Contacts of the helix formed by residues 222 - 231 (chain 3) in PDB entry 5IY8
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 SER 222 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 ARG* 3.7 25.6 + - - -
612 PHE* 5.1 9.0 - - - -
2193 GLN* 3.2 12.4 + - - +
2203 MET 3.0 1.6 - - - -
2213 PRO* 1.3 73.4 - - - +
2233 LEU* 1.3 56.2 - - - +
2243 LEU* 3.2 3.4 - - - -
2253 GLN* 2.7 52.8 + - - +
2263 TYR* 2.7 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 CYS* 5.2 13.9 - - + +
403 ALA* 4.4 15.7 - - + -
413 VAL* 5.5 0.7 - - + -
1643 ILE* 5.0 11.0 - - + -
1943 CYS* 4.2 13.2 - - - -
1963 LEU* 3.0 44.4 - - + -
2203 MET* 3.0 13.9 + - - +
2213 PRO* 2.9 6.0 - - + +
2223 SER* 1.3 76.7 - - - +
2243 LEU* 1.3 66.2 + - - +
2263 TYR* 3.1 8.9 + - - +
2273 LEU* 3.0 51.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612 PHE* 6.0 8.5 - - + -
992 GLN* 5.4 14.1 - - + +
403 ALA* 3.6 35.9 - - + +
433 VAL* 4.3 20.0 - - + -
443 LEU* 4.3 22.0 - - + +
2213 PRO 4.5 2.3 + - - +
2223 SER 3.2 1.0 - - - -
2233 LEU* 1.3 83.5 - - - +
2253 GLN* 1.3 64.6 + - - +
2273 LEU* 3.2 2.9 + - + +
2283 LEU* 3.0 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 ARG* 5.1 9.8 + - - +
612 PHE* 5.7 7.4 - - + -
2223 SER* 2.7 49.2 + - - +
2243 LEU* 1.3 79.6 - - - +
2263 TYR* 1.3 73.4 + - + +
2283 LEU* 3.2 3.3 + - - +
2293 TRP* 2.6 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1943 CYS* 4.3 11.0 - - - -
2153 LEU* 4.6 7.9 - - + -
2173 VAL* 2.9 48.2 - - + -
2183 PRO* 2.6 31.8 + - + +
2193 GLN* 3.4 1.8 + - - +
2223 SER* 2.7 44.4 - - - -
2233 LEU* 3.1 7.5 + - - +
2253 GLN* 1.3 95.8 + - + +
2273 LEU* 1.3 59.3 + - - +
2293 TRP* 4.9 0.9 - + - -
2303 VAL* 2.6 61.5 + - + +
2313 PHE* 3.8 1.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ILE* 6.4 0.2 - - + -
403 ALA 4.7 1.3 - - - +
413 VAL* 4.3 22.0 - - + +
443 LEU* 3.7 36.5 - - + +
1623 LEU* 3.7 28.7 - - + -
1643 ILE* 4.8 12.3 - - + -
1943 CYS* 4.8 7.0 - - + -
2233 LEU* 3.0 46.7 + - + +
2243 LEU* 3.7 6.3 - - - +
2263 TYR* 1.3 79.3 - - - +
2283 LEU* 1.3 65.6 + - - +
2313 PHE* 3.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012 LEU 5.9 2.7 - - - +
443 LEU* 3.7 16.6 - - + +
473 SER* 5.6 7.2 - - - +
2243 LEU* 3.0 20.7 + - + +
2253 GLN* 4.0 3.4 - - - +
2273 LEU* 1.3 82.1 - - - +
2293 TRP* 1.3 68.8 + - + +
2313 PHE 4.1 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 229 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2253 GLN* 2.6 47.5 + - + +
2263 TYR* 4.9 1.1 - + - -
2283 LEU* 1.3 80.7 - - + +
2303 VAL* 1.3 67.6 + - + +
2313 PHE 3.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1943 CYS* 6.1 0.2 - - - -
2133 LEU* 2.9 28.0 - - + +
2153 LEU* 2.9 34.1 - - + -
2263 TYR* 2.6 66.0 + - + +
2293 TRP* 1.3 79.0 - - + +
2313 PHE* 1.3 78.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603 ARG* 3.5 17.1 + - - +
1623 LEU* 3.7 26.2 - - + -
1923 ASP* 2.9 42.4 - - + +
1933 ALA 3.7 16.6 - - - -
1943 CYS* 4.3 13.0 - - + -
2133 LEU* 3.6 26.2 - - + -
2153 LEU* 5.2 1.1 - - + -
2263 TYR 3.8 4.4 + - - -
2273 LEU* 3.9 23.8 + - + +
2283 LEU 4.2 8.7 - - - -
2293 TRP 3.3 6.7 - - - -
2303 VAL* 1.3 106.2 - - + +
----------------------------------------------------------
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