Contacts of the strand formed by residues 540 - 544 (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 LYS 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507B GLY* 4.2 11.0 - - - +
508B GLY 2.9 10.3 + - - +
509B THR* 3.4 25.2 - - + +
510B PHE 3.0 22.8 + - - -
538B LYS 4.8 2.5 - - - +
539B LEU* 1.3 71.9 - - - +
541B PHE* 1.3 59.3 + - - +
542B TYR* 3.5 33.3 + - + -
570B LEU* 6.0 0.6 - - - +
615B GLU* 3.4 31.0 - - - +
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Residues in contact with PHE 541 (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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510B PHE* 3.4 42.0 - + + +
512B LEU* 4.0 12.8 - - + -
522B MET* 3.5 32.1 - - + -
526B LEU* 4.1 8.7 - - + -
534B ILE* 3.9 27.8 - - + -
539B LEU* 3.4 3.2 + - + -
540B LYS* 1.3 74.2 - - - +
542B TYR* 1.3 72.8 + - - +
543B ASN* 4.7 1.3 - - + -
615B GLU* 3.5 7.5 + - - +
616B PHE* 2.6 70.6 + + + +
618B TYR* 4.3 8.5 - + + -
622B TRP* 4.0 18.2 - + - -
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Residues in contact with TYR 542 (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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509B THR* 4.3 10.8 - - + -
510B PHE 3.0 10.7 + - - +
511B VAL* 3.2 12.2 - - + -
512B LEU 2.9 25.5 + - - +
540B LYS* 3.5 49.2 + - + -
541B PHE* 1.3 84.4 - - - +
543B ASN* 1.3 60.6 + - - +
570B LEU* 3.8 46.3 - - + +
613B LEU* 3.9 15.0 - - + -
614B GLN* 3.3 29.8 - - - +
615B GLU* 3.6 27.5 - - + +
616B PHE 4.3 0.2 - - - +
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Residues in contact with ASN 543 (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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512B LEU* 3.2 24.7 - - - +
514B SER* 2.7 44.6 + - - -
516B TRP 4.0 11.7 + - - -
517B SER* 4.3 9.2 + - - +
522B MET* 3.6 21.9 - - + +
541B PHE* 4.7 1.6 - - + -
542B TYR* 1.3 76.2 - - - +
544B ILE* 1.3 73.4 + - - +
545B ASP 4.2 1.0 - - - +
612B SER 4.9 6.8 - - - +
613B LEU* 5.4 1.0 - - - +
614B GLN 4.6 7.5 + - - +
616B PHE* 4.2 17.1 - - + +
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Residues in contact with ILE 544 (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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511B VAL* 4.3 2.9 - - + -
512B LEU 2.8 15.1 + - - +
513B ASN* 3.2 1.9 - - - -
514B SER 3.1 19.7 + - - -
543B ASN* 1.3 77.3 - - - +
545B ASP* 1.3 62.8 + - - +
546B ALA 2.9 8.5 + - - +
549B ILE* 3.8 23.8 - - + -
562B ILE* 3.8 22.4 - - + -
563B MET* 3.8 33.0 - - + -
566B ALA* 5.5 0.7 - - + -
609B ALA* 4.2 7.9 - - - +
612B SER* 4.3 8.7 - - - +
613B LEU* 3.3 41.5 - - + +
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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
------------------------------------------------------------
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