Contacts of the strand formed by residues 460 - 465 (chain L) in PDB entry 1YKN
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 HIS 460 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401L GLN* 4.1 6.1 - - - +
402L ALA 4.9 0.9 + - - -
444L PRO* 3.2 21.7 - - - +
445L GLY 5.1 0.6 + - - -
447L TYR* 3.4 28.3 - + - -
457L ARG* 3.6 15.8 + - + -
458L PRO 2.6 22.4 + - - -
459L ALA* 1.3 76.6 - - - +
461L ILE* 1.3 65.5 + - - +
462L HIS* 3.7 11.2 - + - -
477L GLN* 3.1 23.8 - - + +
478L LEU 3.1 16.2 - - - +
479L TYR* 3.6 16.2 - + + -
480L PHE* 4.3 2.5 - - - -
5550L DHB 3.3 1.8 + - - -
5600L FE 2.2 30.4 - - - -
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Residues in contact with ILE 461 (chain L).
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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380L VAL* 4.1 21.5 - - + -
399L MET* 3.9 22.2 - - + -
400L TRP 3.9 10.1 - - - +
401L GLN* 3.6 23.1 - - + +
441L THR* 4.3 4.9 - - + -
444L PRO* 4.0 14.4 - - + -
460L HIS* 1.3 80.5 - - - +
462L HIS* 1.3 70.8 + - - +
463L PHE* 3.6 25.3 - - + -
477L GLN* 3.6 0.5 - - - -
478L LEU* 2.9 33.6 + - + -
480L PHE* 4.0 20.9 - - + -
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Residues in contact with HIS 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K THR 4.2 2.4 + - - -
13K ALA* 3.8 20.6 + - - -
14K GLY* 4.7 1.1 - - - -
15K PRO* 6.0 0.2 - - - +
399L MET* 3.2 25.5 - - - +
400L TRP* 2.9 58.1 + + + -
401L GLN* 5.0 4.0 - - - -
408L GLU* 4.8 2.8 + - - -
460L HIS* 3.5 5.3 + + - -
461L ILE* 1.3 74.0 - - - +
463L PHE* 1.3 59.2 + - - +
475L ILE* 5.4 0.2 - - - +
476L THR 3.5 6.0 + - - +
477L GLN* 3.5 23.8 + - - +
5550L DHB 3.4 20.2 - + - -
5600L FE 2.3 31.6 - - - -
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Residues in contact with PHE 463 (chain L).
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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380L VAL* 4.1 9.6 - - + -
397L VAL* 3.6 32.5 - - + -
398L GLU 3.3 6.3 - - - -
399L MET* 4.3 7.6 - - + -
400L TRP* 4.4 5.4 - - - -
437L TYR* 3.9 27.1 - + - -
439L PHE* 4.2 7.4 - + - -
461L ILE* 3.6 24.4 + - + -
462L HIS* 1.3 80.4 - - - +
464L GLY* 1.4 56.4 + - - +
465L ILE* 4.2 5.4 - - + -
475L ILE* 3.3 7.1 - - - +
476L THR* 2.8 50.5 + - + +
478L LEU* 3.4 37.0 - - + -
523L PHE* 4.1 5.8 - + + -
525L ILE* 4.3 11.0 - - + -
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Residues in contact with GLY 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 5.6 1.6 - - - -
396L LEU 3.5 1.0 - - - +
397L VAL* 3.4 4.9 - - - +
398L GLU* 2.7 43.2 + - - +
400L TRP* 4.6 4.0 - - - -
463L PHE* 1.4 73.4 - - - +
465L ILE* 1.3 61.2 + - - +
473L LYS* 5.0 5.8 - - - -
474L LEU 3.3 9.2 - - - -
475L ILE* 3.8 12.6 - - - -
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Residues in contact with ILE 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L VAL* 4.2 10.1 - - + -
395L THR* 4.0 19.1 - - + -
396L LEU 3.4 4.3 - - - +
397L VAL* 4.5 11.2 - - + -
463L PHE* 4.2 9.9 - - + -
464L GLY* 1.3 84.4 - - - +
466L SER* 1.3 67.6 + - - +
472L THR 4.2 1.6 - - - +
473L LYS* 3.2 5.4 - - - +
474L LEU* 2.9 45.2 + - + +
476L THR* 4.4 11.4 - - + -
525L ILE* 4.1 36.1 - - + -
527L LEU* 3.9 33.0 - - + -
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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