3 20.0 - - + -
167A PRO* 3.7 24.5 - - + -
947A PHE* 4.7 0.7 - - - -
1018A LEU* 6.5 0.4 - - + -
1020A HIS* 4.3 15.7 - - + +
1021A CYS 3.1 20.6 - - - +
1022A HIS* 3.7 19.1 - - + +
1023A VAL 2.8 33.3 + - - +
1024A THR 2.8 2.9 + - - +
1026A HIS* 1.3 70.5 - - - +
1028A HIS* 1.3 61.4 + - + +
1029A ALA 3.0 0.2 - - - -
1030A GLY* 3.1 15.1 + - - -
1031A MET 4.6 7.2 - - - -
1032A GLU* 3.4 32.9 - - - +
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Residues in contact with HIS1028 (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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165A ASP* 2.7 43.3 + - - -
167A PRO* 3.2 36.1 - - + +
168A LYS* 4.4 8.4 - - + +
209A PHE* 5.3 4.0 - + - -
737A HIS* 5.9 6.2 - + - -
742A GLN* 5.4 2.9 - - - -
746A ASN* 5.7 0.5 + - - -
748A PHE* 4.6 5.4 - - - -
947A PHE* 3.9 12.6 - - - -
1024A THR* 3.0 31.5 + - + +
1025A ASP* 3.3 9.4 - - - +
1027A ILE* 1.3 77.1 - - + +
1029A ALA* 1.3 55.6 + - - +
1030A GLY 3.3 3.3 + - - -
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Residues in contact with ALA1029 (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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748A PHE* 3.7 21.5 - - + -
940A HIS* 3.2 46.1 + - + +
946A MET* 3.4 17.2 - - - +
947A PHE* 3.7 5.2 - - - -
1025A ASP* 2.7 15.9 + - - +
1026A HIS 3.3 4.7 - - - +
1027A ILE 3.0 1.0 - - - -
1028A HIS* 1.3 78.1 - - - +
1030A GLY* 1.3 59.1 + - - +
1031A MET 3.3 3.1 + - - -
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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