Contacts of the strand formed by residues 388 - 392 (chain C) in PDB entry 1TYE
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 GLN 388 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C THR* 5.2 5.7 + - - -
378C ALA* 3.2 31.7 + - + +
381C GLY* 4.2 2.2 - - - -
382C GLY* 3.3 36.8 + - - +
383C PRO* 4.1 5.5 - - - +
387C GLY* 1.3 74.2 - - - +
389C VAL* 1.3 62.1 + - - +
390C LEU* 3.7 24.8 - - + +
406C VAL* 3.5 17.3 - - + +
407C LEU 3.0 19.1 - - - +
408C ASP* 3.4 23.7 + - - -
417C PHE* 3.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ALA* 3.8 26.2 - - + -
376C VAL 3.3 13.2 - - - +
377C ALA* 4.7 1.1 - - + -
388C GLN* 1.3 76.5 - - - +
390C LEU* 1.3 66.0 + - - +
391C VAL* 4.2 1.1 + - + -
406C VAL* 3.5 2.9 - - - -
407C LEU* 2.8 52.6 + - + +
417C PHE* 3.6 26.5 - - + -
418C GLY* 4.6 5.4 - - - -
421C LEU* 3.9 25.4 - - + -
435C LEU* 4.5 3.1 - - + -
437C VAL* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C THR* 6.4 1.6 - - + -
356C PHE* 4.0 27.6 - - + -
375C ALA* 3.5 1.0 - - - -
376C VAL 2.8 39.8 + - - +
378C ALA* 5.1 2.2 - - + -
388C GLN* 3.7 37.2 - - + +
389C VAL* 1.3 80.1 - - - +
391C VAL* 1.3 59.2 + - - +
392C PHE* 3.3 25.9 - - + -
403C PRO* 4.2 21.1 - - + -
405C GLN 3.7 5.2 - - - +
406C VAL* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C LEU 5.8 0.2 - - - +
3C LEU* 4.2 21.3 - - + -
363C LEU* 4.0 11.2 - - + -
366C LEU* 3.8 23.1 - - + -
373C ASP* 4.8 0.4 - - + -
374C ILE 3.5 11.0 - - - +
375C ALA* 4.4 5.8 - - + +
389C VAL* 5.4 0.2 - - + -
390C LEU* 1.3 72.5 - - - +
392C PHE* 1.3 63.1 + - - +
393C LEU* 4.0 17.3 - - + -
403C PRO* 3.5 6.6 - - - +
404C SER* 3.0 26.7 + - - +
405C GLN* 3.4 28.2 + - + +
407C LEU* 4.9 14.4 - - + -
435C LEU* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 3.5 39.5 - - + -
356C PHE* 4.3 17.0 - + - -
373C ASP* 3.6 1.2 - - - +
374C ILE* 2.9 37.5 + - + -
376C VAL* 4.3 11.9 - - + -
390C LEU* 3.3 39.0 - - + -
391C VAL* 1.3 73.4 - - - +
393C LEU* 1.3 65.5 + - - +
399C LEU* 3.5 19.9 - - + +
400C ARG 3.3 19.7 - - - +
401C SER 3.8 7.2 - - - -
402C ARG 4.2 0.7 - - - -
403C PRO* 3.8 33.9 - - + -
404C SER 4.8 1.3 - - - +
----------------------------------------------------------
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