Contacts of the helix formed by residues 317 - 325 (chain B) in PDB entry 1YSD
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 317 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 4.6 3.4 - - - +
125A ARG* 3.6 51.7 - - - +
292B ASP* 4.1 2.7 + - - +
316B SER* 1.3 75.3 - - - +
318B GLY* 1.3 57.3 + - - +
319B GLU 3.4 0.4 - - - -
320B LYS* 3.4 9.8 + - - +
321B TYR* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.7 8.9 + - - -
295B THR* 3.3 31.7 - - - +
316B SER* 2.9 13.1 + - - -
317B LYS* 1.3 77.4 - - - +
319B GLU* 1.3 63.7 + - - -
321B TYR* 4.0 3.8 - - - -
322B LEU* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 2.6 31.4 + - - +
290B PRO* 4.4 4.8 + - + -
295B THR* 4.3 0.2 + - - -
308B VAL* 5.0 1.2 - - + +
311B ASN* 3.0 36.4 + - - +
315B LYS* 3.4 22.7 + - + +
316B SER* 3.5 11.9 + - - +
317B LYS 3.4 0.8 - - - -
318B GLY* 1.3 76.4 - - - +
320B LYS* 1.3 61.7 + - - +
322B LEU* 3.5 20.0 + - + +
323B GLN* 3.3 21.9 + - - +
329B VAL* 3.9 20.6 - - + +
331B VAL* 4.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY* 3.7 22.9 - - - +
199B SER* 2.8 47.5 + - - +
202B VAL* 3.1 28.1 - - - +
315B LYS* 5.7 4.9 - - - +
316B SER 4.7 0.8 + - - +
317B LYS* 3.4 9.9 + - - +
318B GLY 3.2 0.2 - - - -
319B GLU* 1.3 76.4 - - - +
321B TYR* 1.3 66.7 + - - +
323B GLN* 3.0 22.1 + - - +
324B THR* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 4.3 3.5 + - + -
117A LYS* 4.7 4.3 - - - +
121A TYR* 3.6 68.1 - + - +
292B ASP* 6.0 0.4 - - - -
295B THR* 4.1 7.6 - - + -
296B GLY* 6.2 0.7 - - - -
299B ILE* 3.5 33.2 - - + -
317B LYS 3.0 18.2 + - - +
318B GLY* 3.2 7.2 + - - +
320B LYS* 1.3 77.6 - - - +
322B LEU* 1.3 56.0 + - - +
324B THR* 3.1 18.4 + - + -
325B ARG* 2.8 70.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PRO* 4.1 25.1 - - + -
295B THR* 3.6 24.9 - - + +
298B ILE* 3.9 27.8 - - + -
299B ILE* 3.8 17.9 - - + -
306B CYS* 4.4 9.6 - - + -
318B GLY 2.8 20.3 + - - +
319B GLU* 3.5 8.7 - - - +
320B LYS 3.2 0.2 - - - -
321B TYR* 1.3 77.4 - - - +
323B GLN* 1.3 55.1 + - - +
325B ARG* 3.2 2.6 + - - -
326B GLY 3.1 5.0 + - - -
327B HIS* 2.7 42.9 + - + +
329B VAL* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.5 22.7 - - + +
203B THR 2.9 28.7 - - - +
204B GLY* 4.4 4.0 - - - -
319B GLU* 3.3 24.0 + - - +
320B LYS* 3.0 24.9 + - - +
322B LEU* 1.3 72.6 - - - +
324B THR* 1.3 60.9 + - - +
326B GLY* 2.9 18.5 + - - -
327B HIS 3.5 13.0 - - - +
329B VAL* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY 4.2 16.4 + - - +
199B SER* 5.3 1.9 + - - -
320B LYS* 2.9 20.0 + - - +
321B TYR* 3.3 26.8 - - + -
323B GLN* 1.3 76.2 - - - +
325B ARG* 1.3 61.6 + - + +
326B GLY* 3.1 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 2.9 37.4 + - - -
117A LYS* 3.5 40.4 - - - +
299B ILE* 3.5 23.0 - - + +
321B TYR* 2.8 63.3 + - + +
322B LEU 3.5 4.9 - - - +
323B GLN 3.1 0.2 - - - -
324B THR* 1.3 80.5 - - - +
326B GLY* 1.3 58.9 + - - +
327B HIS* 3.5 19.2 + - + +
----------------------------------------------------------
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