Contacts of the strand formed by residues 476 - 485 (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 PHE 476 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B THR* 3.7 27.4 - - + -
472B PRO 3.7 7.0 - - - -
473B GLY* 3.5 42.2 + - - +
474B THR 3.3 1.7 - - - -
475B THR* 1.3 95.5 - - - +
477B THR* 1.3 74.8 + - - +
478B GLU* 3.9 5.8 - - + -
563B ARG* 3.4 50.9 - - + -
564B ILE 3.1 16.2 - - - +
565B ALA* 3.7 12.6 - - + -
570B TRP* 3.6 8.4 - - - -
572B PRO* 5.9 0.5 - - - +
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Residues in contact with THR 477 (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* 5.7 2.2 - - + -
471B THR 5.5 0.2 - - - -
473B GLY 5.9 0.4 - - - +
476B PHE* 1.3 76.2 + - - +
478B GLU* 1.3 61.3 + - - +
479B ILE* 3.8 28.7 - - + +
501B TYR* 3.8 16.6 + - + +
562B PHE 3.8 1.4 - - - +
563B ARG* 3.3 1.9 - - - -
564B ILE* 2.9 35.8 + - - +
570B TRP* 2.8 31.1 + - - -
572B PRO* 3.7 15.8 - - - +
575B ASP* 4.9 0.5 + - - -
578B PHE* 3.9 15.7 - - + -
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Residues in contact with GLU 478 (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* 3.7 6.9 - - - +
470B ASN* 2.8 57.0 + - + +
471B THR* 2.8 42.1 + - - +
476B PHE* 3.8 11.1 - - + -
477B THR* 1.3 74.4 - - - +
479B ILE* 1.3 59.4 + - - +
561B GLN* 4.9 4.1 + - + -
562B PHE 3.4 12.6 - - - +
563B ARG* 2.8 42.7 + - + +
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Residues in contact with ILE 479 (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* 4.1 15.0 - - + -
468B GLN 3.5 12.6 - - - +
469B ILE* 4.6 5.8 - - + -
470B ASN* 4.3 1.8 - - - -
477B THR* 3.8 26.0 - - + -
478B GLU* 1.3 78.3 - - - +
480B LYS* 1.3 73.5 + - - +
481B ALA* 3.9 2.7 - - + +
501B TYR* 4.0 18.2 - - + +
560B VAL 3.8 0.7 - - - +
561B GLN* 3.3 3.6 - - - +
562B PHE* 2.9 60.9 + - + +
564B ILE* 5.9 0.4 - - + -
578B PHE* 4.8 1.8 - - + -
581B ILE* 4.1 27.6 - - + -
591B ILE* 5.0 3.1 - - + -
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Residues in contact with LYS 480 (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* 3.4 3.6 - - - -
468B GLN* 2.9 56.0 + - + +
470B ASN* 3.7 28.9 + - - +
479B ILE* 1.3 73.2 - - - +
481B ALA* 1.3 64.5 + - - +
482B MET* 4.7 13.2 - - - +
559B GLU* 3.6 28.7 + - + +
560B VAL 3.6 2.7 - - - -
561B GLN* 4.1 15.9 + - + +
585B LEU* 3.8 11.1 - - + +
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Residues in contact with ALA 481 (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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465B VAL* 4.2 9.0 - - + -
466B GLU 3.3 11.0 - - - +
467B ALA* 4.3 2.7 - - + +
479B ILE* 3.9 4.9 - - + -
480B LYS* 1.3 76.2 - - - +
482B MET* 1.3 62.0 + - - +
483B ILE* 5.8 0.2 - - - -
499B PHE* 3.8 29.4 - - + -
559B GLU* 3.7 6.8 - - - +
560B VAL* 2.7 41.4 + - + +
562B PHE* 4.2 9.6 - - + -
591B ILE* 5.3 1.6 - - + -
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Residues in contact with MET 482 (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 3.8 0.2 - - - +
465B VAL* 3.3 5.2 - - - -
466B GLU* 2.8 48.2 + - + +
480B LYS* 4.7 8.5 - - - -
481B ALA* 1.3 75.7 - - - +
483B ILE* 1.3 63.5 + - - +
484B ARG* 3.4 35.8 + - - +
557B ARG* 3.6 35.4 - - + +
558B ARG 3.5 13.0 - - - +
559B GLU* 4.1 23.3 - - + +
585B LEU* 4.0 23.6 - - + -
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Residues in contact with ILE 483 (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 3.6 7.9 - - - +
465B VAL* 4.6 6.5 - - + +
482B MET* 1.3 74.1 - - - +
484B ARG* 1.3 62.9 + - - +
494B LEU* 4.1 17.3 - - + -
497B GLY* 5.9 0.7 - - - +
499B PHE* 3.9 30.1 - - + -
523B CYS* 4.5 2.7 - - - -
543B CYS* 3.3 35.9 - - + -
548B ILE* 4.0 23.8 - - + -
556B HIS 4.4 0.2 - - - -
557B ARG* 3.0 30.7 - - - +
558B ARG* 3.0 16.8 + - + +
560B VAL* 4.7 2.7 - - + -
593B LEU* 4.2 16.2 - - + -
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Residues in contact with ARG 484 (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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463B ILE* 3.2 8.1 - - - +
464B PHE* 2.8 71.9 + - + +
466B GLU* 2.8 34.7 + - + +
482B MET* 3.4 28.0 - - - +
483B ILE* 1.3 83.3 - - - +
485B ASN* 1.3 60.7 + - - +
486B GLN* 3.9 13.4 + - + +
553B GLN* 4.5 4.8 + - - -
556B HIS* 3.1 32.9 + - - -
557B ARG* 3.7 14.3 - - - +
585B LEU* 4.3 5.5 - - - +
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Residues in contact with ASN 485 (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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462B GLU 3.7 2.2 - - - -
463B ILE* 3.5 14.1 - - + +
484B ARG* 1.3 73.4 - - - +
486B GLN* 1.3 59.1 + - - +
487B SER* 2.7 29.0 + - - -
492B ARG 2.9 21.3 + - - -
494B LEU* 3.6 15.8 - - + +
548B ILE* 2.8 37.8 + - + +
549B PHE* 3.7 0.8 - - - +
550B PRO* 3.6 12.7 - - - +
556B HIS* 2.9 36.0 + - - +
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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