Contacts of the strand formed by residues 365 - 370 (chain A) in PDB entry 1DY7
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 365 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLU* 4.4 12.5 + - + +
358A THR 3.7 0.2 - - - +
359A ALA* 3.5 5.4 - - - -
360A ALA* 2.9 40.0 + - + +
363A ARG* 3.1 29.0 + - + +
364A ASN* 1.3 78.7 - - - +
366A LEU* 1.3 65.9 + - - +
367A VAL* 5.1 0.2 - - + -
379A ILE* 3.8 26.0 - - + -
380A GLU* 3.3 4.3 - - - +
381A ASP* 2.9 46.4 + - - +
382A THR* 4.8 0.2 - - - -
387A PRO* 4.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ILE* 4.4 9.6 - - + -
358A THR 3.4 9.2 - - - +
359A ALA* 4.2 12.6 - - + -
365A LYS* 1.3 77.9 - - - +
367A VAL* 1.3 62.4 + - - +
368A VAL* 4.0 2.7 + - + +
378A ALA 3.8 1.2 - - - +
379A ILE* 3.3 4.3 - - - -
380A GLU* 2.7 35.9 + - - +
382A THR* 3.6 26.9 - - + -
387A PRO* 4.5 2.7 - - + -
404A TRP* 3.7 41.7 - - + -
406A THR* 4.4 9.9 - - + -
415A ALA* 5.7 2.0 - - + +
416A LEU 6.1 0.2 - - - -
417A ILE* 4.3 18.3 - - + +
431A ILE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.8 23.3 - - + -
340A ALA* 3.9 6.1 - - + -
341A GLU* 4.0 28.0 - - + +
344A LEU* 4.2 12.6 - - + -
356A PHE 3.4 1.9 - - - +
357A ILE* 3.3 4.9 - - - -
358A THR* 2.8 44.6 + - + +
360A ALA* 4.5 5.6 - - + -
365A LYS* 5.1 0.2 - - + -
366A LEU* 1.3 77.1 - - - +
368A VAL* 1.3 63.2 + - - +
369A ILE* 4.3 2.2 - - + -
376A LEU* 3.5 24.5 - - + -
378A ALA 3.5 3.4 - - - -
379A ILE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 4.1 9.4 - - + -
356A PHE 3.3 7.2 - - - +
357A ILE* 4.4 10.5 - - + -
366A LEU 4.6 2.7 - - - +
367A VAL* 1.3 79.4 - - - +
369A ILE* 1.3 65.3 + - - +
376A LEU* 3.5 5.4 - - - +
377A VAL* 2.8 30.7 + - + -
378A ALA* 2.9 29.0 + - + +
417A ILE* 4.2 16.8 - - + -
429A TRP* 3.6 54.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.2 1.6 - - + -
322A ILE* 3.8 30.5 - - + -
324A LEU* 3.9 30.1 - - + -
338A ILE* 4.2 21.3 - - + -
355A TYR* 3.3 10.1 - - - +
356A PHE* 2.9 71.9 + - + +
367A VAL* 4.3 4.9 - - + -
368A VAL* 1.3 80.1 - - - +
370A ASP* 1.3 60.2 + - - +
371A THR* 3.6 8.0 + - + +
375A LYS 3.4 6.3 - - - +
376A LEU* 4.1 13.0 - - - -
377A VAL* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.8 0.9 - - - +
354A ARG* 2.9 44.5 + - - +
355A TYR* 3.7 20.7 + - + -
369A ILE* 1.3 71.1 - - - +
371A THR* 1.3 58.6 + - - +
372A LYS 2.9 11.8 + - - -
373A GLU* 3.3 23.9 + - + +
374A GLY* 2.8 26.5 + - - -
375A LYS* 2.8 21.4 + - + +
377A VAL* 3.9 14.6 - - + +
----------------------------------------------------------
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