Contacts of the helix formed by residues 171 - 187 (chain A) in PDB entry 1XGG
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 THR 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER 5.5 0.7 - - - -
169A GLU 5.0 3.4 - - - +
170A ILE* 1.3 76.1 - - - +
172A PHE* 1.3 63.3 + - - +
173A ASP* 3.4 10.7 + - - +
174A GLU* 3.1 52.0 + - - +
175A ILE* 3.1 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 4.3 10.5 - - - -
170A ILE 4.8 1.3 - - - -
171A THR* 1.3 76.2 - - - +
173A ASP* 1.3 59.4 + - - +
175A ILE* 3.2 12.3 + - + +
176A LEU* 3.1 31.1 + - - +
212A ALA 5.4 0.4 - - - -
213A SER* 2.9 34.5 - - - -
214A LEU* 3.8 14.4 - - + -
216A THR* 3.6 34.1 - - + -
217A SER* 3.3 37.5 + - - +
220A ARG* 3.6 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 3.2 8.7 + - - +
172A PHE* 1.3 79.2 - - - +
174A GLU* 1.3 56.2 + - + +
176A LEU* 3.1 21.2 + - - +
177A GLN* 3.0 39.2 + - - +
220A ARG* 3.4 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 5.7 1.0 - - - +
143A TYR* 4.3 5.4 + - - -
169A GLU 4.0 3.8 - - - +
170A ILE* 3.2 21.3 - - + +
171A THR* 3.1 47.0 + - - +
173A ASP* 1.3 76.3 - - + +
175A ILE* 1.3 57.7 + - - +
177A GLN* 3.1 25.4 + - - +
178A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 6.0 0.4 - - - -
165A TRP* 3.4 28.7 - - + +
170A ILE* 3.8 32.5 - - + +
171A THR 3.1 18.2 - - - +
172A PHE* 3.2 11.8 + - + +
174A GLU* 1.3 76.3 - - - +
176A LEU* 1.3 57.9 + - - +
178A ALA* 3.1 26.0 - - + +
179A TYR* 3.5 4.0 + - - +
214A LEU* 4.2 22.4 - - + -
217A SER* 3.7 14.8 - - - +
221A LYS* 3.3 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE 3.1 17.8 + - - +
173A ASP* 3.1 24.9 + - - +
175A ILE* 1.3 76.2 - - - +
177A GLN* 1.3 58.6 + - + +
178A ALA 3.2 0.2 - - - -
179A TYR* 3.2 10.7 + - + +
180A CYS* 3.1 36.0 + - - -
217A SER 5.0 0.4 - - - +
220A ARG* 3.7 27.6 - - + -
221A LYS* 3.4 33.0 - - + +
224A ASP* 3.3 26.5 - - + +
295A RET 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.0 22.4 + - - +
132A PRO* 3.8 34.7 - - + +
143A TYR* 5.0 0.2 - - - -
173A ASP* 3.0 22.3 + - - +
174A GLU* 3.1 30.4 + - - +
176A LEU* 1.3 75.0 - - + +
178A ALA* 1.3 64.3 + - - +
180A CYS* 3.2 8.7 + - - +
181A PHE 3.0 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 4.7 0.9 - - - -
135A VAL* 5.9 0.7 - - - -
143A TYR* 3.1 43.7 + - + +
160A PHE* 5.4 6.1 - - + -
174A GLU 3.1 8.6 + - - +
175A ILE* 3.1 20.0 - - + +
177A GLN* 1.3 78.7 - - - +
179A TYR* 1.3 62.2 + - + +
181A PHE* 3.2 17.7 + - - +
182A ILE* 3.3 16.5 - - - +
221A LYS* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 3.6 36.6 - - + +
160A PHE* 3.5 30.5 - + + -
175A ILE 3.5 5.3 + - - +
176A LEU* 3.2 13.2 + - + +
178A ALA* 1.3 79.4 - - - +
180A CYS* 1.3 61.9 + - - +
182A ILE* 3.3 5.9 + - + +
183A LEU* 2.9 58.9 + - + +
