Contacts of the strand formed by residues 1005 - 1011 (chain C) in PDB entry 3KBU
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 GLU1005 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004C ARG* 1.3 78.9 - - - +
1006C LEU* 1.3 67.2 + - - +
1007C VAL* 3.5 9.4 - - - +
1066C MET 3.6 0.2 - - - +
1067C SER* 3.1 7.3 - - - -
1068C ARG* 3.0 80.0 + - + +
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Residues in contact with LEU1006 (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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972C ALA* 4.2 6.1 - - + -
995C HIS* 3.3 42.8 - - + +
998C SER* 4.9 9.6 - - - +
1004C ARG 4.2 4.2 + - - +
1005C GLU* 1.3 80.7 - - - +
1007C VAL* 1.3 66.8 + - - +
1008C VAL* 6.0 0.2 - - - -
1052C CYS* 4.2 11.9 - - - -
1065C ILE* 4.1 15.7 - - + -
1066C MET 3.4 5.6 - - - +
1067C SER* 3.3 25.4 - - - +
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Residues in contact with VAL1007 (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 GLU* 3.5 12.3 - - - +
1006C LEU* 1.3 78.8 - - - +
1008C VAL* 1.3 66.1 + - - +
1009C LEU* 4.2 14.6 - - + -
1019C GLU* 4.1 13.0 - - + +
1065C ILE* 3.7 5.9 - - - +
1066C MET* 3.1 57.8 + - + +
1068C ARG* 3.3 48.9 - - + +
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Residues in contact with VAL1008 (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 VAL* 1.3 78.0 - - - +
1009C LEU* 1.3 59.8 + - - +
1019C GLU* 3.4 9.3 - - - +
1020C HIS* 2.8 50.0 + - + +
1052C CYS* 5.2 7.9 - - + -
1053C ARG 5.5 3.6 - - - +
1054C ILE* 4.0 24.5 - - + -
1063C PHE* 3.7 28.3 - - + -
1064C VAL 3.5 9.0 - - - +
1065C ILE* 4.0 15.9 - - + -
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Residues in contact with LEU1009 (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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963C PRO* 4.3 18.2 - - + -
964C PRO 5.6 2.9 - - - +
965C LEU* 5.5 2.0 - - + -
1007C VAL* 4.2 10.5 - - + -
1008C VAL* 1.3 76.6 - - - +
1010C ARG* 1.3 63.5 + - - +
1017C TRP* 4.0 16.2 - - + +
1018C LYS* 3.2 23.6 - - - +
1019C GLU* 3.9 9.0 - - + +
1020C HIS* 4.8 0.2 - - - -
1063C PHE* 3.3 8.1 - - - -
1064C VAL* 2.9 51.1 + - + -
1066C MET* 3.9 33.9 - - + -
1068C ARG* 5.8 1.6 - - - +
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Residues in contact with ARG1010 (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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1009C LEU* 1.3 75.5 - - - +
1011C SER* 1.3 60.4 + - - +
1012C GLU* 2.7 38.1 + - - +
1016C VAL 3.7 0.3 - - - +
1017C TRP* 3.5 5.5 - - - -
1018C LYS* 2.8 58.4 + - + +
1019C GLU 5.0 0.4 - - - -
1020C HIS* 3.3 42.3 + - + +
1056C THR* 3.5 12.7 + - - -
1058C ASP* 2.9 34.5 + - - -
1060C PRO* 3.8 14.5 - - + +
1062C TYR 3.5 12.1 - - - +
1063C PHE* 3.7 18.9 - - + -
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Residues in contact with SER1011 (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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1010C ARG* 1.3 74.6 - - - +
1012C GLU* 1.3 60.1 + - - +
1014C GLY* 2.8 35.8 + - - -
1015C SER 3.5 0.3 + - - -
1016C VAL 3.1 21.1 + - - -
1017C TRP* 3.6 30.0 - - - -
1018C LYS* 6.5 0.2 - - - +
1060C PRO* 3.6 4.0 - - - +
1061C LEU* 3.1 21.3 + - - +
1062C TYR* 3.3 13.8 + - - -
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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