Contacts of the strand formed by residues 458 - 463 (chain X) in PDB entry 1T6B
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 ASN 458 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X TYR* 4.7 14.4 + - - +
376X ASN* 2.7 38.8 + - - +
377X VAL* 5.4 1.2 - - - +
399X ASN* 5.1 0.5 + - - -
456X TYR 4.6 1.6 - - - +
457X GLY* 1.3 79.0 - - - -
459X ILE* 1.3 61.3 + - - +
460X ALA 4.3 0.5 + - - -
471X VAL* 3.7 14.9 - - + +
472X ASP 3.6 9.2 - - - +
473X THR* 3.3 31.5 + - - +
475X SER 3.1 21.4 + - - +
476X ASN* 4.0 14.1 + - - +
477X TRP* 3.9 9.4 + - - -
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Residues in contact with ILE 459 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X PRO* 3.9 25.1 - - + -
233X TYR* 4.1 11.0 - - + +
375X TYR* 5.4 0.2 - - - -
458X ASN* 1.3 75.2 - - - +
460X ALA* 1.3 69.2 + - - +
461X THR* 3.4 17.9 + - + -
471X VAL* 4.1 2.5 - - - -
472X ASP* 2.9 27.9 + - - +
475X SER* 3.1 17.9 + - - +
476X ASN 3.4 33.9 - - - +
477X TRP* 3.5 35.0 - - + +
480X VAL* 3.9 16.8 - - + -
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Residues in contact with ALA 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X TYR* 3.7 15.1 + - - -
244X ASP* 3.9 6.4 - - - +
375X TYR* 3.5 36.8 - - + +
458X ASN 4.3 0.6 + - - -
459X ILE* 1.3 73.0 - - - +
461X THR* 1.3 59.4 + - - +
469X VAL* 3.8 19.9 - - + +
470X ARG* 3.2 16.8 - - - +
471X VAL* 3.7 6.0 - - + +
803X NA 3.2 12.5 - - - -
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Residues in contact with THR 461 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X LYS* 4.4 8.0 + - - -
232X PRO* 4.4 17.5 - - + +
233X TYR* 5.0 2.2 - - + -
237X GLU* 6.0 0.4 - - - -
459X ILE* 3.4 28.2 + - + +
460X ALA* 1.3 73.5 - - - +
462X TYR* 1.3 67.5 + - - +
463X ASN* 3.9 1.7 + - - +
469X VAL* 3.4 1.4 - - - -
470X ARG* 2.9 30.9 + - - +
472X ASP* 3.7 17.7 + - - +
475X SER* 3.7 20.4 - - - +
803X NA 3.7 6.5 - - - -
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Residues in contact with TYR 462 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X SER* 3.4 22.6 - - - -
153X LEU* 4.5 4.4 - - + +
157X LYS* 2.6 29.3 + - - +
233X TYR* 5.7 0.4 - - - -
237X GLU* 3.9 15.1 + - - +
242X ARG* 3.4 53.0 + - + +
243X ILE 4.9 0.2 - - - -
461X THR* 1.3 78.9 + - - +
463X ASN* 1.3 74.8 + - - +
464X PHE* 3.6 50.4 - + - -
467X GLY* 3.3 36.7 - - - -
468X ARG 3.7 7.2 - - - -
469X VAL* 4.2 11.2 - - + +
803X NA 3.5 7.9 - - - -
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Residues in contact with ASN 463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X GLU* 3.9 5.3 - - - +
157X LYS* 4.8 1.3 - - - +
461X THR 4.9 1.8 - - - +
462X TYR* 1.3 80.1 - - - +
464X PHE* 1.3 53.0 + - - +
465X GLU* 2.9 35.1 + - - +
466X ASN* 3.3 30.5 + - + +
467X GLY* 2.7 36.7 + - - -
468X ARG 2.9 14.3 + - - +
470X ARG* 5.8 6.1 - - + +
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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