Contacts of the helix formed by residues 642 - 648 (chain B) in PDB entry 1KEK
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 VAL 642 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B PHE* 2.8 50.8 + - + +
641B ASN* 1.3 90.7 - - + +
643B VAL* 1.3 68.3 + - - +
644B LYS 3.5 0.7 - - - -
645B PRO* 3.2 3.0 - - - +
646B ILE* 3.2 43.5 + - + +
654B LEU* 4.1 7.5 - - + +
658B ALA* 4.2 25.1 - - + +
659B PHE* 4.7 6.7 - - + -
665B PHE* 4.6 9.0 - - + -
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Residues in contact with VAL 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B PHE* 3.1 35.3 + - + -
639B PHE* 3.2 41.1 - - + -
642B VAL* 1.3 75.8 - - - +
644B LYS* 1.4 57.9 + - - +
646B ILE* 3.0 5.5 + - - +
647B LEU* 2.8 40.9 + - + +
669B THR* 3.8 19.7 - - + +
673B GLU* 5.1 2.7 - - + -
849B PRO* 3.6 26.5 - - + +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B GLU* 5.6 6.5 - - - +
633B PRO* 5.6 9.1 - - - +
639B PHE* 2.8 45.3 + - + +
640B LYS* 4.5 6.3 - - + +
643B VAL* 1.4 73.0 - - - +
645B PRO* 1.3 63.8 - - + +
647B LEU* 3.2 6.7 + - + +
648B THR* 2.8 49.7 + - + +
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Residues in contact with PRO 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B LYS 3.6 15.0 - - - +
641B ASN* 3.6 19.3 - - - +
642B VAL 3.2 13.5 - - - +
644B LYS* 1.3 98.1 - - + +
646B ILE* 1.4 57.5 + - - +
648B THR* 3.4 9.8 + - - +
650B GLN* 2.7 44.7 + - + +
651B GLY 4.0 1.8 - - - -
654B LEU* 4.4 15.5 - - + -
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Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASP* 3.4 24.5 - - - +
224A ILE* 3.8 24.5 - - + -
642B VAL* 3.2 28.4 + - + +
643B VAL 3.0 8.1 + - - +
645B PRO* 1.4 78.9 - - - +
647B LEU* 1.3 64.7 + - - +
649B GLN* 3.2 19.2 + - - -
650B GLN 4.1 0.2 + - - -
651B GLY* 3.8 13.5 - - - +
654B LEU* 3.6 24.9 - - + -
659B PHE* 4.6 0.7 - - + -
665B PHE* 5.0 0.7 - - + -
848B ALA 5.0 2.5 - - - +
849B PRO* 3.6 33.9 - - + -
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B LYS* 5.0 8.1 - - - -
498B TYR* 3.5 18.0 + - - -
639B PHE* 4.3 10.8 - - + -
643B VAL* 2.8 32.0 + - + +
644B LYS* 3.7 6.7 - - + +
646B ILE* 1.3 74.0 - - + +
648B THR* 1.3 61.3 + - + +
649B GLN* 3.2 11.2 + - - +
673B GLU* 3.7 42.6 - - + +
849B PRO* 3.8 25.4 - - + -
850B SER* 5.4 0.4 - - - -
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Residues in contact with THR 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ILE* 4.2 21.1 - - + +
498B TYR* 4.1 15.9 - - + +
499B ASP 5.4 2.1 + - - -
644B LYS* 2.8 47.2 + - + +
645B PRO* 3.4 11.1 + - - +
646B ILE 3.1 0.6 - - - -
647B LEU* 1.3 79.6 - - + +
649B GLN* 1.3 66.2 + - - +
650B GLN* 3.1 22.4 - - - +
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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