Contacts of the strand formed by residues 458 - 467 (chain A) in PDB entry 1D0N
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 ARG 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A THR* 4.7 2.0 - - - +
453A TYR* 3.7 17.5 - - + +
455A HIS* 2.8 38.8 + - - +
456A GLY 3.2 1.5 - - - -
457A SER* 1.3 101.4 + - - +
459A GLN* 1.3 66.6 + - - +
723A GLY 5.9 1.2 + - - -
724A PHE* 5.7 1.8 - - - +
725A GLU* 3.3 29.4 + - - +
726A PRO 4.9 0.7 - - - -
727A PRO* 4.4 11.8 - - + +
730A VAL* 4.2 19.2 - - - +
736A TRP* 3.1 31.1 - - - +
738A ASP* 2.5 41.5 + - - +
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Residues in contact with GLN 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A TYR* 3.4 15.4 + - - +
454A ARG* 4.2 27.1 - - + +
455A HIS 4.8 0.7 - - - +
456A GLY 5.5 3.6 - - - +
458A ARG* 1.3 81.6 - - - +
460A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A ASN* 3.4 5.9 - - - +
453A TYR* 2.9 48.2 + - - +
459A GLN* 1.3 76.4 - - - +
461A GLN* 1.3 65.2 + - - +
493A THR* 5.9 5.8 - - - -
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Residues in contact with GLN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A LEU* 4.0 21.3 - - + +
451A TYR 3.1 8.3 - - - +
452A ASN* 2.8 29.6 + - - +
453A TYR* 3.7 1.3 - - - -
460A GLY* 1.3 76.8 - - - -
462A ILE* 1.3 67.7 + - - +
490A LEU* 3.3 36.2 - - - +
493A THR* 5.5 7.3 + - + +
494A PRO* 3.5 18.4 - - + +
495A VAL* 3.0 26.1 + - - +
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ASP* 3.4 27.1 - - + +
449A ILE 3.3 2.8 - - - +
450A LEU* 3.6 0.9 - - - -
451A TYR* 2.8 42.2 + - + +
453A TYR* 3.6 24.5 - - + -
461A GLN* 1.3 80.7 - - - +
463A ILE* 1.3 68.1 + - - +
464A TYR* 3.7 34.5 + - + +
495A VAL* 3.4 26.7 - - + +
497A SER* 4.9 2.5 - - - -
507A HIS* 4.0 24.5 - - + +
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ILE* 3.8 29.6 - - + -
449A ILE 3.1 8.1 - - - +
450A LEU* 3.8 16.4 - - + -
462A ILE* 1.3 76.5 - - - +
464A TYR* 1.3 62.9 + - - +
465A ASN 4.0 0.3 + - - -
483A THR* 4.0 19.0 - - + +
486A LEU* 3.8 15.0 - - + -
487A ASP* 3.7 39.7 - - + +
490A LEU* 4.6 0.4 - - + -
494A PRO* 3.9 20.0 - - + -
495A VAL 2.7 12.4 + - - +
496A GLN* 3.7 4.6 - - + +
497A SER* 3.0 28.2 + - - +
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Residues in contact with TYR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ASP* 5.4 0.5 + - - -
447A TYR 3.8 0.9 - - - +
448A ILE* 3.1 6.6 - - - +
449A ILE* 2.7 61.4 + - + +
451A TYR* 5.1 3.6 - - + -
462A ILE* 3.7 25.5 - - + +
463A ILE* 1.3 73.3 - - - +
465A ASN* 1.3 61.2 + - - +
466A TRP 3.8 1.1 + - - +
497A SER* 3.7 29.2 - - - -
499A VAL* 4.6 6.5 - - + -
505A PRO* 4.1 18.0 - - + +
507A HIS* 2.9 44.0 - + - +
508A LEU* 3.7 33.0 + - + -
511A LEU* 4.1 17.3 - - + -
679A GLN* 6.3 0.2 - - - -
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Residues in contact with ASN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A TYR 3.3 13.8 + - - -
448A ILE* 4.5 1.0 - - - +
463A ILE 4.0 0.4 + - - -
464A TYR* 1.3 71.6 - - - +
466A TRP* 1.3 63.5 + - - +
467A GLN* 3.1 23.5 + - - +
479A SER* 3.4 23.2 + - - -
480A ALA* 3.5 20.3 + - - +
483A THR* 3.4 27.8 + - + +
497A SER 2.9 14.9 + - - +
498A ARG* 3.7 7.2 - - + +
499A VAL* 2.9 31.3 + - - +
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Residues in contact with TRP 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PHE* 4.3 12.3 - + + -
442A TYR 3.6 8.3 - - - -
443A GLY* 3.9 6.3 - - - -
445A ASP 3.6 2.5 - - - -
446A SER* 3.2 8.5 - - - -
447A TYR* 2.9 77.9 + + + +
449A ILE* 5.3 8.5 - - + -
464A TYR* 3.8 2.0 - - + -
465A ASN* 1.3 73.1 + - - +
467A GLN* 1.3 61.5 + - - +
468A GLY* 3.4 28.7 - - - -
499A VAL* 3.3 29.2 - - + -
501A GLN* 3.3 41.7 - - + +
504A GLU* 3.2 26.7 + - + +
508A LEU* 4.3 8.7 - - + -
517A MET* 3.9 8.7 - - + +
519A VAL* 3.8 17.3 - - + -
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Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A SER* 4.1 5.6 - - - +
465A ASN* 3.1 26.7 + - - +
466A TRP* 1.3 79.0 - - - +
468A GLY* 1.3 66.5 + - - +
469A ALA 3.5 0.5 + - - -
476A VAL* 3.4 35.1 + - + +
479A SER* 4.2 10.1 + - - +
480A ALA* 4.8 6.3 - - - +
498A ARG* 3.8 30.8 + - - +
499A VAL 2.8 14.4 + - - +
500A VAL* 3.7 15.5 - - + +
501A GLN 2.9 24.3 + - - -
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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