Contacts of the helix formed by residues 185 - 195 (chain D) in PDB entry 3IFS
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 GLY 185 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LYS 4.9 0.2 - - - -
146D SER* 3.6 17.7 - - - -
184D ARG* 1.3 80.6 - - - +
186D ALA* 1.3 63.6 + - - -
187D LEU 3.2 2.7 - - - -
188D LYS 4.1 0.2 - - - -
189D THR* 2.9 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 3.2 49.7 - - + +
349C ASP* 3.8 5.8 - - + +
146D SER 2.9 13.0 + - - +
147D GLY 4.1 4.9 - - - +
148D THR* 4.0 11.7 - - + +
185D GLY* 1.3 72.3 - - - -
187D LEU* 1.3 57.4 + - - +
189D THR* 4.8 0.9 - - - -
190D LEU* 3.2 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D VAL* 4.1 37.0 - - + +
144D SER* 3.6 36.6 - - - +
146D SER 3.5 2.2 + - - -
147D GLY* 3.7 16.4 - - - +
156D PHE* 4.2 18.6 - - + -
178D ALA* 4.4 7.9 - - + -
179D THR 4.1 2.7 - - - +
180D THR* 3.6 20.4 - - + +
185D GLY 3.2 0.8 - - - -
186D ALA* 1.3 78.2 - - - +
188D LYS* 1.3 61.1 + - - +
190D LEU* 3.6 8.6 + - + +
191D ALA* 2.8 32.5 + - + +
196D TYR* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D THR* 3.8 14.7 + - + +
181D ASP 3.4 22.0 - - - +
182D LYS* 3.5 19.2 + - - +
183D ALA* 3.8 21.3 - - - +
184D ARG 3.4 21.8 - - - +
185D GLY 3.6 2.0 + - - -
186D ALA 3.6 0.2 - - - -
187D LEU* 1.3 75.4 - - - +
189D THR* 1.3 59.0 - - - +
191D ALA* 3.7 1.7 - - + +
192D ASP* 3.1 65.8 + - - +
198D THR* 3.4 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 4.1 17.9 - - + -
183D ALA 5.0 5.7 + - - -
184D ARG* 5.4 0.5 - - - -
185D GLY 2.9 22.7 + - - -
186D ALA* 4.0 3.8 - - - -
187D LEU 3.3 0.6 - - - -
188D LYS* 1.3 75.9 - - - +
190D LEU* 1.3 67.7 + - - +
192D ASP* 3.2 6.9 + - - +
193D ASN* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLU* 5.9 0.9 - - - +
346C ASN* 3.4 33.7 - - + +
348C LEU* 3.6 11.8 - - + +
156D PHE* 3.8 30.1 - - + -
160D ARG* 4.2 22.0 - - - +
186D ALA 3.2 17.6 + - - +
187D LEU* 3.8 7.9 - - + +
189D THR* 1.3 78.5 - - - +
191D ALA* 1.3 57.8 + - - +
193D ASN* 3.1 5.0 + - - +
194D GLU* 2.8 59.2 + - + +
196D TYR* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ALA* 4.2 12.1 - - + -
180D THR* 5.3 0.9 - - + -
187D LEU* 2.8 20.7 + - + +
188D LYS* 3.7 9.2 - - + +
190D LEU* 1.3 76.1 - - - +
192D ASP* 1.3 57.9 + - - +
194D GLU 3.6 0.3 - - - -
195D GLY* 2.8 27.0 + - - -
196D TYR* 3.2 33.6 + - + +
198D THR* 4.0 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ALA 5.4 0.7 - - - +
188D LYS* 3.1 53.2 + - - +
189D THR* 3.2 5.7 + - - +
191D ALA* 1.3 77.0 - - - +
193D ASN* 1.3 64.4 + - - +
194D GLU 3.5 0.2 + - - -
195D GLY* 3.6 8.1 + - - +
198D THR* 4.4 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ASN* 4.3 18.3 - - - +
348C LEU* 4.8 1.8 - - - +
189D THR* 2.9 35.6 + - - +
190D LEU* 3.5 8.7 - - - +
192D ASP* 1.3 78.0 - - - +
194D GLU* 1.3 64.9 + - + +
195D GLY 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU* 5.5 5.2 - - - +
346C ASN* 4.4 7.4 + - - -
160D ARG* 4.4 3.5 + - - -
169D LYS* 3.8 28.1 + - - -
173D ARG* 2.9 25.5 - - - +
190D LEU* 2.8 41.3 + - + +
191D ALA 3.9 0.2 - - - +
193D ASN* 1.3 82.7 - - + +
195D GLY* 1.3 57.4 + - - +
196D TYR* 3.6 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 2.9 33.4 + - - +
191D ALA 2.8 9.5 + - - -
192D ASP* 3.6 7.6 + - - -
193D ASN 3.6 2.4 - - - -
194D GLU* 1.3 78.8 - - - +
196D TYR* 1.3 62.3 + - - -
197D GLU 3.9 0.2 + - - -
----------------------------------------------------------
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