Contacts of the strand formed by residues 538 - 544 (chain A) in PDB entry 1CK7
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 ASN 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A GLY* 1.3 72.2 - - - -
539A GLU* 1.3 63.4 + - - +
555A PRO* 3.2 11.6 - - + +
556A LEU* 2.7 44.1 + - + +
565A VAL 5.2 0.9 - - - +
566A GLN* 3.7 37.6 + - + +
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Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A PHE* 3.8 0.7 - - - -
536A ALA 2.9 29.8 + - - +
538A ASN* 1.3 95.8 - - - +
540A TYR* 1.3 64.7 + - - +
541A TRP* 3.6 30.2 - - + -
553A PRO* 3.7 24.5 - - + +
554A LYS 3.3 12.8 - - - +
555A PRO* 5.2 1.1 - - + -
556A LEU* 3.8 5.7 - - - +
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Residues in contact with TYR 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A VAL* 4.0 7.2 - - + -
534A PHE 3.0 16.4 - - - +
535A PHE* 4.0 8.5 - - + -
539A GLU* 1.3 76.9 - - - +
541A TRP* 1.3 63.4 + - - +
542A ILE* 3.7 29.2 - - + -
552A TYR* 3.6 18.1 + + - -
553A PRO* 3.2 20.8 - - - +
554A LYS* 3.1 25.9 + - + +
555A PRO 3.4 20.2 - - - -
556A LEU* 3.7 19.5 - - + -
558A SER* 3.6 11.4 + - - -
559A LEU* 3.3 56.4 + - + +
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Residues in contact with TRP 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A LYS* 5.9 0.9 - - - -
515A GLU* 3.8 21.2 + - + +
516A LEU* 3.7 20.2 - - + -
517A PRO* 3.6 28.5 - - + -
532A ALA 3.5 1.2 - - - +
533A VAL* 3.2 4.9 - - - +
534A PHE* 2.9 39.8 + - + +
536A ALA* 3.7 20.4 - - + -
539A GLU* 3.6 48.0 - - + -
540A TYR* 1.3 82.2 - - - +
542A ILE* 1.3 63.6 + - - +
543A TYR* 3.7 19.9 - - + -
548A LEU* 3.6 23.1 - - + -
552A TYR* 4.3 3.1 - - - -
553A PRO* 3.3 32.7 - - + +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A ALA* 5.8 0.9 - - + -
531A LYS* 3.8 22.2 - - + -
532A ALA 3.2 1.6 - - - +
533A VAL* 3.3 38.6 - - + -
540A TYR* 3.7 26.2 - - + -
541A TRP* 1.3 74.5 - - - +
543A TYR* 1.3 65.5 + - - +
548A LEU* 4.1 0.3 - - - +
549A GLU* 2.8 47.2 + - + +
552A TYR* 3.1 40.9 - - + +
559A LEU* 5.7 0.9 - - + -
593A GLU* 6.0 0.4 - - - +
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Residues in contact with TYR 543 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A PHE 4.7 0.2 - - - -
513A TRP* 3.1 44.3 - + + +
514A PRO* 5.3 0.2 - - + -
515A GLU* 2.4 39.5 + - - +
516A LEU* 3.4 36.1 + - + +
531A LYS* 3.0 9.7 - - - +
532A ALA* 2.6 38.2 + - + +
534A PHE* 4.0 13.5 - + - -
541A TRP* 3.7 11.9 - - + -
542A ILE* 1.3 79.3 - - - +
544A SER* 1.3 64.4 - - - +
545A ALA 4.1 1.1 - - - +
546A SER 4.1 8.1 - - - +
547A THR 3.4 7.9 - - - +
548A LEU* 3.3 35.8 - - + +
549A GLU* 4.3 2.7 - - - -
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Residues in contact with SER 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ARG* 3.2 20.0 + - - +
529A GLU 5.2 0.9 + - - -
531A LYS* 3.8 27.3 - - - -
543A TYR* 1.3 77.8 - - - +
545A ALA* 1.3 69.4 + - - +
546A SER 3.4 0.2 - - - -
547A THR* 3.1 25.0 + - - -
549A GLU* 4.0 6.6 + - - -
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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