Contacts of the strand formed by residues 463 - 471 (chain B) in PDB entry 1TF4
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 ILE 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B PRO* 4.8 0.3 - - - +
462B GLU* 1.3 79.8 + - + +
464B PHE* 1.3 64.5 + - - +
484B ARG 3.2 9.4 - - - +
485B ASN* 3.5 33.2 - - - +
487B SER* 4.4 4.3 - - - -
492B ARG* 4.0 32.5 - - + +
493B MET 5.5 1.1 - - - +
494B LEU* 3.8 27.1 - - + -
593B LEU* 3.5 24.7 - - + -
595B ASP* 5.9 2.0 - - - +
600B VAL* 3.9 24.8 - - + +
601B TRP* 3.7 17.2 - - - +
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B PRO* 3.4 39.0 - - + -
462B GLU 3.9 4.7 - - - -
463B ILE* 1.3 77.6 - - - +
465B VAL* 1.3 70.0 + - - +
466B GLU* 3.5 35.2 - - + -
482B MET 3.8 0.2 - - - +
483B ILE* 3.6 4.3 - - - +
484B ARG* 2.8 54.0 + - + +
486B GLN* 3.8 24.0 - - - -
587B PRO* 4.5 17.5 - - + -
593B LEU* 4.3 2.2 - - - -
601B TRP* 3.6 32.5 - - + -
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Residues in contact with VAL 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B PHE* 1.3 82.4 - - - +
466B GLU* 1.3 74.8 + - - +
481B ALA* 4.2 13.9 - - + -
482B MET 3.3 9.0 - - - +
483B ILE* 4.7 7.2 - - + -
499B PHE* 4.8 7.2 - - + -
587B PRO* 3.4 4.9 - - - +
588B ALA* 2.9 22.7 + - + +
591B ILE* 4.1 33.0 - - + -
593B LEU* 3.8 33.9 - - + -
601B TRP* 3.6 18.7 + - + +
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Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B PHE* 3.5 30.6 - - + -
465B VAL* 1.3 77.5 - - - +
467B ALA* 1.3 64.9 + - - +
481B ALA* 3.3 2.4 - - - -
482B MET* 2.8 34.2 + - + +
484B ARG* 2.8 44.9 + - + -
585B LEU* 3.6 27.3 - - + +
586B ALA* 3.2 18.1 - - - +
587B PRO* 4.4 7.0 - - - +
588B ALA* 4.5 0.2 - - - -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B GLU* 1.3 77.9 - - - +
468B GLN* 1.3 63.3 + - - +
479B ILE* 4.1 10.5 - - + -
480B LYS 3.4 10.8 - - - +
481B ALA* 4.6 1.6 - - - -
581B ILE* 4.2 13.8 - - + +
582B GLY 5.1 1.0 + - - -
584B GLU 3.4 3.1 - - - +
585B LEU* 3.8 3.1 - - - -
586B ALA* 2.8 28.3 + - - +
588B ALA* 3.7 21.7 - - + +
591B ILE* 4.1 14.6 - - + -
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B ALA* 1.3 78.8 - - - +
469B ILE* 1.3 75.1 + - - +
470B ASN* 4.8 4.2 + - - +
479B ILE* 3.5 4.7 - - - +
480B LYS* 2.9 55.9 + - + +
581B ILE* 3.7 8.7 - - - -
582B GLY 3.3 13.2 - - - +
583B ASN 3.4 16.5 + - - -
584B GLU 3.7 1.1 - - - -
585B LEU* 3.5 43.3 + - + +
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B GLN* 1.3 85.0 + - - +
470B ASN* 1.3 64.9 + - - +
471B THR 3.8 24.7 - - - +
472B PRO* 4.0 11.0 - - + -
477B THR* 5.7 1.6 - - + -
478B GLU 3.7 8.3 - - - +
479B ILE* 4.6 4.5 - - + -
578B PHE* 4.1 29.8 - - + -
581B ILE* 4.0 23.6 - - + +
582B GLY* 2.9 12.7 + - - +
583B ASN* 3.8 28.7 + - - +
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Residues in contact with ASN 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B GLN* 3.4 6.1 + - - +
469B ILE* 1.3 75.3 - - - +
471B THR* 1.3 60.5 + - - +
472B PRO* 4.3 3.4 - - - +
478B GLU* 2.8 45.7 + - + +
479B ILE 4.3 0.4 - - - -
480B LYS* 3.7 36.7 - - + +
561B GLN* 3.5 26.3 - - - +
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Residues in contact with THR 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B ILE* 3.8 9.5 - - - +
470B ASN* 1.3 82.4 + - - +
472B PRO* 1.3 82.6 - - + +
473B GLY 3.6 1.6 + - - -
476B PHE* 3.7 18.3 - - + -
478B GLU* 2.8 41.3 + - - +
563B ARG* 4.6 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