Contacts of the strand formed by residues 460 - 465 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401H GLN* 4.1 7.3 - - - +
402H ALA* 4.9 1.0 + - - +
444H PRO* 3.4 20.1 - - - +
445H GLY 5.1 0.6 + - - -
447H TYR* 3.3 31.9 - + - -
457H ARG* 3.5 16.1 + - + +
458H PRO 2.7 22.6 + - - -
459H ALA* 1.3 74.9 - - - +
461H ILE* 1.3 66.6 + - - +
462H HIS* 3.6 12.3 - + - -
477H GLN* 3.0 23.5 + - + +
478H LEU 3.1 17.0 - - - +
479H TYR* 3.7 14.1 - + + -
480H PHE* 4.3 3.8 - - - -
3550H DHB 3.3 2.4 + - - -
3600H FE 2.4 26.1 - - - -
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Residues in contact with ILE 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380H VAL* 4.0 27.6 - - + -
399H MET* 4.1 20.0 - - + -
400H TRP 3.9 11.0 - - - +
401H GLN* 3.8 21.8 - - + +
441H THR* 4.4 3.6 - - + -
444H PRO* 4.0 14.6 - - + -
460H HIS* 1.3 83.2 - - - +
462H HIS* 1.4 65.6 + - - +
463H PHE* 3.7 21.0 + - + -
477H GLN* 3.5 1.2 - - - -
478H LEU* 2.9 39.2 + - + +
480H PHE* 4.0 17.5 - - + -
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Residues in contact with HIS 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G THR 4.0 2.6 + - - -
13G ALA* 3.6 19.3 + - - -
14G GLY* 4.5 0.4 - - - -
399H MET* 3.1 7.6 - - - +
400H TRP* 2.8 81.2 + + + +
401H GLN* 5.1 3.4 - - - -
408H GLU* 5.2 2.6 + - - -
460H HIS* 3.4 6.3 + + - -
461H ILE* 1.4 72.9 - - - +
463H PHE* 1.4 59.5 - - - +
475H ILE* 5.4 0.8 - - + +
476H THR 3.4 6.3 + - - +
477H GLN* 3.4 25.2 + - - +
3550H DHB 3.2 21.1 - + - -
3600H FE 2.2 32.0 - - - -
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Residues in contact with PHE 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380H VAL* 4.0 14.6 - - + -
397H VAL* 3.7 25.8 - - + -
398H GLU 3.3 6.1 - - - -
399H MET* 4.4 4.9 - - + -
400H TRP* 4.4 5.4 - - - -
437H TYR* 3.8 29.2 - + - -
439H PHE* 4.1 10.8 - + - -
461H ILE* 3.7 25.1 - - + -
462H HIS* 1.4 76.7 - - - +
464H GLY* 1.3 57.5 + - - +
465H ILE* 4.1 11.7 - - + -
474H LEU 4.0 0.3 - - - +
475H ILE* 3.3 6.4 - - - +
476H THR* 2.9 46.5 + - + +
478H LEU* 3.4 37.5 - - + -
523H PHE* 4.2 6.5 - + - -
525H ILE* 4.1 12.1 - - + -
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Residues in contact with GLY 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G LEU* 5.7 1.8 - - - -
396H LEU 3.5 1.6 - - - +
397H VAL* 3.4 5.0 - - - +
398H GLU* 2.8 44.4 + - - +
400H TRP* 4.4 4.0 - - - -
463H PHE* 1.3 75.0 - - - +
465H ILE* 1.3 62.5 + - - +
473H LYS* 5.1 6.7 - - - -
474H LEU 3.4 6.5 - - - -
475H ILE* 4.1 11.7 - - - -
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Residues in contact with ILE 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H VAL* 4.4 7.4 - - + -
395H THR* 4.2 17.9 - - + -
396H LEU 3.4 4.3 - - - +
397H VAL* 4.5 11.7 - - + -
463H PHE* 4.1 14.4 - - + -
464H GLY* 1.3 80.3 - - - +
466H SER* 1.3 64.2 + - - +
472H THR 4.3 1.0 - - - +
473H LYS* 3.3 5.7 - - - +
474H LEU* 2.8 46.8 + - + +
476H THR* 4.4 11.7 - - + -
525H ILE* 3.9 37.7 - - + -
527H LEU* 4.0 32.5 - - + -
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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
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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