Contacts of the helix formed by residues 477 - 487 (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 TRP 477 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232X PRO* 3.7 21.5 - - + -
233X TYR* 3.7 12.1 - - - -
258X ALA 3.3 26.9 - - - -
259X TYR* 3.7 18.4 - - + -
260X PRO* 3.6 16.5 - - + +
372X ALA* 3.7 20.6 - - + -
373X PRO 3.7 16.2 + - - -
374X ILE* 5.1 1.3 - - + +
375X TYR* 6.1 0.2 - - - -
456X TYR* 3.8 38.6 - - + +
457X GLY 2.9 24.7 + - - +
458X ASN 3.9 9.7 + - - -
459X ILE* 3.5 26.1 - - + +
476X ASN* 1.3 71.7 + - - +
478X SER* 1.3 57.4 + - - +
479X GLU 3.1 0.2 - - - -
480X VAL* 3.7 18.1 - - + +
481X LEU* 3.0 40.9 + - + +
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Residues in contact with SER 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454X GLN 4.5 9.5 + - - -
455X VAL* 4.6 17.0 - - - +
456X TYR 5.0 0.5 + - - -
476X ASN* 2.8 19.9 + - - -
477X TRP* 1.3 78.6 - - - +
479X GLU* 1.3 61.1 + - - +
481X LEU* 5.0 4.9 - - - -
482X PRO* 3.2 22.7 - - - +
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Residues in contact with GLU 479 (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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474X GLY 3.9 14.3 - - - +
475X SER* 4.6 0.9 - - - -
476X ASN* 3.1 37.6 + - + +
478X SER* 1.3 82.7 - - - +
480X VAL* 1.3 63.6 + - + +
482X PRO* 3.9 7.4 - - - +
483X GLN* 3.5 22.5 - - - +
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Residues in contact with VAL 480 (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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230X SER 3.9 15.5 - - - +
231X ASP* 4.0 10.3 - - - -
232X PRO* 4.0 11.2 - - + -
459X ILE* 3.9 14.6 - - + -
476X ASN 3.9 11.9 - - - +
477X TRP* 3.2 31.8 + - + +
479X GLU* 1.3 83.6 - - + +
481X LEU* 1.3 68.5 + - - +
482X PRO 3.4 0.4 - - - -
483X GLN* 3.0 25.5 + - - +
484X ILE* 3.1 18.5 + - + +
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Residues in contact with LEU 481 (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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259X TYR* 3.7 41.7 - - + -
260X PRO* 4.5 3.8 - - + -
454X GLN* 3.6 46.0 - - + +
456X TYR* 3.9 15.7 - - + -
477X TRP* 3.0 30.0 + - + +
478X SER* 5.0 2.9 - - - -
480X VAL* 1.3 77.0 - - - +
482X PRO* 1.3 63.0 - - + +
484X ILE* 3.1 9.0 + - + +
485X GLN* 2.9 42.7 + - + +
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Residues in contact with PRO 482 (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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478X SER 3.2 24.0 - - - +
479X GLU 3.9 6.1 - - - +
480X VAL 3.4 3.4 - - - -
481X LEU* 1.3 94.5 - - + +
483X GLN* 1.3 61.7 + - + +
485X GLN* 3.3 16.3 + - - +
486X GLU* 3.0 31.2 + - + +
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Residues in contact with GLN 483 (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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230X SER* 3.7 22.3 + - - +
479X GLU 3.5 21.0 + - - +
480X VAL* 3.0 17.1 + - - +
482X PRO* 1.3 76.8 - - + +
484X ILE* 1.3 66.7 + - - +
486X GLU* 3.4 4.8 + - - +
487X THR* 3.1 31.5 + - + +
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Residues in contact with ILE 484 (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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229X ALA 4.0 10.5 - - - +
230X SER* 3.6 12.6 - - - +
231X ASP* 3.6 23.6 - - + -
257X ALA* 3.8 19.3 - - + -
258X ALA 4.0 0.7 - - - +
259X TYR* 3.6 36.8 - - + -
480X VAL* 3.1 23.6 + - + +
481X LEU* 3.3 10.1 - - + +
483X GLN* 1.3 75.7 - - - +
485X GLN* 1.3 60.1 + - + +
486X GLU 3.1 0.9 + - - -
487X THR 3.2 8.3 + - - -
488X THR* 2.8 28.6 + - + +
504X ARG* 3.6 23.3 - - - -
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Residues in contact with GLN 485 (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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259X TYR* 6.3 1.9 - - + -
326X ASN* 3.5 42.2 + - - +
454X GLN* 3.1 31.1 + - - +
481X LEU* 2.9 26.6 + - + +
482X PRO* 3.6 17.5 - - - +
484X ILE* 1.3 78.0 - - + +
486X GLU* 1.3 60.3 + - + +
488X THR 4.1 4.2 - - - +
504X ARG* 3.5 30.3 + - - +
586X LYS* 4.2 9.5 - - - +
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Residues in contact with GLU 486 (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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482X PRO* 3.0 20.7 + - + +
483X GLN* 3.8 6.7 - - - +
484X ILE 3.1 0.2 - - - -
485X GLN* 1.3 80.4 - - + +
487X THR* 1.3 66.7 + - + +
488X THR 3.5 0.7 - - - -
509X ASN* 5.3 1.2 - - - +
585X ALA* 3.5 14.7 - - - +
586X LYS* 3.2 47.0 + - + +
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Residues in contact with THR 487 (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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225X LYS* 4.1 6.6 + - - +
229X ALA 4.0 4.9 + - - -
230X SER* 2.8 29.2 + - - +
483X GLN* 3.1 17.0 + - + +
484X ILE 3.2 3.6 + - - -
486X GLU* 1.3 86.7 - - + +
488X THR* 1.3 59.3 + - - +
506X ALA* 4.0 0.2 - - - -
507X ALA 3.3 7.3 + - - +
515X GLU* 4.6 9.2 - - - +
518X LYS* 3.1 30.3 + - - +
585X ALA* 3.8 10.8 - - - -
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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