Contacts of the helix formed by residues 685 - 692 (chain E) in PDB entry 1KKQ
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 LEU 685 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A VAL* 4.9 9.6 - - + -
310A LYS* 4.1 14.6 - - + +
313A VAL* 4.2 24.9 - - + -
314A TYR* 4.0 24.2 - - + +
683E MET* 2.6 29.4 - - + +
684E GLY* 1.3 77.9 - - - -
686E GLU* 1.3 55.2 + - - +
687E ALA* 2.7 21.4 + - - +
688E ILE* 3.1 20.9 + - + +
689E ILE* 3.1 23.9 + - + +
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Residues in contact with GLU 686 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.5 17.9 - - + -
310A LYS* 3.8 24.8 + - + +
684E GLY* 4.1 4.1 - - - -
685E LEU* 1.3 81.7 - - - +
687E ALA* 1.3 67.2 + - + +
689E ILE* 3.5 17.7 - - + -
690E ARG* 2.5 68.6 + - - +
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Residues in contact with ALA 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A TYR* 3.9 24.1 + - + +
684E GLY 5.1 0.9 - - - +
685E LEU* 2.7 8.2 + - - +
686E GLU* 1.3 88.2 - - + +
688E ILE* 1.3 67.8 + - + +
690E ARG* 3.3 10.6 + - - +
691E LYS* 3.4 13.3 + - - +
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Residues in contact with ILE 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A SER 5.4 1.1 - - - +
281A VAL* 3.8 33.0 - - + -
284A VAL* 4.9 9.2 - - + -
285A THR* 4.8 6.7 - - - +
460A LEU* 3.3 35.7 - - + -
464A TYR* 3.9 17.2 - - + -
685E LEU* 3.1 14.0 + - + +
687E ALA* 1.3 80.3 - - + +
689E ILE* 1.3 63.1 + - + +
691E LYS* 3.5 26.1 - - - +
692E ALA* 3.5 19.6 + - - +
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Residues in contact with ILE 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A VAL* 3.8 25.8 - - + -
288A THR* 3.9 21.5 - - - +
306A VAL* 3.3 46.9 - - + +
309A LEU* 4.2 14.4 - - + +
310A LYS* 4.1 14.4 - - + +
313A VAL* 6.2 0.2 - - + -
685E LEU* 3.1 29.4 - - + +
686E GLU* 3.5 14.1 - - + +
687E ALA 3.3 0.2 - - - -
688E ILE* 1.3 75.0 - - + +
690E ARG* 1.3 66.5 + - - +
691E LYS 3.2 0.6 + - - -
692E ALA* 3.5 2.0 + - - +
693E LEU* 3.5 20.3 + - + +
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Residues in contact with ARG 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 4.4 16.1 - - + +
303A ASN* 4.9 14.3 + - - +
306A VAL* 3.9 28.8 - - + +
686E GLU* 2.5 66.9 + - - +
687E ALA* 3.3 5.2 + - - +
689E ILE* 1.3 77.0 - - - +
691E LYS* 1.3 57.5 + - - +
692E ALA 3.5 0.2 - - - -
693E LEU* 3.2 21.6 - - - +
694E MET* 3.3 16.6 - - - +
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Residues in contact with LYS 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 4.7 7.8 - - - +
285A THR* 5.7 2.0 - - - -
464A TYR* 3.4 47.9 + - + +
465A ARG* 4.3 4.7 - - - +
467A MET* 6.2 0.4 - - - +
468A TYR* 3.8 37.8 - - + +
687E ALA 3.4 8.2 + - - +
688E ILE* 3.5 38.0 - - - +
689E ILE 3.2 0.6 - - - -
690E ARG* 1.3 79.3 - - - +
692E ALA* 1.3 56.7 + - - +
693E LEU 3.0 5.6 - - - -
694E MET* 2.8 26.8 - - - +
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Residues in contact with ALA 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A THR* 3.2 37.9 - - + +
288A THR* 4.0 17.5 - - + +
289A GLU* 3.0 24.7 - - - +
292A LYS* 4.1 2.9 + - - -
468A TYR* 5.1 7.4 - - + -
688E ILE 3.5 14.0 + - - +
689E ILE* 3.5 6.2 + - - +
691E LYS* 1.3 81.0 - - - +
693E LEU* 1.3 62.0 + - - +
694E MET 3.3 2.9 + - - -
695E GLY* 5.0 1.8 + - - -
696E LYS* 5.2 0.7 - - - +
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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