Contacts of the strand formed by residues 454 - 463 (chain D) in PDB entry 4PKY
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 ILE 454 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369D ILE* 4.3 23.4 - - + +
416D VAL* 3.7 44.6 - - + +
419D LYS* 4.3 16.6 - - + -
445D THR* 3.8 33.9 - - + +
446D PHE 3.6 3.8 - - - +
447D GLN* 4.4 9.6 - - + +
453D GLU* 1.3 81.2 + - - +
455D GLU* 1.3 63.3 + - - +
456D TYR 3.8 15.7 - - - +
457D ILE* 5.0 0.9 - - + -
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Residues in contact with GLU 455 (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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368D ASN* 5.5 2.3 - - - -
369D ILE* 6.3 0.2 - - - -
446D PHE* 2.9 37.9 + - + +
448D ASN* 3.4 36.8 + - + +
449D PRO* 4.5 2.4 - - - +
453D GLU 3.5 0.2 + - - -
454D ILE* 1.3 75.3 - - - +
456D TYR* 1.3 79.5 + - + +
619E ARG* 3.8 21.2 + - - +
623E ASP* 4.7 1.9 - - - +
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Residues in contact with TYR 456 (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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366D ARG* 3.2 29.2 - - + +
367D HIS 3.4 14.4 - - - +
368D ASN* 5.1 4.0 - - - +
369D ILE* 5.7 0.9 - - - +
374D THR* 5.3 0.4 - - - +
445D THR* 3.5 2.9 - - - -
446D PHE* 3.0 38.7 + + + -
454D ILE* 3.5 7.8 - - - +
455D GLU* 1.3 93.3 - - + +
457D ILE* 1.3 62.8 + - - +
458D ILE* 3.3 34.8 - - + +
619E ARG* 3.2 39.5 + - - -
620E ILE* 4.0 15.4 - - + -
623E ASP* 2.7 36.0 + - - +
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Residues in contact with ILE 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D SER 3.6 0.5 - - - +
366D ARG* 3.4 3.6 - - - -
367D HIS* 2.8 45.5 + - + +
368D ASN 3.9 11.0 - - - +
369D ILE* 4.0 13.0 - - - -
412D PHE* 3.5 32.1 - - + -
415D VAL* 3.8 17.7 - - + -
416D VAL* 4.2 8.5 - - + -
443D SER* 4.2 9.6 - - - -
444D PHE 3.5 11.7 - - - +
445D THR* 3.8 16.2 - - + -
454D ILE* 5.0 2.2 - - + -
456D TYR* 1.3 77.2 - - - +
458D ILE* 1.3 71.1 + - - +
459D CYS* 4.0 15.0 - - - -
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Residues in contact with ILE 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ILE* 3.9 24.7 - - + -
365D SER 3.6 3.4 - - - +
366D ARG* 5.1 3.4 - - + -
442D SER 4.2 0.2 - - - +
443D SER* 3.2 6.1 - - - -
444D PHE* 3.0 51.2 + - + +
446D PHE* 5.1 5.4 - - + -
456D TYR* 3.3 35.0 - - + +
457D ILE* 1.3 73.6 - - - +
459D CYS* 1.3 64.8 + - - +
620E ILE* 3.9 18.8 - - + -
623E ASP* 5.9 0.2 - - + -
624E LEU* 3.9 26.7 - - + +
625F ILE* 4.3 16.8 - - + -
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Residues in contact with CYS 459 (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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364D ILE* 3.3 7.8 - - - +
365D SER* 2.8 45.3 + - - +
367D HIS* 3.4 26.7 - - - +
396D ILE* 5.7 2.0 - - + -
412D PHE* 4.4 9.9 - - - -
441D THR* 3.8 13.0 - - + -
442D SER 3.9 3.8 - - - -
443D SER* 3.0 25.4 - - - +
457D ILE* 4.0 8.3 - - - -
458D ILE* 1.3 78.5 - - - +
460D THR* 1.3 63.8 + - - +
461D ASN* 3.7 5.2 + - - +
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Residues in contact with THR 460 (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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362D ARG* 3.2 41.7 - - + +
363D PHE 3.8 3.4 - - - +
364D ILE* 4.5 9.5 - - + +
440D ARG 3.3 13.0 - - - +
441D THR* 4.3 0.2 - - - -
442D SER* 3.2 32.9 + - - -
444D PHE* 5.3 0.5 - - - -
458D ILE* 5.0 0.7 - - - +
459D CYS* 1.3 73.8 + - - +
461D ASN* 1.3 61.2 + - - +
462D THR* 3.7 2.5 + - - +
622F ASP* 5.1 4.0 - - + -
625F ILE* 3.7 33.8 - - + +
629F GLU* 5.6 0.9 - - - +
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Residues in contact with ASN 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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361D THR 4.2 0.3 - - - +
362D ARG* 3.4 2.5 - - - -
363D PHE* 3.0 62.5 + - + -
365D SER* 3.0 26.7 + - - -
373D PHE* 5.7 0.6 - - - -
396D ILE* 4.6 12.2 - - - +
427D PHE* 4.8 2.1 - - + -
439D MET* 3.5 20.1 - - + +
440D ARG 3.6 4.3 - - - -
441D THR* 2.7 33.1 + - - +
459D CYS* 3.7 7.3 + - - +
460D THR* 1.3 72.9 - - - +
462D THR* 1.3 61.1 + - - +
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Residues in contact with THR 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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361D THR 3.7 15.5 - - - +
362D ARG* 3.2 40.4 + - - +
439D MET* 3.6 6.4 - - - +
440D ARG* 3.0 61.1 + - - +
460D THR* 4.3 4.2 + - - +
461D ASN* 1.3 73.7 - - - +
463D ASN* 1.3 73.4 + - - +
464D VAL* 3.4 2.4 + - + +
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Residues in contact with ASN 463 (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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361D THR* 3.1 27.2 + - - +
383D THR* 3.8 31.8 + - + +
437D LEU* 4.4 21.0 - - - +
438D TRP 3.5 11.9 + - - +
439D MET* 3.9 7.6 - - - +
462D THR* 1.3 79.6 - - - +
464D VAL* 1.3 72.9 + - - +
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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