Contacts of the strand formed by residues 465 - 471 (chain A) in PDB entry 2DB3
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 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A CYS* 2.9 30.0 - - + +
463A SER 3.3 0.8 - - - -
464A ASP* 1.3 79.2 - - - +
466A LYS* 1.3 64.1 + - - +
467A GLN* 3.2 15.3 + - + +
577A ILE* 3.6 42.6 - - + +
580A THR* 3.1 36.1 - - + +
581A GLY* 3.9 7.6 - - - +
587A GLY 3.2 8.1 - - - +
588A ARG 5.1 0.2 - - - +
589A ALA* 5.0 5.6 - - + -
614A GLN* 3.5 10.4 + - - +
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Residues in contact with LYS 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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464A ASP 3.7 2.2 + - - -
465A VAL* 1.3 70.5 - - - +
467A GLN* 1.3 67.2 + - - +
468A THR* 4.0 17.7 + - - +
587A GLY 2.6 14.8 + - - +
588A ARG* 3.2 10.6 - - + +
589A ALA 2.8 26.9 + - - +
614A GLN* 3.3 11.5 + - - +
615A THR* 5.3 12.9 + - - +
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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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461A ALA* 3.9 5.7 - - - +
462A CYS 4.2 0.2 + - - -
465A VAL* 3.4 22.3 + - + +
466A LYS* 1.3 78.2 + - - +
468A THR* 1.3 64.7 + - - +
469A ILE* 5.2 1.3 - - - +
573A TYR* 2.7 40.1 + - - +
577A ILE* 3.3 27.0 - - + +
589A ALA* 3.3 10.1 - - + +
608A ILE* 4.3 3.8 - - - +
609A LEU* 3.6 19.8 - - + +
612A SER* 3.2 26.6 + - - -
614A GLN* 2.8 29.4 + - - +
615A THR* 5.0 6.8 + - - +
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Residues in contact with THR 468 (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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466A LYS* 4.0 20.1 + - - +
467A GLN* 1.3 77.9 + - - +
469A ILE* 1.3 67.8 + - - +
470A TYR* 3.9 35.8 + - + +
589A ALA 2.8 10.0 + - - +
590A THR* 3.4 10.7 - - - +
591A SER 2.9 25.3 + - - -
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Residues in contact with ILE 469 (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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468A THR* 1.3 90.1 - - - +
470A TYR* 1.3 65.5 + - - +
573A TYR* 3.8 18.4 - - + +
591A SER* 3.5 28.0 - - - +
593A PHE* 3.7 19.5 - - + -
605A LEU* 4.1 26.7 - - + -
609A LEU* 4.2 21.8 - - + -
615A THR 5.9 0.2 - - - +
617A PRO* 3.8 17.3 - - + +
619A PHE* 3.4 34.1 - - + -
620A LEU* 4.4 2.9 - - + -
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Residues in contact with TYR 470 (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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468A THR* 3.9 21.7 - - + +
469A ILE* 1.3 78.6 - - - +
471A GLU* 1.3 57.1 + - - +
472A VAL* 3.2 18.0 + - + -
480A LYS* 3.7 31.1 - - - -
484A ILE* 4.4 5.4 - - + -
590A THR* 3.8 31.0 - - + -
591A SER 2.9 9.5 + - - +
592A PHE* 3.6 7.1 - + + -
593A PHE* 2.7 32.9 + - - +
619A PHE* 3.8 3.4 - - - -
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Residues in contact with GLU 471 (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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470A TYR* 1.3 70.2 - - - +
472A VAL* 1.3 60.5 + - - +
473A ASN* 4.4 1.4 + - - -
593A PHE* 3.3 4.2 - - + +
595A PRO* 3.4 35.0 - - + +
619A PHE* 3.0 58.8 - - + +
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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