Contacts of the strand formed by residues 1066 - 1071 (chain C) in PDB entry 4KSL
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 THR1066 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004C PHE* 3.3 26.5 - - + +
1006C LYS* 4.6 23.8 - - + +
1044C ILE 4.5 0.9 - - - +
1045C PHE* 3.5 19.1 - - - -
1046C ALA 5.2 0.3 + - - -
1064C GLU 4.2 2.9 + - - -
1065C SER* 1.3 77.8 + - - +
1067C LEU* 1.3 72.9 + - - +
1068C HIS* 4.4 16.3 + - + +
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Residues in contact with LEU1067 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C ILE* 3.7 26.7 - - + -
1004C PHE 2.6 17.1 + - - +
1005C VAL* 4.1 15.7 - - + -
1006C LYS* 2.8 26.3 + - - -
1026C VAL* 5.0 3.4 - - + -
1043C LEU* 4.6 18.8 - - + -
1044C ILE 3.4 7.0 - - - +
1045C PHE* 3.6 36.6 - - + -
1050C LEU* 3.9 19.1 - - + -
1056C LEU* 5.2 1.8 - - + -
1061C ILE* 4.0 20.2 - - + -
1065C SER* 4.9 0.9 - - - +
1066C THR* 1.3 81.5 - - - +
1068C HIS* 1.3 63.3 + - - +
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Residues in contact with HIS1068 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C LYS* 3.7 22.1 + - + +
1042C ARG 3.3 4.2 - - - +
1043C LEU* 3.5 3.2 - - - -
1044C ILE* 2.9 63.6 + - + +
1046C ALA 5.3 5.6 - - - -
1047C GLY 5.9 0.9 - - - -
1066C THR* 4.7 17.6 + - + +
1067C LEU* 1.3 79.5 + - - +
1069C LEU* 1.3 60.1 - - - +
1070C VAL* 5.1 5.2 - - + -
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Residues in contact with LEU1069 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005C VAL* 3.5 22.0 - - + -
1006C LYS 3.2 10.6 + - - +
1007C THR* 3.9 17.6 - - + -
1008C LEU* 3.7 22.7 + - - +
1013C ILE* 4.7 1.6 - - + -
1030C ILE* 4.2 15.7 - - + -
1036C ILE* 3.8 28.7 - - + -
1041C GLN* 3.7 23.6 - - + +
1042C ARG 3.4 13.9 - - - +
1043C LEU* 3.9 11.7 - - + -
1067C LEU 4.1 1.0 + - - -
1068C HIS* 1.3 72.3 - - - +
1070C VAL* 1.3 63.2 + - - +
1071C LEU* 3.7 24.8 - - + +
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Residues in contact with VAL1070 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008C LEU* 5.0 25.4 - - + -
1042C ARG* 2.9 65.4 + - + +
1044C ILE* 4.4 16.6 - - + -
1068C HIS* 4.6 5.6 - - + +
1069C LEU* 1.3 79.5 - - - +
1071C LEU* 1.3 70.8 + - - +
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Residues in contact with LEU1071 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C THR* 5.8 5.8 - - + -
1008C LEU* 6.0 4.5 - - + +
1009C THR* 6.1 4.9 - - + -
1036C ILE* 4.0 31.2 - - + -
1040C GLN* 3.2 18.6 - - + +
1041C GLN* 4.2 1.1 - - - -
1042C ARG* 6.0 0.4 - - - -
1069C LEU* 3.7 31.0 - - + +
1070C VAL* 1.3 90.7 - - - +
1072C ARG* 1.3 64.3 + - - +
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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