Contacts of the strand formed by residues 1055 - 1060 (chain A) in PDB entry 3KZ1
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 GLN1055 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A LYS* 3.4 28.0 + - - -
1020A GLN* 3.4 20.4 + - - +
1021A THR 3.9 18.3 + - - -
1022A PHE* 3.2 39.2 - - + +
1045A ILE 3.7 1.0 - - - +
1046A ILE* 3.3 6.4 - - - +
1047A CYS* 2.8 41.1 + - + +
1053A PRO* 3.6 12.2 + - - +
1054A PRO* 1.3 81.2 + - - +
1056A ILE* 1.3 61.7 + - - +
1057A TYR* 3.9 11.5 + - + +
72F LEU* 3.9 12.0 - - + +
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Residues in contact with ILE1056 (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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974A TRP* 5.0 1.0 + - - -
975A ARG 5.6 1.2 - - - +
1022A PHE* 3.8 16.4 - - - -
1044A PHE* 3.6 32.3 - - + -
1045A ILE 3.8 0.9 - - - +
1046A ILE* 3.3 38.1 - - + -
1055A GLN* 1.3 74.8 - - - +
1057A TYR* 1.3 63.9 + - - +
1058A GLU* 3.7 4.0 + - + +
39F PHE* 4.5 16.4 - - + -
58F TRP* 5.7 3.6 - - + -
72F LEU* 3.8 38.1 - - + +
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Residues in contact with TYR1057 (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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974A TRP* 3.6 29.6 - + - +
995A LEU* 3.9 20.9 - - + -
1022A PHE* 3.5 26.4 - + + +
1023A SER 2.7 43.0 + - - -
1026A LEU* 3.5 35.2 - - + +
1043A PHE 3.7 1.0 - - - +
1044A PHE* 3.4 3.8 - - - -
1045A ILE* 2.8 55.0 + - + +
1047A CYS* 4.0 13.7 - - + +
1055A GLN* 4.1 10.6 - - + +
1056A ILE* 1.3 75.7 - - - +
1058A GLU* 1.3 59.5 + - - +
1059A LEU* 3.7 11.7 + - + +
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Residues in contact with GLU1058 (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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974A TRP* 3.4 7.7 - - - +
975A ARG* 2.9 78.1 + - + +
1036A VAL* 4.3 11.3 - - + +
1039A ASP* 5.1 0.3 - - - +
1042A ALA* 4.2 17.7 - - + +
1043A PHE 3.8 2.9 - - - -
1044A PHE* 3.8 30.3 - - + -
1056A ILE* 3.7 6.5 + - + +
1057A TYR* 1.3 70.3 - - - +
1059A LEU* 1.3 62.3 + - - +
1060A VAL* 5.3 0.2 - - + -
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Residues in contact with LEU1059 (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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972A LEU* 3.8 33.0 - - + -
973A THR 3.6 3.4 - - - +
974A TRP* 3.9 35.4 - - + -
984A LEU* 4.3 10.3 - - + -
986A VAL* 5.4 0.4 - - + -
993A LEU* 4.9 2.0 - - + -
995A LEU* 4.2 18.8 - - + -
1042A ALA* 3.3 1.3 - - - -
1043A PHE* 2.9 54.7 + - + +
1045A ILE* 3.6 28.7 - - + -
1057A TYR* 4.7 10.8 - - + +
1058A GLU* 1.3 73.7 - - - +
1060A VAL* 1.3 61.3 + - - +
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Residues in contact with VAL1060 (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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972A LEU* 3.5 10.0 - - - -
973A THR* 2.7 50.3 + - + +
975A ARG* 3.6 44.4 - - + +
1039A ASP* 5.0 0.2 - - - +
1041A ARG* 3.8 33.9 - - + +
1042A ALA* 4.1 6.3 - - + +
1058A GLU* 4.9 3.4 - - + +
1059A LEU* 1.3 75.5 - - - +
1061A ALA* 1.3 73.6 + - - +
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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