Contacts of the helix formed by residues 219 - 229 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D TYR* 4.5 9.2 - - - +
192D HIS 4.6 1.8 - - - -
217D ALA* 3.1 3.4 - - + +
218D ASN* 1.3 87.0 + - - +
220D LEU* 1.3 65.4 + - - +
221D ASN* 3.3 18.6 - - - +
222D VAL* 3.4 19.7 + - + +
223D VAL* 3.4 17.4 + - - +
99E TYR* 5.9 5.6 - - + -
126E THR* 4.4 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D TYR* 5.1 0.4 + - - -
100D ASN* 3.3 43.8 + - + +
191D GLY* 3.5 32.3 - - - +
192D HIS 3.7 11.0 - - - +
193D PRO* 4.5 4.5 - - + -
194D LEU* 4.6 12.1 - - + -
219D ALA* 1.3 69.5 - - - +
221D ASN* 1.3 65.5 + - - +
222D VAL 3.1 2.7 - - - -
223D VAL* 3.2 7.2 + - + +
224D ARG* 2.9 24.5 + - - +
234D THR* 6.0 0.4 - - - +
235D LEU 4.7 3.8 - - - +
236D MET* 4.2 20.9 - - - +
237D PRO* 4.2 13.7 - - + -
240D MET* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA* 3.3 21.1 - - - +
220D LEU* 1.3 76.9 - - - +
222D VAL* 1.3 80.6 + - - +
224D ARG* 3.5 12.3 + - - +
225D SER* 3.3 19.2 + - - -
240D MET* 5.0 7.8 - - + +
100E ASN* 5.8 2.6 + - - +
102E THR* 6.1 0.2 - - - -
103E LYS* 3.9 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D PHE* 3.5 19.9 - - + -
217D ALA* 4.3 7.4 - - + -
219D ALA* 3.7 14.8 - - + +
220D LEU 3.1 0.8 - - - -
221D ASN* 1.3 99.4 + - - +
223D VAL* 1.3 64.8 + - - +
224D ARG 3.2 0.2 - - - -
225D SER* 3.1 16.8 + - - -
226D ALA 3.2 8.8 + - - -
102E THR* 4.0 24.5 - - + -
103E LYS* 4.8 3.6 - - - +
107E MET* 3.4 34.2 - - + +
124E LEU* 4.4 6.7 - - + -
126E THR* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 3.7 23.6 - - + +
190D LYS 3.9 3.8 - - - +
191D GLY* 3.5 30.5 - - - +
215D PHE* 4.2 11.0 - - + -
217D ALA* 3.8 15.9 - - + +
219D ALA 3.4 11.6 + - - +
220D LEU* 3.2 10.2 + - + +
222D VAL* 1.3 75.8 - - - +
224D ARG* 1.3 63.1 + - - +
226D ALA* 3.1 2.9 + - - +
227D CYS* 3.0 20.8 + - - +
234D THR* 3.1 29.4 - - + +
236D MET* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D LEU 2.9 15.9 + - - +
221D ASN* 3.6 11.3 + - - +
222D VAL 3.2 0.4 - - - -
223D VAL* 1.3 77.2 - - - +
225D SER* 1.3 67.2 + - - +
227D CYS* 3.4 4.8 + - + +
228D SER* 2.5 65.1 + - - +
236D MET* 3.8 23.7 - - + +
240D MET* 5.6 2.9 - - + -
241D ILE* 4.2 13.7 - - + -
244D TYR* 4.0 46.2 + - - -
250D LEU* 4.8 6.8 - - + +
103E LYS* 4.0 27.5 - - - +
104E ARG* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ASN 3.3 10.6 + - - -
222D VAL* 3.1 11.3 + - - -
224D ARG* 1.3 93.6 - - - +
226D ALA* 1.3 62.1 + - - +
228D SER* 3.4 4.5 + - - -
229D GLU* 3.2 25.3 + - - +
103E LYS* 4.6 10.8 + - - -
107E MET* 3.3 21.3 - - - +
111E ASN* 3.2 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 4.0 12.1 - - + -
215D PHE* 3.6 31.4 - - + -
222D VAL 3.2 2.0 + - - +
223D VAL 3.1 9.0 + - - +
225D SER* 1.3 78.3 + - - +
227D CYS* 1.3 64.1 + - - +
229D GLU* 2.9 14.6 + - - +
230D GLY 3.4 0.2 + - - -
231D LEU* 3.4 24.9 + - + +
107E MET* 4.4 0.2 - - - +
111E ASN* 3.5 22.0 + - - +
114E MET* 4.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D VAL* 3.4 33.4 - - - -
166D ALA* 3.7 8.7 - - - -
167D SER* 3.5 12.9 + - - -
189D LEU* 3.5 15.3 - - + +
223D VAL 3.0 12.4 + - - +
224D ARG* 3.6 10.5 - - + +
226D ALA* 1.3 76.2 - - - +
228D SER* 1.3 57.7 + - - +
230D GLY* 2.8 20.1 + - - +
231D LEU 4.2 0.6 + - - +
232D GLY 3.6 12.9 - - - +
234D THR* 3.8 20.4 - - + -
250D LEU* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER* 3.9 10.0 - - - -
169D GLU* 5.2 1.6 - - - +
224D ARG* 2.5 51.8 + - - -
225D SER* 3.7 6.7 - - - -
226D ALA 3.3 0.2 - - - -
227D CYS* 1.3 74.0 - - - +
229D GLU* 1.3 66.5 + - - +
230D GLY 3.2 1.0 + - - -
249D SER 5.3 1.6 - - - +
250D LEU* 4.1 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLU* 3.7 20.4 - - - +
225D SER* 3.2 13.6 + - - +
226D ALA 2.9 10.0 + - - +
228D SER* 1.3 81.8 - - - +
230D GLY* 1.3 60.9 + - - +
231D LEU* 3.5 9.6 + - + +
108E PRO* 6.5 0.7 - - - -
111E ASN* 3.5 30.7 - - + +
115E SER* 6.0 0.5 - - - -
----------------------------------------------------------
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