Contacts of the strand formed by residues 497 - 504 (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 GLY 497 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ILE* 5.9 0.4 - - - -
494B LEU* 4.3 17.4 - - - +
495B ASP 3.7 1.4 - - - -
496B LYS* 1.3 74.9 - - - +
498B THR* 1.3 66.1 + - - +
543B CYS* 2.8 38.6 + - - +
544B THR* 3.3 3.9 + - - +
548B ILE* 5.9 2.1 - - - +
593B LEU* 4.6 6.5 - - - -
594B TYR 3.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS 4.6 2.4 + - - +
497B GLY* 1.3 81.0 - - - +
499B PHE* 1.3 66.7 + - - +
540B GLU* 4.4 18.7 + - - +
541B ILE 3.1 11.9 - - - -
542B ASP* 3.6 26.2 - - + +
543B CYS* 4.3 0.9 - - - +
544B THR* 3.8 10.8 - - + -
593B LEU* 3.4 4.7 - - - +
594B TYR* 2.8 46.4 + - - +
597B GLY* 5.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B VAL* 4.8 4.0 - - + -
481B ALA* 3.8 23.3 - - + -
483B ILE* 3.9 36.3 - - + -
498B THR* 1.3 76.5 - - - +
500B ARG* 1.3 67.2 + - - +
501B TYR* 4.9 2.2 - - + -
539B VAL 5.6 0.2 - - - -
540B GLU* 3.3 5.2 - - - +
541B ILE* 2.9 70.6 + - + -
543B CYS* 5.0 0.2 - - - -
560B VAL* 4.1 10.5 - - + -
562B PHE* 4.0 20.2 - + - -
591B ILE* 3.5 27.6 - - + -
592B VAL 3.1 16.6 - - - +
593B LEU* 3.9 11.2 - - + -
594B TYR* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B PHE* 1.3 83.6 - - - +
501B TYR* 1.3 59.9 + - - +
502B TRP* 3.7 31.0 - - + -
538B TYR* 3.4 48.5 + - + -
539B VAL 3.3 4.7 - - - +
540B GLU* 3.2 27.7 + - + -
591B ILE* 3.5 10.4 - - - +
592B VAL 2.9 25.6 + - - -
594B TYR* 3.7 36.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B THR* 3.8 11.3 - - + +
479B ILE* 4.0 20.6 - - + +
499B PHE* 4.9 4.2 - - + -
500B ARG* 1.3 73.3 - - - +
502B TRP* 1.3 71.5 + - - +
503B PHE* 4.1 11.8 + + + -
538B TYR* 3.2 3.2 - - - -
539B VAL* 2.9 37.6 + - + +
562B PHE* 3.9 27.4 - + + -
564B ILE* 3.7 25.6 - - + -
570B TRP* 5.9 0.7 - + - -
575B ASP* 4.7 5.7 + - - -
577B SER* 3.4 29.6 - - - -
578B PHE* 3.4 35.5 - - - +
581B ILE* 4.2 7.4 - - + -
591B ILE* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ARG* 3.7 33.0 - - + -
501B TYR* 1.3 77.0 - - - +
503B PHE* 1.3 62.3 + - - +
532B VAL* 4.0 7.5 - - + +
536B LEU* 3.9 18.4 - - + +
537B TYR 3.2 9.0 - - - +
538B TYR* 3.5 29.3 - - + +
575B ASP* 3.9 1.0 - - - +
576B TRP* 3.6 12.0 + + + -
577B SER* 2.8 42.4 + - - +
590B TYR 4.0 4.5 - - - -
592B VAL* 3.4 33.0 - - + -
594B TYR* 3.4 26.5 - - - -
604B ALA* 3.8 10.1 - - + -
605B PRO* 3.5 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B TYR* 4.2 17.3 - + + -
502B TRP* 1.3 78.4 - - - +
504B THR* 1.3 70.1 + - - +
505B LEU* 4.5 7.0 - - + -
514B ILE* 3.7 32.8 - - + -
529B VAL* 4.0 13.7 - - + -
535B ASP 3.6 0.5 - - - +
536B LEU* 3.7 5.8 - - - +
537B TYR* 2.8 66.2 + + + +
538B TYR 4.2 1.1 - - - -
539B VAL* 3.9 25.1 - - + -
564B ILE* 4.6 4.0 - - + -
570B TRP* 3.8 21.5 - + + -
575B ASP* 3.4 27.1 - - + +
576B TRP 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B PHE* 1.3 78.1 - - - +
505B LEU* 1.3 73.8 + - - +
506B ASP* 3.4 1.6 + - - +
535B ASP* 3.3 20.0 + - + +
536B LEU* 4.8 7.5 - - - +
570B TRP* 5.5 0.3 - - - -
574B ASN* 2.9 41.3 + - + +
575B ASP* 3.1 7.4 + - - +
576B TRP 5.1 1.2 + - - -
3004B CA 2.4 27.5 - - - -
----------------------------------------------------------
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