Contacts of the helix formed by residues 219 - 223 (chain B) in PDB entry 1H8F
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 219 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASP* 3.6 16.2 - - - +
261A SER* 4.2 6.2 - - - -
181B ASP* 2.9 12.1 + - - -
182B ILE 5.7 0.4 + - - -
183B LYS* 2.8 39.9 + - - -
218B CYS* 1.3 76.6 - - - +
220B ARG* 1.3 81.0 + - - +
222B TYR* 3.0 21.7 + - - +
223B ARG* 3.2 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASP* 3.1 49.8 + - + +
140B TYR* 5.5 4.0 - - - -
183B LYS* 5.5 1.2 - - - +
185B GLN* 3.2 26.3 + - - +
218B CYS 4.0 0.2 + - - -
219B SER* 1.3 79.9 - - - +
221B TYR* 1.3 116.3 + - + +
222B TYR* 3.1 20.6 + - - -
223B ARG* 3.3 19.0 + - - +
259B GLY 4.7 2.0 - - - +
265B GLN* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 1.3 122.9 + - + +
222B TYR* 1.3 73.5 + - + +
223B ARG 3.6 1.9 - - - +
245B CYS* 3.8 15.9 - - - +
255B PRO* 3.6 39.0 - - + -
256B ILE* 5.6 0.3 - - - +
257B PHE* 3.9 25.7 + - - +
258B PRO* 3.7 17.3 - - + +
259B GLY 3.6 31.5 + - - -
260B ASP* 4.7 7.9 + - - -
265B GLN* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 6.0 0.7 - - - -
182B ILE 3.6 18.2 - - - +
183B LYS* 3.7 15.3 - - + -
184B PRO* 3.4 27.2 - - + +
185B GLN* 4.8 2.5 + - - -
218B CYS* 3.7 4.0 - - - -
219B SER* 3.0 15.9 + - - +
220B ARG* 3.6 29.1 + - - -
221B TYR* 1.3 93.2 - - + +
223B ARG* 1.3 64.5 + - - +
224B ALA 3.5 1.0 + - - -
241B TRP* 3.6 9.6 - - - -
242B SER* 3.0 28.7 + - - +
245B CYS* 3.7 29.2 - - + -
246B VAL* 4.4 6.3 - - + -
249B GLU* 2.6 35.8 + - - -
255B PRO* 4.6 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 5.5 6.7 - - - +
260A ASP 5.7 0.2 - - - -
261A SER* 6.0 0.2 - - - +
262A GLY 5.7 0.6 - - - +
215B SER 2.9 22.0 + - - -
216B TYR* 4.0 5.6 - - - +
217B ILE 2.8 24.3 + - - +
218B CYS* 3.1 29.6 + - - +
219B SER 3.2 17.7 - - - +
220B ARG* 3.3 16.7 + - - +
221B TYR 5.0 1.7 - - - +
222B TYR* 1.3 76.5 - - - +
224B ALA* 1.3 66.7 + - - +
225B PRO 3.9 0.7 - - - -
227B LEU* 3.4 32.1 + - + +
228B ILE* 4.0 27.6 + - + +
241B TRP* 3.3 12.1 + - - -
265B GLN* 4.9 5.1 + - - +
269B ILE* 4.8 1.9 - - - +
----------------------------------------------------------
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