Contacts of the helix formed by residues 176 - 189 (chain A) in PDB entry 4I7Z
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 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.4 1.3 - - - -
140A TRP* 3.7 18.1 - - - -
145A TYR* 5.3 0.7 - - - -
174A SER* 3.8 2.2 + - - -
175A VAL* 1.3 77.5 - - - +
177A GLN* 1.3 65.5 + - - -
178A ALA* 3.3 3.8 - - - +
179A THR* 3.1 17.3 + - - -
180A LEU 3.2 9.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
60A PRO 3.1 21.8 + - - -
61A THR* 3.2 15.6 + - - +
62A VAL* 2.9 46.6 + - + +
176A GLY* 1.3 70.9 - - - -
178A ALA* 1.3 65.8 + - - +
180A LEU* 3.1 4.3 + - - +
181A THR* 2.8 51.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
170A ARG 3.7 13.5 - - - +
171A GLY* 3.9 18.4 - - - +
176A GLY 5.1 0.9 - - - +
177A GLN* 1.3 78.9 - - - +
179A THR* 1.3 58.6 + - - +
181A THR* 3.3 7.1 + - - -
182A ARG* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TRP* 4.8 2.2 - - + -
148A VAL* 4.2 12.1 - - + -
152A SER* 5.7 0.9 - - - -
169A LEU 4.6 1.1 - - - -
170A ARG* 2.8 39.9 + - + +
175A VAL* 3.4 16.2 - - + -
176A GLY 3.1 25.6 + - - -
178A ALA* 1.3 78.3 - - - +
180A LEU* 1.3 57.1 + - - +
182A ARG* 3.2 1.7 + - - -
183A TYR* 2.8 61.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.6 19.7 - - - +
60A PRO* 3.5 10.5 - - + +
61A THR* 3.4 43.3 - - - +
62A VAL* 3.5 11.4 - - + +
65A ALA* 4.5 4.7 - - + -
137A SER* 4.3 1.3 - - - +
138A LEU* 4.1 18.8 - - + +
140A TRP* 3.8 35.1 - - + -
176A GLY 3.2 4.9 + - - +
177A GLN* 3.1 9.5 + - - +
179A THR* 1.3 78.0 - - - +
181A THR* 1.3 53.3 + - - +
183A TYR* 3.4 5.6 + - + +
184A TYR* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 4.5 5.3 + - - -
177A GLN* 2.8 33.8 + - - +
178A ALA* 3.4 11.2 - - - -
180A LEU* 1.3 77.3 - - - +
182A ARG* 1.3 61.5 + - + +
184A TYR* 3.0 6.9 + - - +
185A SER* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP 4.2 0.4 + - - -
168A LEU* 2.7 60.5 + - - +
169A LEU 4.1 10.3 - - - +
171A GLY* 3.6 26.2 + - - +
178A ALA* 2.9 23.4 + - - +
179A THR 3.8 2.5 - - - +
181A THR* 1.3 76.5 - - + +
183A TYR* 1.3 58.7 + - + +
185A SER* 3.4 8.2 + - - -
186A ALA* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 4.6 10.1 - - + +
134A THR* 3.7 35.4 - - + +
137A SER* 3.4 22.0 - - - +
138A LEU* 4.5 4.5 - - + -
148A VAL* 3.1 27.3 - - + +
151A VAL* 3.9 15.1 - - - +
152A SER* 4.4 11.7 - - - -
169A LEU* 3.7 28.9 - - + +
179A THR* 2.8 47.5 + - + +
180A LEU* 3.7 6.7 - - + +
182A ARG* 1.3 75.2 - - + +
184A TYR* 1.3 57.2 + - - +
186A ALA* 3.3 7.0 + - - +
187A HIS* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.8 30.6 + - + +
58A TYR* 3.4 40.1 + + + -
60A PRO* 3.6 31.8 - - + +
138A LEU* 3.7 22.8 - - + +
180A LEU 2.8 21.2 + - - +
181A THR* 3.6 4.0 - - - +
183A TYR* 1.3 70.0 - - - +
185A SER* 1.3 59.4 + - - +
187A HIS* 3.2 1.1 + - - +
188A THR* 2.6 69.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 2.9 14.6 + - - -
182A ARG* 3.5 11.9 - - - -
184A TYR* 1.3 79.7 - - - +
186A ALA* 1.3 57.1 + - - +
188A THR* 4.2 3.1 - - - -
189A PHE* 2.8 44.2 + - - +
190A VAL* 3.3 9.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
134A THR* 4.2 13.7 - - + -
182A ARG 2.8 17.5 + - - +
183A TYR* 3.4 9.0 - - - +
185A SER* 1.3 78.5 - - - +
187A HIS* 1.3 59.4 + - - +
190A VAL* 4.1 15.9 - - + -
191A LEU* 3.1 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 4.3 20.0 + + - -
131A PHE* 3.1 53.5 + + + -
132A GLY* 5.5 0.2 - - - -
134A THR* 2.9 26.6 + - - +
135A GLY* 3.2 16.5 + - - -
138A LEU* 3.5 29.4 - - + +
183A TYR 2.8 20.1 + - - +
184A TYR 3.8 2.7 - - - +
186A ALA* 1.3 74.6 - - - +
188A THR* 1.3 68.4 + - + +
189A PHE 3.7 0.2 - - - -
191A LEU* 4.3 3.1 - - - -
192A PRO* 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 6.4 0.4 - - - -
55A THR* 4.4 15.7 - - + -
184A TYR* 2.6 69.3 + - + +
185A SER* 4.2 2.3 + - - -
187A HIS* 1.3 90.7 - - + +
189A PHE* 1.3 60.9 + - - +
192A PRO* 3.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 2.8 26.7 + - - +
187A HIS 3.7 0.8 - - - -
188A THR* 1.3 77.9 - - - +
190A VAL* 1.3 78.7 + - + +
191A LEU 3.6 0.7 - - - -
192A PRO* 3.4 4.2 - - - +
193A TRP* 3.0 55.6 + + + -
----------------------------------------------------------
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