Contacts of the strand formed by residues 504 - 509 (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 MET 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE 5.0 11.0 - - - +
82A GLY* 5.0 11.7 - - - +
83A LEU* 5.4 10.8 - - + -
92A ASN* 4.8 17.0 - - - +
493A ILE 4.4 0.3 - - - +
494A TRP* 3.3 4.5 - - - -
495A ARG* 2.9 66.2 + - + +
496A THR* 4.9 1.5 - - - -
502A LYS 3.7 3.6 + - - -
503A PRO* 1.3 70.7 - - - +
505A GLY* 1.3 79.9 + - - +
506A PRO 5.1 0.7 - - - +
507A LEU* 3.3 34.5 - - + +
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Residues in contact with GLY 505 (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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82A GLY* 5.7 2.5 + - - -
493A ILE 4.5 1.1 - - - -
494A TRP* 3.5 12.0 - - - -
503A PRO 3.4 4.5 + - - +
504A MET* 1.3 91.6 - - - +
506A PRO* 1.3 75.4 - - - +
507A LEU* 4.0 1.6 - - - -
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Residues in contact with PRO 506 (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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417A PRO* 3.0 37.9 - - + +
465A THR* 4.4 9.2 - - - +
466A PRO 3.8 17.9 - - - +
467A GLU* 6.0 1.3 - - + -
492A PHE* 3.9 16.8 - - + -
493A ILE 4.0 1.6 - - - +
494A TRP* 3.5 32.1 - - + +
504A MET* 5.1 0.7 - - - +
505A GLY* 1.3 83.9 - - - +
507A LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 507 (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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99A LYS* 4.6 18.2 - - - +
417A PRO* 4.4 6.3 - - + -
492A PHE* 3.3 4.6 - - - -
493A ILE* 2.8 46.0 + - + +
495A ARG* 6.1 1.3 - - - +
504A MET* 3.3 40.6 - - + -
505A GLY* 4.9 0.4 - - - -
506A PRO* 1.3 76.1 - - - +
508A LEU* 1.3 70.4 + - - +
509A VAL 3.3 0.2 + - - -
511A THR* 4.7 7.4 - - + +
512A PHE* 4.5 21.3 - - + -
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Residues in contact with LEU 508 (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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417A PRO* 3.4 26.9 - - - +
418A GLY* 3.9 15.5 - - - +
426A THR* 4.6 7.2 - - + +
428A THR* 4.9 17.5 - - + -
491A ARG* 3.1 43.5 - - + +
492A PHE* 4.0 9.6 - - + -
507A LEU* 1.3 79.9 - - - +
509A VAL* 1.3 70.9 + - + +
510A ALA* 3.1 20.6 - - + +
511A THR* 3.2 33.7 + - + +
512A PHE* 4.4 1.7 - - - -
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Residues in contact with VAL 509 (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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488A PHE* 4.6 7.4 - - + -
490A ASP 4.4 7.6 - - - +
491A ARG* 3.5 24.2 + - + -
492A PHE 3.9 0.9 - - - +
493A ILE* 3.3 34.5 - - + -
507A LEU 3.3 2.6 + - - -
508A LEU* 1.3 69.0 - - + +
510A ALA* 1.3 62.3 + - - +
511A THR 3.0 2.2 - - - -
512A PHE* 2.8 24.2 + - - +
513A TRP* 2.9 22.4 + - + +
516A LEU* 4.2 27.4 - - + -
517A PRO 5.9 3.6 - - - +
518A GLU 5.7 0.4 - - - +
520A ILE* 5.9 3.1 - - + -
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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