Contacts of the helix formed by residues 931 - 937 (chain C) in PDB entry 3KKA
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 ALA 931 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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941B THR* 6.2 0.9 - - - -
907C THR* 5.7 1.1 - - - +
908C VAL* 3.7 4.9 - - - +
930C THR* 1.3 83.6 + - - +
932C ILE* 1.3 65.6 + - - +
933C GLU* 3.3 22.9 - - + +
934C LYS* 3.1 14.2 + - + +
935C VAL* 3.1 22.5 + - - +
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Residues in contact with ILE 932 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941B THR* 6.1 1.1 - - + -
907C THR* 3.3 42.2 - - - +
908C VAL* 3.8 6.4 - - - +
911C TRP* 3.7 25.4 - - + -
931C ALA* 1.3 72.0 - - - +
933C GLU* 1.3 65.7 + - - +
935C VAL* 3.0 34.5 + - + +
936C VAL* 3.3 11.4 + - + +
964C LEU* 4.6 18.2 - - + -
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Residues in contact with GLU 933 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941B THR* 3.0 44.1 + - - +
943B GLU* 3.6 26.9 - - - +
931C ALA* 3.8 18.1 - - + +
932C ILE* 1.3 79.5 + - - +
934C LYS* 1.3 64.6 + - - +
936C VAL* 3.7 20.4 - - + +
937C GLN* 4.1 13.3 + - - +
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Residues in contact with LYS 934 (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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928C GLY 4.7 4.3 - - - +
929C TYR* 3.9 26.5 - - + -
930C THR* 4.6 1.1 - - - +
931C ALA* 3.1 23.3 + - + +
933C GLU* 1.3 78.9 - - - +
935C VAL* 1.3 63.6 + - - +
936C VAL 3.1 1.6 - - - -
937C GLN* 3.1 27.8 + - - +
938C MET 4.0 0.3 + - - -
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Residues in contact with VAL 935 (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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908C VAL* 3.7 32.8 - - + -
911C TRP* 4.4 9.6 - - + -
924C PHE* 5.0 0.2 - - + -
929C TYR* 4.3 13.9 - - + -
931C ALA 3.1 13.9 + - - +
932C ILE* 3.0 24.4 + - + +
934C LYS* 1.3 74.4 - - - +
936C VAL* 1.3 63.9 + - + +
937C GLN 3.3 0.2 - - - -
938C MET* 3.1 31.8 + - + +
961C LEU* 3.1 22.6 - - + +
964C LEU* 4.3 22.2 - - + -
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Residues in contact with VAL 936 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932C ILE* 3.4 20.4 - - + +
933C GLU* 3.7 15.5 - - - +
934C LYS 3.1 0.8 - - - -
935C VAL* 1.3 80.2 - - + +
937C GLN* 1.3 62.1 - - - +
938C MET 3.1 4.7 + - - -
961C LEU* 4.4 2.0 - - - -
964C LEU* 3.9 16.8 - - + +
965C LYS* 3.1 54.2 + - + +
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Residues in contact with GLN 937 (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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929C TYR* 5.2 5.1 + - + -
933C GLU 4.1 14.3 + - - +
934C LYS* 3.1 16.6 + - - +
936C VAL* 1.3 80.3 - - - +
938C MET* 1.3 63.5 + - - +
939C THR* 3.7 2.3 + - - -
942C ASP* 4.2 4.3 - - - +
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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