Contacts of the strand formed by residues 497 - 504 (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 GLY 497 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ILE* 6.2 0.4 - - - -
494A LEU* 4.2 18.1 + - - +
495A ASP 3.7 2.2 - - - -
496A LYS* 1.3 78.5 - - - +
498A THR* 1.3 64.6 + - - +
543A CYS* 2.8 35.4 + - - -
544A THR* 3.3 6.3 + - - +
548A ILE* 5.9 2.6 - - - +
593A LEU* 4.7 7.2 - - - -
594A TYR 3.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LYS 4.8 1.9 + - - +
497A GLY* 1.3 80.1 - - - +
499A PHE* 1.3 64.8 + - - +
500A ARG* 6.0 0.2 - - - +
540A GLU* 4.4 21.2 + - - +
541A ILE 3.1 11.2 - - - -
542A ASP* 3.6 26.5 - - - +
543A CYS* 4.4 0.9 - - - +
544A THR* 3.9 10.5 - - + -
593A LEU* 3.5 5.2 - - - +
594A TYR* 2.8 47.5 + - - +
597A GLY 5.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 4.8 3.8 - - + -
481A ALA* 3.9 23.6 - - + -
483A ILE* 3.7 35.4 - - + -
498A THR* 1.3 75.2 - - - +
500A ARG* 1.3 67.0 + - - +
501A TYR* 4.9 1.8 - - + -
539A VAL 3.8 0.4 - - - +
540A GLU* 3.3 4.7 - - - +
541A ILE* 2.9 70.9 + - + -
543A CYS* 5.0 0.4 - - - -
560A VAL* 4.1 11.0 - - + -
562A PHE* 4.0 20.9 - + - -
591A ILE* 3.5 26.7 - - + -
592A VAL 3.0 21.1 - - - +
593A LEU* 4.0 8.7 - - + -
594A TYR* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PHE* 1.3 82.5 - - - +
501A TYR* 1.3 60.9 + - - +
502A TRP* 3.6 32.5 - - + -
538A TYR* 3.4 48.0 + - + -
539A VAL 3.3 4.0 - - - +
540A GLU* 3.1 28.5 + - + -
591A ILE* 3.6 8.7 - - - +
592A VAL 3.0 26.5 + - - -
594A TYR* 3.9 37.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A THR* 3.9 11.7 - - + +
479A ILE* 4.0 20.3 - - + +
499A PHE* 4.9 3.8 - - + -
500A ARG* 1.3 71.6 - - - +
502A TRP* 1.3 71.6 + - - +
503A PHE* 4.2 12.3 - + + -
538A TYR* 3.3 2.3 - - - -
539A VAL* 3.0 34.9 + - + +
541A ILE* 6.6 0.2 - - + -
562A PHE* 3.9 26.7 - + + -
564A ILE* 3.7 27.4 - - + -
570A TRP* 5.9 0.4 - + - -
575A ASP* 4.8 5.8 + - + -
577A SER* 3.4 33.0 - - - -
578A PHE* 3.4 33.6 - - - +
581A ILE* 4.0 6.5 - - + -
591A ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ARG* 3.6 36.6 - - + -
501A TYR* 1.3 77.1 - - - +
503A PHE* 1.3 62.5 + - - +
532A VAL* 4.1 8.0 - - + +
536A LEU* 3.9 18.7 - - + +
537A TYR 3.3 8.7 - - - -
538A TYR* 3.5 29.4 - - + +
575A ASP* 4.1 0.7 - - - +
576A TRP* 3.6 10.7 + + + -
577A SER* 2.8 45.3 + - - +
590A TYR 4.1 3.8 - - - -
592A VAL* 3.5 29.8 - - + -
594A TYR* 3.3 26.5 - - - -
604A ALA* 3.8 10.1 - - + -
605A PRO* 3.6 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A TYR* 4.2 17.7 - + + -
502A TRP* 1.3 76.4 - - - +
504A THR* 1.3 71.0 + - - +
505A LEU* 4.5 8.7 - - + -
514A ILE* 3.8 31.6 - - + -
529A VAL* 4.3 12.1 - - + -
535A ASP 3.7 0.2 - - - +
536A LEU* 3.8 5.2 - - - +
537A TYR* 2.9 66.6 + + + +
538A TYR 4.2 0.9 - - - -
539A VAL* 4.0 24.2 - - + -
564A ILE* 4.6 4.3 - - + -
570A TRP* 3.7 24.0 - + + -
575A ASP* 3.4 27.1 - - + +
576A TRP 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 1.3 77.2 - - - +
505A LEU* 1.3 74.2 + - - +
506A ASP* 3.4 1.4 - - - +
535A ASP* 3.3 23.9 + - - +
536A LEU* 4.8 8.0 - - - +
574A ASN* 3.0 39.4 + - + +
575A ASP* 3.0 7.5 + - - +
576A TRP* 5.0 1.9 + - - +
3002A CA 2.4 30.0 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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