Contacts of the strand formed by residues 495 - 500 (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 VAL 495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ASP* 5.6 1.1 - - - +
453A TYR* 5.0 4.0 - - + +
461A GLN 3.0 15.8 + - - +
462A ILE* 3.4 21.8 - - + +
463A ILE* 2.7 28.9 + - - +
493A THR 5.3 0.4 - - - +
494A PRO* 1.3 75.4 - - - +
496A GLN* 1.3 62.6 + - - +
718A THR* 3.3 30.5 - - + -
719A VAL 3.6 7.0 - - - +
720A VAL* 4.3 7.0 - - + -
724A PHE 4.3 9.4 - - - +
726A PRO* 3.9 38.1 - - + -
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Residues in contact with GLN 496 (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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463A ILE* 3.7 7.6 - - + +
480A ALA 5.2 1.8 + - - -
483A THR* 3.6 33.1 - - + +
484A ALA* 4.2 14.4 - - - +
487A ASP* 3.6 32.1 - - + +
494A PRO 3.9 0.8 + - - +
495A VAL* 1.3 74.1 - - - +
497A SER* 1.3 64.9 + - - +
498A ARG 4.4 0.2 + - - -
697A LEU* 3.9 27.4 - - + +
717A ILE 3.8 0.7 - - - +
718A THR* 3.3 1.1 - - - -
719A VAL* 2.6 56.1 + - + +
721A LYS* 5.2 3.1 + - - -
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Residues in contact with SER 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 4.9 4.3 - - - -
463A ILE 3.0 9.2 + - - +
464A TYR* 3.7 31.4 - - - -
465A ASN* 2.9 29.3 + - - +
496A GLN* 1.3 79.5 - - - +
498A ARG* 1.3 63.1 + - - +
499A VAL* 3.8 1.4 + - - +
505A PRO* 5.2 2.8 - - - +
679A GLN* 4.5 2.4 + - - -
716A PRO* 4.9 4.9 - - - +
717A ILE 3.1 7.4 + - - -
718A THR* 3.1 26.3 + - - -
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Residues in contact with ARG 498 (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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465A ASN* 3.7 7.0 - - + +
467A GLN* 3.8 31.2 + - - +
496A GLN 4.4 0.2 - - - -
497A SER* 1.3 71.5 - - - +
499A VAL* 1.3 61.6 + - - +
500A VAL* 3.5 24.5 - - - +
697A LEU* 4.1 22.3 - - + +
701A LYS* 3.7 34.6 - - - +
713A ARG 3.4 24.2 + - - -
714A ARG 3.7 0.8 + - - -
715A THR 3.6 13.3 + - - -
716A PRO* 3.4 4.1 - - - +
717A ILE* 2.7 48.0 + - - +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A TYR* 4.6 8.3 - - + -
465A ASN 2.9 22.5 + - - +
466A TRP* 3.6 20.0 - - + -
467A GLN* 2.8 27.2 + - - +
497A SER* 5.1 1.1 - - - +
498A ARG* 1.3 76.1 - - - +
500A VAL* 1.3 70.8 + - - +
503A LYS 3.7 4.5 - - - +
504A GLU* 3.6 15.0 - - - -
505A PRO* 3.5 32.5 - - + -
508A LEU* 3.7 19.5 - - + -
716A PRO* 4.8 4.7 - - + -
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Residues in contact with VAL 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A TRP* 4.5 0.9 - - - -
467A GLN* 3.7 22.4 - - + +
469A ALA* 5.5 6.3 - - + +
498A ARG* 3.5 34.5 - - - +
499A VAL* 1.3 85.5 - - - +
501A GLN* 1.3 78.2 + - + +
502A GLY 3.1 0.2 + - - -
503A LYS* 3.1 16.5 + - - -
504A GLU* 3.5 3.9 - - - +
714A ARG* 3.9 35.2 + - + +
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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