Contacts of the strand formed by residues 475 - 485 (chain A) in PDB entry 6T2C
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 TYR 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ASN* 4.4 0.7 - - - -
355A LEU* 2.9 47.2 + - + +
357A LYS* 3.4 44.4 - - + +
361A LEU* 3.6 27.4 - - + -
362A LYS* 3.5 12.3 - - + +
365A LEU* 3.6 19.7 - - + +
367A GLU* 2.3 36.7 + - - +
474A GLU* 1.3 74.4 - - - +
476A GLN* 1.3 62.5 + - - +
477A VAL 3.5 2.1 + - - -
500A ILE* 4.4 4.7 - - + -
501A LYS 3.4 21.8 - - - +
502A GLY* 3.8 16.2 - - - -
503A ARG* 4.3 11.0 + - + +
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Residues in contact with GLN 476 (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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352A PHE* 3.9 11.7 - - - +
353A LEU 3.6 7.6 - - - +
354A ASN* 2.8 26.8 + - - +
467A SER* 3.0 19.0 + - - +
471A ALA* 3.7 19.0 - - - +
474A GLU* 3.3 7.0 + - + +
475A TYR* 1.3 71.5 - - - +
477A VAL* 1.3 72.7 + - - +
478A ILE* 3.4 4.2 + - + +
499A ILE 3.6 0.3 - - - +
500A ILE* 4.7 0.2 - - - -
501A LYS* 3.1 42.9 + - - +
31V U 2.8 42.4 + - - +
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Residues in contact with VAL 477 (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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304A MET* 4.4 24.1 - - + +
341A LEU* 3.7 30.5 - - + -
353A LEU* 3.1 24.9 + - + +
355A LEU* 3.7 34.5 - - + -
476A GLN* 1.3 78.7 - - - +
478A ILE* 1.3 62.5 + - - +
479A PRO* 4.0 5.0 - - - +
498A PHE* 4.2 23.3 - - + -
499A ILE 3.6 4.9 - - - +
500A ILE* 4.2 7.4 - - + +
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Residues in contact with ILE 478 (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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460A ILE* 5.3 3.8 - - + +
463A ALA* 3.7 42.0 - - + +
464A LEU* 3.9 27.6 - - + +
467A SER* 3.9 22.4 - - - +
476A GLN* 3.8 11.4 - - + +
477A VAL* 1.3 80.8 - - - +
479A PRO* 1.3 75.8 - - + +
498A PHE* 3.4 1.9 - - - -
499A ILE* 2.5 59.8 + - + +
501A LYS* 4.6 5.6 - - + -
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Residues in contact with PRO 479 (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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303A PRO* 3.7 39.9 - - + +
304A MET* 4.0 16.6 - - + -
307A ALA* 4.0 20.4 - - + -
459A TYR 6.1 0.5 - - - -
460A ILE* 5.4 3.1 - - - +
463A ALA* 5.2 3.2 - - + +
477A VAL 4.0 1.8 - - - +
478A ILE* 1.3 100.4 - - + +
480A ILE* 1.3 62.1 + - - +
481A ILE* 3.8 12.7 + - + +
495A LEU* 4.4 0.9 - - + -
497A GLY 3.6 6.3 - - - +
498A PHE* 4.1 11.7 - - + -
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Residues in contact with ILE 480 (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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282A PHE* 5.3 0.2 - - + -
456A LYS* 3.9 11.0 - - + -
459A TYR* 6.4 0.7 - - + -
460A ILE* 3.7 37.2 - - + -
479A PRO* 1.3 74.4 - - - +
481A ILE* 1.3 60.7 + - - +
495A LEU* 3.4 6.5 - - - +
496A TYR* 2.9 46.0 + - + -
497A GLY* 2.8 34.0 + - - +
498A PHE 4.4 0.7 - - - +
499A ILE* 4.0 24.2 - - + -
519A GLU* 3.3 33.2 - - + +
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Residues in contact with ILE 481 (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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303A PRO* 4.6 19.7 - - + +
306A ASP* 4.9 6.1 - - + +
307A ALA 4.7 7.2 - - - +
456A LYS* 5.2 0.3 - - - -
459A TYR* 3.2 33.1 - - + +
479A PRO* 3.8 23.1 + - + +
480A ILE* 1.3 82.0 - - - +
482A THR* 1.3 74.7 + - - +
483A LYS* 4.4 15.3 - - + -
493A THR* 3.8 23.6 - - + -
494A ASN 3.4 6.7 - - - +
495A LEU* 3.7 28.5 - - + -
496A TYR* 4.8 0.2 - - - -
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Residues in contact with THR 482 (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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417A TRP* 3.9 13.4 - - + -
452A GLU 4.6 2.2 - - - +
455A MET* 4.3 11.0 - - + +
456A LYS* 3.8 33.4 - - + +
459A TYR* 4.8 4.0 - - - -
481A ILE* 1.3 80.1 - - - +
483A LYS* 1.3 65.0 + - - +
493A THR* 3.7 2.1 - - - -
494A ASN* 2.9 43.1 + - - +
496A TYR* 3.2 36.1 + - + +
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLY* 4.2 21.2 + - - -
306A ASP* 4.6 12.6 - - - -
417A TRP 4.6 0.3 - - - +
455A MET* 3.6 27.9 - - - +
459A TYR* 4.3 14.1 + - + +
481A ILE* 4.4 13.9 - - + -
482A THR* 1.3 79.5 - - - +
484A CYS* 1.3 62.7 + - - +
491A ARG* 4.2 21.4 - - - +
492A ARG 3.5 7.4 - - - +
493A THR* 4.1 15.9 - - - +
568B LEU* 5.1 4.9 - - - +
32V G 3.8 6.5 + - - -
33V C 3.0 34.3 + - - +
34V U 4.2 22.1 - - - +
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Residues in contact with CYS 484 (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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415A SER* 3.9 20.2 - - - -
416A ASN 4.2 9.0 - - - +
417A TRP* 3.6 29.6 - - + -
483A LYS* 1.3 75.7 - - - +
485A ARG* 1.3 69.4 + - - +
491A ARG* 3.6 4.5 - - - +
492A ARG* 2.9 44.8 + - - +
494A ASN* 3.2 27.4 - - - -
34V U 3.9 7.9 + - - -
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Residues in contact with ARG 485 (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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415A SER* 3.3 10.9 + - - -
416A ASN* 3.1 40.9 + - + +
419A GLU* 4.0 18.5 + - - -
484A CYS* 1.3 78.3 - - - +
486A ASP* 1.3 68.4 + - - +
489A GLY* 2.5 41.6 + - - +
490A GLN 3.7 7.9 - - - +
491A ARG* 4.6 8.6 - - - +
492A ARG* 5.4 2.0 - - - -
34V U 2.5 55.8 + - - +
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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