Contacts of the helix formed by residues 219 - 229 (chain C) in PDB entry 5FHK
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 ALA 219 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 4.2 13.2 - - - +
191C GLY* 4.8 0.4 - - - -
192C HIS 4.2 5.1 + - - -
217C ALA* 3.2 3.4 + - - +
218C ASN* 1.3 85.0 - - - +
220C LEU* 1.3 63.2 + - - +
221C ASN* 3.5 16.4 - - - +
222C VAL* 3.0 27.0 - - + +
223C VAL* 3.7 11.3 - - - +
99F TYR* 6.3 2.5 - - + -
126F THR* 4.9 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 5.1 0.2 + - - -
100C ASN* 4.1 30.9 + - - +
191C GLY* 3.7 33.9 - - - +
192C HIS 3.7 9.2 + - - +
193C PRO* 4.6 2.2 - - + -
194C LEU* 4.4 11.4 - - + -
219C ALA* 1.3 71.5 - - - +
221C ASN* 1.3 67.4 + - - +
223C VAL* 2.8 16.8 + - + +
224C ARG* 2.9 13.5 + - - +
235C LEU 4.5 7.0 - - - +
236C MET* 4.2 20.6 - - + +
237C PRO* 4.0 28.0 - - + -
240C MET* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ALA* 3.7 11.9 - - - +
220C LEU* 1.3 78.0 - - - +
222C VAL* 1.3 85.3 + - - +
224C ARG* 3.4 9.1 + - - +
225C SER* 3.2 19.6 + - - -
240C MET* 5.3 3.5 - - - +
103F LYS* 3.7 40.0 - - + +
221F ASN* 6.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 3.3 28.4 - - + -
217C ALA* 3.5 13.9 - - + -
219C ALA* 3.0 28.9 - - + +
221C ASN* 1.3 89.5 + - - +
223C VAL* 1.3 61.2 + - - +
225C SER* 3.3 6.5 + - - -
226C ALA 3.3 16.5 + - - -
102F THR* 4.6 8.3 - - + -
103F LYS* 5.2 5.4 - - + -
107F MET* 3.3 29.6 - - + +
124F LEU* 4.5 12.6 - - + -
126F THR* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 3.8 18.5 - - + +
190C LYS 3.6 23.1 - - - +
191C GLY* 3.6 16.4 - - - +
215C PHE* 4.1 12.6 - - + -
217C ALA* 4.0 10.5 - - + -
219C ALA 3.7 9.0 - - - +
220C LEU* 2.8 10.8 + - - +
222C VAL* 1.3 75.8 - - - +
224C ARG* 1.3 59.8 + - - +
226C ALA* 3.2 4.5 + - - +
227C CYS* 2.9 25.1 + - - +
234C THR* 3.1 30.3 - - - +
236C MET* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU 2.9 11.1 + - - +
221C ASN* 3.6 11.2 - - - +
223C VAL* 1.3 76.4 - - - +
225C SER* 1.3 79.2 + - - +
227C CYS* 3.2 6.1 + - + +
228C SER* 2.9 42.5 + - - -
234C THR* 6.2 0.2 - - + -
236C MET* 4.5 13.6 - - + +
240C MET* 6.2 1.1 - - + -
241C ILE* 3.9 23.1 - - + -
244C TYR* 3.2 44.6 + - + -
250C LEU* 4.1 12.1 - - + -
103F LYS* 3.2 35.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN 3.2 10.0 + - - -
222C VAL* 3.5 9.2 - - - -
223C VAL 3.2 0.4 - - - -
224C ARG* 1.3 95.7 - - - +
226C ALA* 1.3 61.5 + - - +
228C SER* 3.3 3.2 + - - -
229C GLU* 3.1 26.3 + - - +
103F LYS* 4.8 11.2 - - - -
107F MET* 3.5 21.0 - - - +
111F ASN* 2.9 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 3.8 10.8 - - + -
215C PHE* 3.8 29.6 - - + -
222C VAL 3.3 4.9 + - - +
223C VAL 3.2 9.3 + - - +
225C SER* 1.3 80.3 + - - +
227C CYS* 1.3 60.3 + - - +
229C GLU* 3.3 7.6 + - - +
231C LEU* 3.3 31.5 + - + +
107F MET* 4.1 1.3 - - + -
111F ASN* 3.2 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.5 20.2 - - - -
166C ALA* 3.7 3.8 - - - -
167C SER* 3.4 13.3 + - - -
189C LEU* 3.5 12.8 - - + +
223C VAL 2.9 15.8 + - - +
224C ARG* 3.2 6.7 + - + +
226C ALA* 1.3 70.3 - - - +
228C SER* 1.3 66.8 + - - +
229C GLU 3.0 1.6 - - - -
230C GLY* 2.9 13.7 + - - -
231C LEU 4.2 0.4 + - - +
232C GLY 3.4 21.2 - - - +
234C THR* 3.7 21.8 - - + -
250C LEU* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C SER* 3.7 11.8 + - - -
224C ARG* 2.9 42.1 + - - -
225C SER 3.7 4.7 - - - -
227C CYS* 1.3 74.5 - - - +
229C GLU* 1.3 66.0 + - - +
230C GLY 3.2 1.3 + - - -
244C TYR* 4.8 6.4 - - - -
249C SER* 4.6 9.2 + - - +
250C LEU* 3.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C GLU* 3.6 11.3 - - - +
225C SER* 3.1 11.6 + - - +
226C ALA 3.7 6.1 - - - +
227C CYS 3.0 1.6 - - - -
228C SER* 1.3 82.4 - - - +
230C GLY* 1.3 60.4 + - - +
231C LEU* 3.5 10.2 + - + +
108F PRO* 6.3 0.4 - - + -
111F ASN* 3.3 41.2 - - + +
115F SER* 6.0 0.9 - - - -
----------------------------------------------------------
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