Contacts of the helix formed by residues 296 - 301 (chain C) in PDB entry 5YL4
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 PHE 296 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C THR* 3.6 18.4 - - + -
293C ASN 3.2 3.4 + - - +
295C CYS* 1.3 75.0 - - + +
297C GLU* 1.3 59.5 + - - +
298C PRO* 3.4 11.3 - - - +
301C GLN* 5.8 0.7 - - - -
308C ARG* 5.0 6.9 - - - +
312C TYR* 3.9 17.5 - + - -
315C CYS* 3.9 2.5 - - - -
317C LEU* 5.0 1.6 - - + -
335C ILE* 3.9 28.3 - - + -
339C ARG* 3.0 39.8 + - + +
341C ILE* 3.8 27.6 - - + -
351C PHE* 3.4 31.0 - + - -
377C MET* 3.4 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C THR* 4.5 0.5 - - - +
293C ASN 3.7 4.0 + - - +
294C ALA* 3.3 18.0 + - - +
295C CYS 4.3 3.8 - - - +
296C PHE* 1.3 76.9 - - - +
298C PRO* 1.4 68.9 - - - +
299C ALA* 3.2 32.2 + - + +
300C ASN* 3.0 37.2 + - - +
301C GLN* 4.3 1.5 + - - -
308C ARG* 4.8 6.2 + - - -
339C ARG* 4.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PHE 3.4 9.8 - - - +
297C GLU* 1.4 95.3 - - - +
299C ALA* 1.3 58.4 + - - +
300C ASN 3.1 1.1 + - - -
301C GLN* 3.3 46.4 + - - +
303C VAL 5.1 0.2 - - - +
304C LYS* 6.0 0.7 - - - -
305C CYS 4.3 8.5 - - - +
306C ASP* 4.4 7.9 - - - +
307C PRO* 4.6 3.4 - - + -
308C ARG* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA 5.1 0.2 - - - +
212C ILE* 3.4 22.9 - - - +
215C ARG* 3.4 39.1 + - - +
297C GLU* 3.1 25.0 + - + +
298C PRO* 1.3 76.6 - - - +
300C ASN* 1.3 60.8 + - - +
301C GLN 3.5 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ILE* 4.0 8.4 - - - +
215C ARG* 5.2 0.5 + - - -
216C ASN* 3.8 22.0 + - - -
271C THR* 3.7 7.4 - - + -
272C TYR 3.4 27.9 + - - +
273C ALA* 5.1 0.9 - - - -
275C VAL* 5.6 2.6 + - - +
294C ALA* 2.9 38.4 + - - +
297C GLU* 3.0 24.5 + - - +
299C ALA* 1.3 81.9 - - - +
301C GLN* 1.3 61.4 + - - +
302C MET* 3.3 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA* 3.3 18.7 - - - +
212C ILE* 3.7 7.6 - - - +
269C LEU* 3.8 12.3 - - + +
270C ALA 3.5 8.1 - - - +
271C THR* 3.5 20.6 - - + +
295C CYS 5.2 1.9 - - - +
296C PHE 5.8 0.9 - - - -
297C GLU 4.6 0.6 - - - +
298C PRO* 3.3 33.8 + - + +
299C ALA 3.5 1.2 - - - +
300C ASN* 1.3 81.4 - - - +
302C MET* 1.3 60.4 + - - +
303C VAL 2.9 23.9 + - - +
304C LYS* 4.7 0.6 - - - +
305C CYS* 3.1 29.7 + - - +
307C PRO* 3.0 26.7 - - - +
----------------------------------------------------------
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