Contacts of the strand formed by residues 338 - 345 (chain C) in PDB entry 1YCH
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 VAL 338 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ARG 2.9 15.0 + - - +
306C ALA* 3.0 9.0 - - + -
307C VAL 2.9 23.2 + - - -
336C ASN* 5.8 1.1 - - - +
337C LYS* 1.3 78.6 - - - +
339C GLY* 1.3 63.0 + - - +
364C ILE* 3.8 3.4 - - - +
365C GLU* 3.4 12.3 - - - +
367C ILE* 3.8 29.6 - - + -
393C ILE* 5.0 6.7 - - + -
396C ARG* 3.9 36.6 - - + +
397C ILE* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL 3.2 13.7 - - - -
308C LEU* 4.4 4.0 - - - -
338C VAL* 1.3 78.8 - - - +
340C LEU* 1.3 63.9 + - - +
359C LEU* 5.0 0.4 - - - -
364C ILE* 3.7 12.6 - - - +
365C GLU 2.9 11.5 + - - -
366C LEU* 3.5 6.9 - - - -
367C ILE* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 3.8 32.8 - - + -
307C VAL 3.3 6.0 + - - +
308C LEU* 3.3 17.6 - - + +
309C VAL 3.0 25.1 + - - +
339C GLY* 1.3 73.9 - - - +
341C ALA* 1.3 69.0 + - - +
342C PHE* 4.4 1.5 - - + -
359C LEU* 4.0 10.0 - - - +
366C LEU* 4.6 4.3 - - - +
367C ILE* 4.0 17.9 - - + -
368C ALA* 4.1 17.0 - - + +
371C GLY* 4.1 8.1 - - - -
372C PRO* 3.7 27.4 - - + -
389C LEU* 4.1 7.6 - - + -
393C ILE* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C VAL 3.3 7.4 - - - +
340C LEU* 1.3 77.1 - - - +
342C PHE* 1.3 65.6 + - - +
352C GLN* 3.0 24.5 + - - +
355C LEU* 3.6 31.0 - - + -
356C GLU* 3.8 19.7 + - + +
359C LEU* 4.3 8.2 - - + +
366C LEU* 5.0 1.8 - - - +
371C GLY* 3.6 1.0 - - - -
372C PRO* 3.5 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 4.1 9.0 - - + -
259C TYR* 4.2 3.6 - - + -
266C THR* 3.6 28.7 - - + -
269C MET* 4.2 11.0 - - + -
270C ALA* 3.9 20.6 - - + -
273C LEU* 3.5 30.1 - - + -
308C LEU* 4.0 16.8 - - + -
309C VAL 3.2 11.6 + - - -
310C GLY* 3.3 28.2 - - - -
311C SER 3.0 22.3 + - - +
340C LEU* 4.4 7.2 - - + -
341C ALA* 1.3 80.4 - - - +
343C GLY* 1.3 62.0 + - - +
352C GLN* 3.5 8.5 + - - -
355C LEU* 3.6 5.7 - - - +
372C PRO* 3.3 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C THR* 3.9 9.6 - - - -
269C MET* 3.1 15.3 - - - +
311C SER 3.3 12.3 - - - -
342C PHE* 1.3 80.2 - - - +
344C ALA* 1.3 62.3 + - - -
352C GLN* 3.9 2.5 + - - +
372C PRO 3.2 4.8 + - - -
373C THR* 3.3 9.7 + - - -
374C VAL 3.2 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C SER* 3.9 14.1 - - - -
266C THR* 3.6 6.9 + - - +
269C MET* 3.3 13.7 - - + +
311C SER 4.0 1.5 + - - +
312C PRO* 3.3 19.4 - - - +
313C THR* 3.3 5.7 + - - -
343C GLY* 1.3 75.6 - - - -
345C TYR* 1.3 67.3 + - - +
374C VAL* 3.2 14.1 - - + +
376C TRP 4.4 2.7 - - - +
721C FMN 3.6 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C THR* 3.9 6.1 - - - +
343C GLY 4.7 0.2 - - - -
344C ALA* 1.3 80.5 - - - +
346C GLY* 1.3 61.3 + - - +
347C TRP 3.6 26.5 - - - -
348C GLY 4.7 2.2 - - - -
349C GLY* 3.8 23.3 - - - -
373C THR* 3.0 29.4 - - + -
374C VAL* 3.1 32.3 + - - -
375C GLN* 3.4 36.7 + - + +
376C TRP 2.8 24.4 + - - -
721C FMN 3.0 24.4 - - - +
----------------------------------------------------------
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