Contacts of the strand formed by residues 1012 - 1017 (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 THR1012 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004C PHE* 5.4 10.3 - - - -
1005C VAL 3.5 7.6 - - - -
1006C LYS* 3.6 34.1 - - + -
1010C GLY 4.0 5.6 - - - +
1011C LYS* 1.3 86.5 - - - +
1013C ILE* 1.3 61.8 + - - +
1014C THR* 4.1 5.4 + - - -
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Residues in contact with ILE1013 (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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95B GLU* 5.2 2.7 - - - +
1004C PHE* 3.4 5.6 - - - +
1005C VAL* 2.9 56.4 + - + +
1007C THR* 4.4 17.7 - - + -
1011C LYS* 4.9 6.1 - - + +
1012C THR* 1.3 76.3 - - - +
1014C THR* 1.3 62.0 + - - +
1015C LEU* 3.8 7.2 + - + +
1030C ILE* 4.3 22.4 - - + -
1033C LYS* 4.1 22.0 - - + -
1034C GLU* 3.6 45.5 - - + +
1036C ILE* 5.4 0.2 - - + -
1069C LEU* 4.7 2.0 - - + -
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Residues in contact with THR1014 (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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95B GLU* 4.1 5.9 + - - +
122B ARG* 3.6 34.6 + - - +
1002C GLN* 3.5 37.5 - - + +
1003C ILE 3.6 3.1 - - - +
1004C PHE* 3.5 27.7 - - + -
1012C THR* 4.1 5.5 + - - -
1013C ILE* 1.3 73.4 - - - +
1015C LEU* 1.3 60.9 + - - +
1016C GLU* 4.1 4.8 + - + +
1033C LYS* 3.6 19.9 + - - -
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Residues in contact with LEU1015 (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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1002C GLN* 3.1 6.7 - - - -
1003C ILE* 2.9 42.9 + - + +
1005C VAL* 3.6 30.3 - - + -
1013C ILE* 4.5 10.3 - - + +
1014C THR* 1.3 75.2 - - - +
1016C GLU* 1.3 60.7 + - - +
1017C VAL* 3.6 14.1 + - + -
1026C VAL* 3.6 29.2 - - + +
1029C LYS* 4.0 15.3 - - + -
1030C ILE* 3.8 17.0 - - + -
1033C LYS* 3.5 31.4 - - + +
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Residues in contact with GLU1016 (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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91B TYR* 4.7 3.8 + - - -
335B GLU* 3.5 37.8 + - - +
336B ASP* 3.9 14.7 - - - +
338B ARG* 3.7 6.9 - - + -
339B HIS* 3.5 45.6 + - + +
341B ASN* 3.3 23.7 + - - -
1001C MET 3.7 4.5 - - - -
1002C GLN* 4.3 7.6 - - - +
1014C THR* 4.1 5.5 + - + +
1015C LEU* 1.3 73.4 - - - +
1017C VAL* 1.3 61.7 + - - +
1029C LYS* 3.0 31.4 + - + +
1033C LYS* 6.1 0.2 - - - +
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Residues in contact with VAL1017 (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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338B ARG* 3.6 16.6 - - - +
75C GLY* 5.0 0.9 - - - -
1001C MET* 3.1 47.1 + - + +
1003C ILE* 4.0 23.8 - - + -
1015C LEU* 4.0 22.2 - - + +
1016C GLU* 1.3 80.2 - - - +
1018C GLU* 1.3 60.8 + - - +
1021C ASP* 3.5 9.2 - - - +
1026C VAL* 4.5 13.0 - - + -
1029C LYS* 4.8 6.1 - - - -
1056C LEU* 3.7 25.6 - - + -
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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