Contacts of the strand formed by residues 465 - 470 (chain D) in PDB entry 4XH9
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 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441D LEU* 3.3 28.5 + - + +
442D GLN 3.7 22.2 - - - +
443D ASP* 4.6 0.4 + - - -
446D VAL* 3.8 37.9 - - + +
448D MET* 4.2 17.9 - - + -
462D ALA 3.9 13.2 - - - +
463D LYS 3.6 16.2 - - - +
464D ASN* 1.3 77.5 - - - +
466D PHE* 1.3 63.2 - - - +
480D THR* 4.3 4.9 - - + -
481D LEU 3.2 6.5 - - - +
482D GLN* 3.7 20.9 - - + +
489D LYS* 2.9 22.5 + - - +
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Residues in contact with PHE 466 (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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393D LEU* 3.8 26.2 - - + -
438D LEU* 3.7 18.2 - - + -
439D GLU 3.4 13.7 - - - +
440D ASP* 4.5 0.2 - - - -
441D LEU* 4.0 9.4 - - - +
464D ASN 4.7 0.9 - - - -
465D ILE* 1.3 78.7 - - - +
467D ARG* 1.3 61.2 + - - +
468D ILE* 4.2 6.1 - - + -
479D HIS 3.8 0.2 - - - +
480D THR* 3.4 2.8 - - - +
481D LEU* 2.8 60.6 + - + +
483D ALA* 4.9 9.2 - - + -
489D LYS* 4.1 20.2 - - + -
492D TRP* 4.0 22.9 - + + -
493D PHE* 4.0 20.0 - + + -
496D ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 467 (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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396D LYS* 6.1 1.2 - - - +
437D VAL 3.8 0.5 - - - +
438D LEU* 3.6 4.0 - - - +
439D GLU* 2.8 70.4 + - + +
441D LEU* 3.9 30.5 - - + +
445D ASP* 6.2 0.2 - - - +
446D VAL* 4.5 9.5 - - - +
466D PHE* 1.3 76.3 - - - +
468D ILE* 1.3 72.7 + - - +
469D ARG* 4.7 4.0 - - - -
478D SER* 4.2 22.5 + - - -
479D HIS 3.3 17.0 - - - +
480D THR* 3.2 20.4 + - - +
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Residues in contact with ILE 468 (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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410D LEU* 3.7 33.9 - - + -
412D LEU* 4.1 11.2 - - + -
431D ILE* 4.2 9.2 - - + -
436D LEU* 4.0 15.7 - - + -
437D VAL 3.3 4.7 - - - +
438D LEU* 4.0 17.3 - - + -
466D PHE* 4.2 13.0 - - + -
467D ARG* 1.3 79.7 - - - +
469D ARG* 1.3 66.4 + - - +
478D SER* 3.3 1.0 - - - -
479D HIS* 2.8 45.3 + - + +
481D LEU* 3.9 19.7 - - + -
496D ILE* 4.3 12.3 - - + -
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Residues in contact with ARG 469 (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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431D ILE* 4.4 8.9 - - - +
435D GLU 3.6 1.6 - - - +
436D LEU* 3.6 5.0 - - - +
437D VAL* 2.8 54.3 + - + +
439D GLU* 3.2 28.4 + - - +
467D ARG* 4.7 7.4 - - - -
468D ILE* 1.3 79.5 - - - +
470D PHE* 1.3 79.7 + - - +
471D HIS* 3.9 7.3 - - - +
472D ASP* 2.9 38.6 + - - +
477D GLN 3.3 16.6 - - - +
478D SER* 3.5 15.0 - - - -
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Residues in contact with PHE 470 (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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429D GLN* 4.2 19.7 - - + -
430D PRO 3.5 21.5 - - - -
431D ILE* 3.6 23.8 - - + -
432D PRO* 3.7 12.1 - - + -
435D GLU* 3.3 36.3 - - + -
469D ARG* 1.3 91.8 + - - +
471D HIS* 1.3 69.4 + - - +
472D ASP* 3.0 12.3 + - - +
474D SER* 3.9 12.1 - - - -
475D PRO* 3.7 22.4 - - + +
477D GLN* 3.4 30.9 + - + +
479D HIS* 6.1 0.2 - - - -
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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