Contacts of the strand formed by residues 476 - 485 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A THR* 3.6 27.8 - - + -
472A PRO 3.7 7.0 - - - -
473A GLY* 3.5 42.2 + - - +
474A THR 3.3 1.4 - - - -
475A THR* 1.3 95.4 - - - +
477A THR* 1.3 74.6 + - - +
478A GLU* 3.8 5.4 - - + -
563A ARG* 3.5 49.1 - - + -
564A ILE 3.2 15.5 - - - +
565A ALA* 3.7 11.7 - - + -
570A TRP* 3.6 9.6 - - - -
572A PRO* 5.8 0.9 - - - +
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Residues in contact with THR 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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469A ILE* 5.6 2.9 - - + -
471A THR 5.5 0.4 - - - -
476A PHE* 1.3 76.6 + - - +
478A GLU* 1.3 61.7 + - - +
479A ILE* 3.9 26.4 - - + +
501A TYR* 3.9 10.9 + - + +
562A PHE 3.8 1.4 - - - +
563A ARG* 3.3 1.2 - - - -
564A ILE* 2.8 36.7 + - - +
570A TRP* 2.8 32.1 + - - -
572A PRO* 3.8 13.3 - - - +
575A ASP* 4.8 0.9 + - - -
578A PHE* 3.9 20.2 - - + -
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Residues in contact with GLU 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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469A ILE* 3.7 8.4 - - - +
470A ASN* 2.7 56.8 + - + +
471A THR* 2.6 41.5 + - - +
476A PHE* 3.8 11.1 - - + -
477A THR* 1.3 74.4 - - - +
479A ILE* 1.3 58.7 + - - +
561A GLN* 5.0 3.5 + - + -
562A PHE 3.4 11.4 - - - +
563A ARG* 2.8 43.4 + - + +
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Residues in contact with ILE 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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467A ALA* 4.0 14.6 - - + -
468A GLN 3.5 8.1 - - - +
469A ILE* 4.6 4.3 - - + -
470A ASN* 4.2 2.0 - - - +
477A THR* 3.9 26.9 - - + +
478A GLU* 1.3 79.8 - - - +
480A LYS* 1.3 73.1 + - - +
481A ALA* 3.8 2.5 - - + +
501A TYR* 4.0 17.0 - - + +
560A VAL 3.9 0.2 - - - +
561A GLN* 3.4 4.0 - - - +
562A PHE* 2.9 60.7 + - + +
564A ILE* 5.9 0.7 - - + -
578A PHE* 4.7 1.3 - - + -
581A ILE* 3.8 34.1 - - + -
591A ILE* 4.9 4.3 - - + -
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Residues in contact with LYS 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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467A ALA* 3.2 4.3 - - - -
468A GLN* 2.9 59.2 + - + +
470A ASN* 3.7 27.5 + - - +
479A ILE* 1.3 75.0 - - - +
481A ALA* 1.3 61.8 + - - +
482A MET* 4.6 12.5 - - + +
559A GLU* 3.4 36.3 + - + +
560A VAL 3.7 2.9 - - - -
561A GLN* 4.1 10.7 + - + +
585A LEU* 3.9 10.1 - - + +
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Residues in contact with ALA 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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465A VAL* 4.3 9.4 - - + -
466A GLU 3.3 8.5 - - - +
467A ALA* 4.3 2.9 - - + +
479A ILE* 3.8 4.9 - - + -
480A LYS* 1.3 75.5 - - - +
482A MET* 1.3 60.8 + - - +
483A ILE 4.3 0.2 - - - -
499A PHE* 3.9 28.9 - - + -
558A ARG 4.6 0.2 - - - -
559A GLU* 3.6 6.2 - - - +
560A VAL* 2.7 43.7 + - + +
562A PHE* 4.2 10.1 - - + -
591A ILE* 5.1 1.3 - - + -
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Residues in contact with MET 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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465A VAL* 3.3 4.8 - - - -
466A GLU* 2.8 46.6 + - + +
480A LYS* 4.6 8.3 - - - +
481A ALA* 1.3 74.6 - - - +
483A ILE* 1.3 67.0 + - - +
484A ARG* 3.6 37.6 + - - +
557A ARG* 4.0 32.5 - - + +
558A ARG 3.5 3.4 - - - +
559A GLU* 3.7 44.0 - - + +
585A LEU* 4.1 17.5 - - + -
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Residues in contact with ILE 483 (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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464A PHE 3.6 3.6 - - - +
465A VAL* 4.6 6.5 - - + +
482A MET* 1.3 75.8 - - - +
484A ARG* 1.3 64.4 + - - +
494A LEU* 4.2 8.1 - - + -
497A GLY* 5.9 1.1 - - - -
499A PHE* 3.7 30.1 - - + -
523A CYS* 4.8 0.4 - - - -
543A CYS* 3.6 33.2 - - + -
548A ILE* 4.2 19.7 - - + -
557A ARG* 3.1 30.5 - - - +
558A ARG* 2.9 20.2 + - + +
560A VAL* 4.9 1.8 - - + -
593A LEU* 4.0 33.2 - - + -
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Residues in contact with ARG 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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462A GLU 4.3 0.2 - - - -
463A ILE* 3.2 8.0 - - - +
464A PHE* 2.8 69.8 + - + +
466A GLU* 2.9 31.7 + - + +
482A MET* 3.6 31.7 - - - +
483A ILE* 1.3 82.3 - - - +
485A ASN* 1.3 60.9 + - - +
486A GLN* 3.9 19.3 + - + +
553A GLN* 5.2 2.0 + - - -
556A HIS* 3.2 32.0 + - - -
557A ARG* 4.0 14.3 - - - +
585A LEU* 4.0 7.3 - - - +
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Residues in contact with ASN 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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462A GLU 3.7 2.2 - - - -
463A ILE* 3.6 16.8 - - + +
484A ARG* 1.3 73.1 - - - +
486A GLN* 1.3 59.6 + - - +
487A SER* 2.7 28.8 + - - -
492A ARG 2.9 21.1 + - - -
493A MET 4.1 0.2 - - - -
494A LEU* 3.7 14.6 - - + +
548A ILE* 2.8 37.5 + - + +
549A PHE* 3.8 1.3 - - - +
550A PRO* 3.6 13.7 - - - +
556A HIS* 2.9 32.5 + - - +
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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