Contacts of the strand formed by residues 1015 - 1021 (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 GLY1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 5.2 6.7 - - - -
1014A PRO* 1.3 74.5 - - - +
1016A ILE* 1.3 64.7 + - - -
1017A TRP* 2.8 24.5 + - - -
1036A THR* 4.8 1.3 - - - -
1037A VAL 2.7 26.7 + - - -
1038A LEU* 6.0 1.5 - - - +
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Residues in contact with ILE1016 (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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109A LYS* 3.2 25.8 + - - +
116A TYR* 3.6 2.8 + - - -
117A PRO 5.8 0.2 - - - +
118A ASP* 4.5 22.7 - - + +
119A ASN* 4.7 13.7 - - + +
1015A GLY* 1.3 74.8 - - - -
1017A TRP* 1.3 63.8 + - - +
1034A THR* 3.5 29.6 - - + +
1035A TYR 3.2 21.5 - - - +
1036A THR* 3.7 26.2 - - + +
1108A NAG 4.6 23.1 - - + +
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Residues in contact with TRP1017 (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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107A TYR* 3.4 44.9 - + - -
109A LYS* 3.6 29.2 - - + -
112A GLU* 4.1 6.5 - - + -
116A TYR* 3.4 18.6 - - - -
980A HIS 3.3 20.0 - - - +
981A GLY* 3.6 17.5 - - - -
982A HIS* 3.6 9.5 - + - -
1013A THR* 3.6 40.0 + - + -
1014A PRO 4.0 9.0 - - - -
1015A GLY 2.8 30.9 + - - -
1016A ILE* 1.3 75.0 - - - +
1018A LEU* 1.3 62.5 + - - +
1019A LEU 3.3 0.3 + - - -
1034A THR* 3.1 28.1 - - - -
1035A TYR* 3.1 40.2 + + + -
1037A VAL* 4.1 3.1 - - + +
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Residues in contact with LEU1018 (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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116A TYR* 3.1 48.9 + - + -
163A HIS* 3.5 20.2 - - + -
732A TRP* 3.9 22.0 - - + -
736A LEU* 5.4 0.9 - - + -
978A HIS 4.0 0.2 - - - +
979A PHE 3.9 0.3 - - - -
980A HIS* 3.0 46.0 + - + +
1017A TRP* 1.3 71.0 - - - +
1019A LEU* 1.3 57.4 + - - +
1020A HIS* 3.7 13.9 - - + -
1027A ILE* 6.5 0.2 - - + -
1032A GLU* 4.1 15.0 - - + +
1033A THR 3.7 7.2 - - - +
1034A THR* 4.1 0.4 - - - -
1035A TYR* 4.7 0.6 - - - -
1102A CU 3.4 24.7 - - - -
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Residues in contact with LEU1019 (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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899A LEU* 4.1 8.7 - - + -
901A PHE* 4.0 26.0 - - + -
942A ILE* 4.1 3.0 - - + +
953A LEU* 3.8 22.0 - - + -
963A TRP* 3.8 6.3 - - + -
977A VAL* 4.9 3.8 - - + -
978A HIS 3.8 5.6 - - - +
979A PHE* 3.7 26.5 - - + -
1017A TRP 3.3 0.6 + - - -
1018A LEU* 1.3 71.2 - - - +
1020A HIS* 1.3 61.0 + - - +
1032A GLU* 3.3 1.3 - - - -
1033A THR* 2.5 61.0 + - + +
1034A THR 4.3 0.2 - - - +
1035A TYR* 3.4 30.7 - - + -
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Residues in contact with HIS1020 (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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163A HIS* 4.9 1.3 - - - -
166A ALA* 5.4 2.7 - - + -
901A PHE* 4.7 4.3 - - - -
942A ILE* 4.9 1.3 - - - -
977A VAL* 4.7 1.3 - - - -
978A HIS* 2.8 48.0 + + - +
980A HIS* 3.3 15.6 + + - -
1018A LEU* 3.7 15.3 - - + -
1019A LEU* 1.3 77.6 - - - +
1021A CYS* 1.3 82.2 + - - +
1022A HIS* 3.5 30.3 - + - -
1027A ILE* 4.1 16.9 - - + +
1031A MET 3.5 6.7 - - - +
1032A GLU* 3.5 23.3 - - + +
1102A CU 2.2 31.3 - - - -
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Residues in contact with CYS1021 (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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901A PHE* 4.3 11.8 - - + -
975A HIS* 3.9 1.1 - - - -
976A THR 3.0 33.0 - - - +
977A VAL* 4.3 1.8 - - - +
1020A HIS* 1.3 97.3 + - - +
1022A HIS* 1.3 67.6 + - - +
1023A VAL* 3.4 24.0 - - - -
1026A HIS* 4.1 2.5 - - + -
1027A ILE* 3.1 13.7 - - - +
1031A MET* 3.4 18.7 + - + +
1106A CU 2.4 31.0 - - - -
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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