Contacts of the strand formed by residues 460 - 465 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401D GLN* 4.0 7.3 - - - +
402D ALA* 4.8 1.4 + - - +
444D PRO* 3.2 22.5 - - - +
445D GLY 5.2 0.4 + - - -
447D TYR* 3.4 27.6 - + - -
457D ARG* 3.3 16.1 + - + -
458D PRO 2.7 21.0 + - - -
459D ALA* 1.3 74.9 - - - +
461D ILE* 1.3 64.9 + - - +
462D HIS* 3.5 13.4 - + - -
477D GLN* 3.0 23.6 - - + +
478D LEU 3.0 17.3 - - - +
479D TYR* 3.7 15.0 - + + -
480D PHE* 4.4 1.8 - - - -
1550D DHB 3.1 3.0 + - - -
1600D FE 2.3 30.5 - - - -
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Residues in contact with ILE 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D VAL* 4.0 26.7 - - + -
399D MET* 4.1 22.0 - - + -
400D TRP 3.6 10.1 - - - +
401D GLN* 3.9 20.0 - - + +
441D THR* 4.4 3.8 - - + -
444D PRO* 4.0 14.8 - - + -
460D HIS* 1.3 81.1 - - - +
462D HIS* 1.3 72.8 + - - +
463D PHE* 3.6 18.2 - - + -
477D GLN* 3.3 1.7 - - - -
478D LEU* 2.7 45.0 + - + +
480D PHE* 4.0 17.0 - - + -
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Residues in contact with HIS 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR 4.3 2.4 + - - -
13C ALA* 3.6 20.1 + - - -
14C GLY* 4.6 1.1 - - - -
399D MET* 3.2 8.5 - - - +
400D TRP* 2.9 78.0 + + + +
401D GLN* 4.9 4.3 - - - -
408D GLU* 4.8 3.9 + - - -
460D HIS* 3.4 5.9 + + - -
461D ILE* 1.3 73.2 - - - +
463D PHE* 1.4 60.3 + - - +
475D ILE* 5.6 0.2 - - - +
476D THR 3.3 5.5 + - - +
477D GLN* 3.6 22.3 + - - +
1550D DHB 3.4 19.5 - + - -
1600D FE 2.4 31.1 - - - -
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Residues in contact with PHE 463 (chain D).
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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380D VAL* 3.9 22.9 - - + -
397D VAL* 3.7 31.4 - - + -
398D GLU 3.3 6.1 - - - -
399D MET* 4.5 5.4 - - + -
400D TRP* 4.4 4.0 - - - -
437D TYR* 3.9 21.3 - + - -
439D PHE* 4.0 10.5 - + - -
461D ILE* 3.6 26.2 - - + -
462D HIS* 1.4 77.0 - - - +
464D GLY* 1.3 57.4 + - - +
465D ILE* 4.3 4.7 - - + -
475D ILE* 3.3 6.2 - - - +
476D THR* 2.6 53.4 + - + +
478D LEU* 3.6 28.5 - - + -
523D PHE* 4.3 5.6 - + - -
525D ILE* 4.4 11.2 - - + -
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Residues in contact with GLY 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 5.8 1.6 - - - -
396D LEU 3.5 1.2 - - - +
397D VAL* 3.4 5.0 - - - +
398D GLU* 2.8 43.9 + - - +
400D TRP* 4.3 6.1 - - - -
463D PHE* 1.3 76.3 - - - +
465D ILE* 1.3 63.3 + - - +
473D LYS* 5.2 5.8 - - - -
474D LEU 3.4 7.9 - - - -
475D ILE* 4.1 11.2 - - - -
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Residues in contact with ILE 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D VAL* 4.2 14.4 - - + -
395D THR* 4.2 9.6 - - + -
396D LEU 3.3 8.1 - - - +
397D VAL* 4.7 11.9 - - + -
463D PHE* 4.3 5.2 - - + -
464D GLY* 1.3 83.5 - - - +
466D SER* 1.3 64.0 + - - +
472D THR 4.4 1.2 - - - +
473D LYS* 3.4 6.6 - - - +
474D LEU* 2.8 44.7 + - + +
476D THR* 4.2 20.9 - - + -
525D ILE* 3.9 37.0 - - + -
527D LEU* 4.1 29.4 - - + -
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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