Contacts of the helix formed by residues 181 - 191 (chain A) in PDB entry 2XFN
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 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 2.6 30.9 + - - -
146A MET 3.6 7.0 - - - -
148A MET 4.3 0.4 - - - -
180A VAL* 1.3 75.0 - - - +
182A ALA* 1.4 58.7 + - - +
183A LEU 3.1 5.7 + - - -
184A TRP* 3.0 20.3 + - - +
185A PHE* 3.0 28.8 + - - +
402A PHE* 2.8 21.4 + - - -
403A PRO 3.7 10.8 - - - -
404A PRO* 3.8 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 3.5 12.8 - - + +
146A MET* 2.9 30.1 + - + +
147A THR 3.9 9.0 - - - +
148A MET* 3.7 20.8 - - - +
151A LEU* 4.1 15.0 - - + -
180A VAL 3.6 1.8 + - - -
181A SER* 1.4 68.8 - - - +
183A LEU* 1.3 67.1 + - - +
185A PHE* 3.3 0.7 + - - +
186A LEU* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.9 24.5 - - + -
134A PRO 3.9 20.6 - - - +
137A ALA* 4.3 5.2 - - + -
140A ALA* 3.6 15.3 - - + +
143A TRP* 3.1 27.2 + - + +
144A ASP* 3.6 24.0 - - + +
181A SER* 3.1 2.1 + - - +
182A ALA* 1.3 77.2 - - - +
184A TRP* 1.3 63.5 + - - +
186A LEU* 3.4 3.5 + - - +
187A TRP* 2.9 22.3 + - - +
407A LEU* 4.0 19.5 - - + -
408A THR* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 3.5 34.3 - - + -
180A VAL* 3.9 24.7 - - + -
181A SER* 3.0 16.2 + - - +
183A LEU* 1.3 77.7 - - - +
185A PHE* 1.3 76.6 + + - +
187A TRP* 3.3 29.2 + + - +
188A TYR* 2.8 44.4 + + - +
399A THR* 5.0 1.1 - - + -
400A THR 3.3 21.9 + - - -
401A TYR* 3.4 23.1 - - + -
402A PHE* 3.4 55.1 - + + -
407A LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 3.4 32.3 - - + -
148A MET* 3.5 34.1 - - + -
168A PHE* 3.5 22.2 - + - -
169A VAL* 3.8 27.4 - - + -
172A CYS* 3.9 10.1 - - + -
173A VAL* 3.8 44.2 - - + -
180A VAL* 4.3 1.6 - - + -
181A SER 3.0 10.8 + - - +
182A ALA 3.3 0.2 + - - -
184A TRP* 1.3 86.9 - + + +
186A LEU* 1.3 63.6 + - - +
188A TYR* 3.2 4.4 + + + +
189A VAL* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 3.6 55.7 - - + +
125A MET* 3.5 38.8 - - + -
126A GLY* 4.4 4.2 - - - +
129A ILE* 3.6 16.1 - - + +
143A TRP* 4.1 14.1 - - + -
148A MET* 4.8 1.3 - - - -
151A LEU* 4.0 13.7 - - + -
182A ALA* 2.9 26.4 + - + +
185A PHE* 1.3 78.2 - - - +
187A TRP* 1.3 60.6 + - - +
189A VAL* 3.6 4.3 + - + +
190A LYS* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.7 20.3 - - + +
130A PRO 3.8 10.3 - - - -
131A SER* 2.9 30.9 + - - +
134A PRO* 3.5 35.0 - - + +
183A LEU 2.9 18.1 + - - +
184A TRP* 3.5 36.1 - + - +
186A LEU* 1.3 75.2 - - - +
188A TYR* 1.3 95.8 + + - +
190A LYS* 3.1 4.8 + - + +
191A GLN* 2.9 42.8 + - + +
402A PHE* 6.1 0.4 - + - -
407A LEU* 5.3 1.3 - - + -
414A LEU* 6.3 1.8 - - + -
415A ARG* 6.1 0.9 - - - -
427A GLU 4.8 5.4 - - - -
429A ALA 3.9 16.8 - - - -
430A THR* 4.9 0.2 - - - -
433A SER* 3.6 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A CYS* 4.0 11.2 + - + -
173A VAL* 3.6 25.4 - - + -
184A TRP* 2.8 38.7 + + + +
185A PHE* 3.2 9.4 + - + +
187A TRP* 1.3 92.4 - + + +
189A VAL* 1.3 67.3 + - + +
191A GLN* 3.1 27.8 + - - +
192A CYS* 3.4 8.6 + - - -
198A ILE* 4.1 21.3 - - + -
398A TYR* 5.1 3.1 - - - -
399A THR* 3.6 25.7 - - + +
400A THR 5.3 0.2 - - - -
433A SER* 3.2 28.3 + - - -
434A GLY* 3.5 10.7 + - - -
435A TYR* 3.4 18.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 4.9 6.3 - - + +
123A ASP* 4.4 2.5 - - - +
168A PHE* 4.0 9.9 - - + -
185A PHE* 3.0 49.2 + - + +
186A LEU* 4.0 4.9 - - - +
188A TYR* 1.3 76.7 - - + +
190A LYS* 1.3 64.0 + - - +
192A CYS* 3.1 11.8 + - - +
193A GLY 3.4 0.3 + - - -
194A GLY* 3.0 43.0 + - - +
195A THR* 3.6 20.2 - - + +
198A ILE* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 5.9 0.7 - - - -
126A GLY* 3.0 32.0 + - - +
127A ARG* 4.0 13.4 + - + +
129A ILE* 2.9 30.6 + - + +
130A PRO* 4.9 1.2 - - - +
131A SER* 3.1 30.7 + - - +
186A LEU 3.1 18.8 + - - +
187A TRP* 3.8 6.1 - - + +
189A VAL* 1.3 77.7 - - - +
191A GLN* 1.3 58.8 + - - +
192A CYS 3.1 0.2 - - - -
193A GLY* 2.9 20.3 + - - -
194A GLY* 3.8 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 4.1 9.0 - - - +
187A TRP* 2.9 45.7 + - + +
188A TYR* 3.1 24.1 + - - +
190A LYS* 1.3 78.7 - - + +
192A CYS* 1.3 63.9 + - - +
193A GLY 3.4 0.2 - - - -
430A THR 3.6 17.8 - - - +
431A HIS* 3.0 21.8 + - - -
432A TRP 2.9 28.3 + - - -
433A SER* 2.7 58.9 + - - +
----------------------------------------------------------
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