Contacts of the strand formed by residues 455 - 460 (chain B) in PDB entry 6TXC
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 LYS 455 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ARG 5.6 3.8 + - - -
452B ASN* 5.8 0.9 - - - +
453B LEU* 3.6 22.0 - - - +
454B PHE* 1.3 72.5 - - - +
456B TYR* 1.3 63.8 + - - +
457B VAL* 3.5 1.0 + - - +
553B TYR* 3.0 5.9 - - - -
554B CYS 2.7 41.4 + - - +
556B LYS 5.0 0.9 - - - +
557B VAL* 3.7 43.2 - - + +
562B LEU* 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LYS* 3.6 48.9 - - + +
378B VAL* 6.0 2.2 - - + -
454B PHE 3.9 2.0 + - - +
455B LYS* 1.3 73.5 - - - +
457B VAL* 1.3 64.2 + - - +
458B GLY* 3.6 28.4 - - - -
459B GLU* 3.2 31.3 + - - +
551B ARG* 3.9 18.2 - - + -
552B VAL 4.2 3.6 - - - -
553B TYR* 3.8 24.9 - + + -
562B LEU* 4.4 4.3 - - - +
566B ARG* 4.2 14.0 + - - -
583B ASP* 5.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LYS 4.0 1.3 - - - +
456B TYR* 1.3 81.4 - - - +
458B GLY* 1.3 60.3 + - - +
498B PHE* 5.2 0.4 - - + -
552B VAL* 2.8 25.6 + - + +
553B TYR 4.0 1.6 - - - -
554B CYS* 3.9 31.0 - - + +
562B LEU* 4.3 6.5 - - + -
565B ALA* 3.9 12.1 - - + +
566B ARG* 3.7 42.6 + - + +
569B PHE* 3.7 22.9 - - + -
583B ASP* 4.3 6.8 - - - +
587B ILE* 4.1 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 3.6 20.1 - - - -
457B VAL* 1.3 82.4 - - - +
459B GLU* 1.3 61.1 + - - -
551B ARG* 3.5 3.1 - - - -
552B VAL 3.1 25.6 + - - +
569B PHE* 3.6 21.0 - - - -
583B ASP* 5.0 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 4.0 8.2 + - - -
456B TYR* 3.2 21.9 + - + +
458B GLY* 1.3 73.7 - - - -
460B THR* 1.3 69.2 + - - +
461B GLN* 6.0 0.2 - - + -
549B LEU* 3.5 34.4 - - + +
550B ILE 3.4 9.4 - - - +
551B ARG* 3.0 34.3 + - + +
569B PHE* 3.8 6.3 - - - -
581B PRO* 3.9 19.2 - - - +
582B GLN* 4.9 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLU* 1.3 79.7 - - - +
461B GLN* 1.3 71.6 + - - +
549B LEU* 3.8 0.9 - - - -
550B ILE* 2.8 50.8 + - + +
569B PHE* 4.0 8.3 - - + -
572B TRP* 4.4 1.1 - - + -
573B CYS* 3.7 25.8 - - - -
578B PHE* 3.3 27.6 - - + +
579B THR* 2.8 29.7 + - - -
581B PRO* 5.0 0.2 - - - -
----------------------------------------------------------
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