Contacts of the helix formed by residues 184 - 194 (chain A) in PDB entry 1IYH
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 ILE 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.7 32.5 - - + -
140A TRP* 4.6 7.6 - - + -
146A VAL* 4.1 19.5 - - + -
151A PHE* 3.9 28.0 - - + -
180A LYS 3.5 14.1 - - - +
181A VAL* 3.2 15.8 + - - +
183A ALA* 1.3 77.1 - - - +
185A PRO* 1.3 65.0 - - + +
186A ALA* 4.3 5.8 - - + +
187A VAL* 3.0 10.2 + - + -
188A ALA* 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA 3.1 9.6 - - - +
184A ILE* 1.3 89.0 - - + +
186A ALA* 1.3 61.8 + - - +
188A ALA* 3.3 6.3 + - + +
189A ASN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 3.4 31.5 - - - +
24A TYR* 4.1 12.3 - - + +
26A ASP* 6.3 0.7 - - + -
184A ILE* 3.5 5.9 - - + +
185A PRO* 1.3 79.1 - - - +
187A VAL* 1.3 62.6 + - + +
189A ASN* 3.5 8.7 + - - +
190A TRP* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.1 30.3 - - + +
23A ALA* 5.1 2.2 - - + -
24A TYR* 4.3 10.3 - - + +
151A PHE* 4.2 26.2 - - + -
181A VAL* 3.5 21.1 - - + +
182A GLN* 4.6 0.2 - - - -
184A ILE* 3.0 25.4 + - + +
186A ALA* 1.3 74.7 - - - +
188A ALA* 1.3 67.6 + - - +
190A TRP* 3.1 6.6 + - + +
191A ILE* 2.9 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLN 3.3 23.5 + - - +
183A ALA* 4.7 3.4 - - - +
184A ILE 2.7 18.4 + - - +
185A PRO* 3.6 7.4 - - + +
187A VAL* 1.3 72.6 - - - +
189A ASN* 1.3 62.4 + - - +
191A ILE* 3.3 7.3 + - - +
192A LYS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO 3.0 18.0 + - - +
186A ALA* 3.6 9.2 + - - +
188A ALA* 1.3 76.5 - - - +
190A TRP* 1.3 63.0 + - - +
192A LYS* 3.3 15.2 + - - +
193A ARG* 2.9 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 2.8 27.3 + - - -
19A ARG* 3.4 35.4 - - + +
20A TYR* 3.7 25.7 - + - -
23A ALA* 3.9 16.6 - - + -
29A TYR* 3.9 12.8 - + - -
31A ASP* 3.9 11.2 - - + -
33A ARG* 3.8 17.3 - - - -
186A ALA 3.2 10.3 + - - +
187A VAL* 3.1 8.8 + - - +
189A ASN* 1.3 81.9 - - - +
191A ILE* 1.3 60.1 + - + +
193A ARG* 4.9 5.8 - - + -
194A ARG* 2.8 60.3 + - + +
195A PRO* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.8 24.5 - - + +
154A GLU* 4.1 3.6 - - - +
182A GLN* 4.0 31.9 - - + +
187A VAL* 2.9 39.0 + - + +
188A ALA* 3.6 6.5 - - - +
190A TRP* 1.3 76.7 - - - +
192A LYS* 1.3 61.5 + - - +
194A ARG* 3.6 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA 3.0 15.8 + - - +
189A ASN* 3.7 20.4 + - - +
190A TRP 3.1 0.2 - - - -
191A ILE* 1.3 82.5 - - - +
193A ARG* 1.3 76.9 + - + +
194A ARG 3.6 2.3 - - - +
196A GLN* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASN* 2.9 46.2 + - - +
190A TRP* 4.3 8.3 - - + +
192A LYS* 1.3 96.0 - - + +
194A ARG* 1.3 66.8 + - - +
195A PRO* 3.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.6 30.5 - - - +
16A GLU* 2.8 37.2 + - - -
20A TYR* 3.2 26.5 + - - -
33A ARG* 5.0 0.7 - - - +
154A GLU* 5.3 2.6 + - - -
158A THR* 5.0 9.5 + - - +
190A TRP* 2.8 47.0 + - + +
191A ILE* 3.6 37.9 + - - +
192A LYS 4.5 3.1 - - - +
193A ARG* 1.3 77.2 - - - +
195A PRO* 1.3 81.8 + - + +
196A GLN* 3.3 10.8 + - + +
----------------------------------------------------------
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