197A PHE* 4.4 5.4 - - - -
199A ILE* 5.4 0.2 - - + -
221A LYS* 5.2 0.4 - - - +
225A MET* 3.4 46.2 - - + +
234A PHE* 5.3 0.2 - - - -
295A RET 4.4 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.7 24.0 - - - +
128A ASP* 4.1 11.4 - - - +
131A SER* 4.6 1.1 - - - -
176A LEU* 3.1 30.0 + - - -
177A GLN* 3.2 11.2 + - - +
179A TYR* 1.3 81.2 - - - +
181A PHE* 1.3 62.6 + - - +
183A LEU* 3.3 6.6 + - - +
184A GLU* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.7 35.0 - - + +
131A SER* 2.9 48.2 - - - +
132A PRO 5.4 1.1 - - - -
135A VAL* 5.2 18.8 - - + -
177A GLN 3.0 5.2 + - - +
178A ALA* 3.3 10.3 - - - +
180A CYS* 1.3 77.5 - - - +
182A ILE* 1.3 70.6 + - + +
184A GLU* 4.2 0.9 - - - -
185A LYS* 3.0 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 5.7 1.1 - - + -
144A PRO* 3.6 32.5 - - + -
146A VAL* 3.7 21.1 - - + -
158A MET* 3.8 15.5 - - + -
160A PHE* 4.2 17.3 - - + -
178A ALA* 3.3 17.9 - - + +
179A TYR* 3.3 5.8 + - - +
181A PHE* 1.3 86.5 - - + +
183A LEU* 1.3 58.1 + - - +
185A LYS* 3.4 5.0 + - - +
186A LEU* 3.0 56.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
125A GLU* 5.2 14.6 - - + +
158A MET* 5.2 2.9 - - + -
179A TYR* 2.9 49.4 + - + +
180A CYS* 3.6 6.7 - - - +
182A ILE* 1.3 77.2 - - - +
184A GLU* 1.3 59.3 + - + +
186A LEU* 3.2 3.5 + - - +
187A LEU* 2.9 52.8 + - + +
197A PHE* 3.8 31.4 - - + -
225A MET* 5.3 4.7 - - + -
233A ARG* 5.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.2 26.1 - - + +
128A ASP* 3.0 43.4 + - - +
129A SER* 2.9 32.0 + - - +
130A LEU* 4.4 2.9 - - - -
131A SER 4.3 1.4 + - - -
180A CYS* 2.9 25.0 + - - +
181A PHE* 3.9 3.7 + - - +
183A LEU* 1.3 79.9 - - + +
185A LYS* 1.3 63.1 + - - +
187A LEU* 3.7 15.6 + - + +
188A GLU* 3.5 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.0 17.4 - - + +
181A PHE* 3.0 39.9 + - + +
182A ILE* 3.9 4.9 - - - +
184A GLU* 1.3 77.3 - - - +
186A LEU* 1.3 70.0 + - + +
188A GLU* 3.2 33.3 + - - +
189A ASN* 4.4 4.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
146A VAL* 4.1 15.5 - - + -
156A VAL* 3.8 30.5 - - + -
158A MET* 4.0 15.0 - - - -
182A ILE* 3.0 41.5 + - + +
183A LEU 3.9 2.9 - - - +
185A LYS* 1.3 86.6 - - + +
187A LEU* 1.3 55.8 + - - +
188A GLU 3.1 0.2 - - - -
189A ASN* 3.1 34.5 + - - +
192A THR* 3.1 34.0 + - + +
197A PHE* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.4 13.9 - - + +
183A LEU* 2.9 52.8 + - + +
184A GLU* 3.9 13.0 - - + +
185A LYS 3.3 0.6 - - - -
186A LEU* 1.3 77.0 - - - +
188A GLU* 1.3 59.2 + - - +
189A ASN 3.3 1.1 - - - -
192A THR* 4.6 13.0 - - + +
193A GLN* 2.9 37.7 + - + +
197A PHE* 4.8 1.6 - - + -
233A ARG* 4.4 22.0 - - - +
----------------------------------------------------------
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