Contacts of the helix formed by residues 163 - 185 (chain A) in PDB entry 4TZQ
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 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 3.5 11.9 - - - -
161A TYR* 3.4 23.9 + - - -
162A GLU* 1.3 78.5 - - - +
164A GLY* 1.3 62.5 + - - -
165A ASP 3.4 2.2 - - - -
166A SER* 2.6 26.7 + - - -
167A VAL* 3.5 6.2 + - - +
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 2.7 18.8 + - - -
18A SER* 5.2 4.0 - - - -
19A ILE* 3.4 28.1 - - - +
30A ARG 5.6 0.4 - - - -
32A VAL* 4.4 3.4 - - - -
161A TYR* 3.2 8.8 + - - -
163A GLY* 1.3 71.4 - - - -
165A ASP* 1.3 57.2 + - - +
167A VAL* 3.1 11.8 + - - +
168A ARG 3.0 21.1 + - - -
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 4.3 6.4 + - - +
19A ILE* 4.1 19.3 - - - +
20A ASP 4.8 1.7 + - - -
163A GLY 3.4 1.0 - - - -
164A GLY* 1.3 73.3 - - - +
166A SER* 1.3 61.1 + - - +
168A ARG* 3.3 34.2 + - - +
169A ASP* 2.9 36.1 + - - +
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 3.6 36.6 + - - +
163A GLY 2.6 21.5 + - - -
165A ASP* 1.3 78.0 - - - +
167A VAL* 1.3 55.9 + - - +
169A ASP* 3.3 9.0 + - - +
170A GLN* 2.8 49.8 + - - +
236A ARG 5.0 0.5 + - - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.9 0.2 - - + -
24A TRP* 4.7 2.9 - - + -
32A VAL* 3.9 15.9 - - + -
41A PHE* 3.3 40.1 - - + -
161A TYR* 3.9 8.3 - - + -
163A GLY 3.8 11.7 - - - +
164A GLY 3.1 9.4 + - - +
166A SER* 1.3 80.1 + - - +
168A ARG* 1.3 65.8 + - - +
170A GLN* 3.2 11.9 + - - +
171A MET* 3.0 22.3 + - - +
236A ARG 3.3 28.9 - - - +
237A PRO* 3.8 11.4 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.2 19.1 - - + -
21A ASP* 4.5 12.3 + - - -
24A TRP* 3.6 23.5 - - + -
71A THR* 3.8 30.8 - - + +
73A LYS* 6.2 1.6 - - - +
164A GLY 3.0 11.3 + - - +
165A ASP* 3.3 41.1 + - - +
166A SER 3.3 0.2 - - - -
167A VAL* 1.3 77.2 - - - +
169A ASP* 1.3 81.3 + - - +
171A MET* 3.1 4.3 + - - +
172A VAL* 2.9 34.9 + - + +
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASP 2.9 13.4 + - - +
166A SER* 3.6 7.6 - - - +
168A ARG* 1.3 109.8 + - - +
170A GLN* 1.3 58.0 + - + +
172A VAL* 3.4 8.7 + - - +
173A THR* 2.9 32.9 + - - +
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Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL 5.7 1.0 + - - -
162A GLU* 5.8 4.2 + - - +
166A SER* 2.8 34.6 + - - +
167A VAL* 3.4 15.5 - - - +
168A ARG 3.2 0.2 - - - -
169A ASP* 1.3 76.7 - - - +
171A MET* 1.3 61.0 + - - +
173A THR* 3.3 7.9 + - - -
174A ILE* 3.1 30.0 + - - +
234A HIS* 3.4 43.0 + - + +
235A LEU* 3.4 5.4 - - + +
236A ARG* 2.8 38.1 + - - +
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Residues in contact with MET 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.8 17.3 - - + -
28A PHE* 4.0 29.8 - - + -
41A PHE* 4.8 2.5 - - + -
45A ALA* 4.1 35.4 - - + +
48A VAL* 4.4 3.6 - - + -
49A ALA* 4.4 8.3 - - + +
70A ILE* 4.3 8.1 - - + -
167A VAL 3.0 12.9 + - - +
168A ARG 3.1 7.8 + - - +
170A GLN* 1.3 76.0 - - - +
172A VAL* 1.3 62.3 + - - +
174A ILE* 3.3 20.8 + - + -
175A VAL* 3.2 40.4 + - + +
235A LEU* 4.0 12.9 - - + +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.2 8.3 - - + -
71A THR* 3.8 31.4 - - + +
74A LEU* 3.7 18.8 - - + -
168A ARG* 2.9 25.1 + - + +
169A ASP* 3.7 10.1 - - - +
170A GLN 3.3 0.2 - - - -
171A MET* 1.3 73.6 - - - +
173A THR* 1.3 65.9 + - - +
175A VAL* 3.4 1.8 + - - +
176A ARG* 3.0 55.1 + - - +
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP 2.9 20.6 + - - -
170A GLN* 3.5 8.2 - - - +
172A VAL* 1.3 76.3 - - - +
174A ILE* 1.3 57.0 + - - +
176A ARG* 3.4 5.4 + - - +
177A SER* 2.8 30.1 + - - -
232A ILE 4.1 13.5 - - - +
233A GLY* 4.8 7.0 - - - -
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Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 4.2 7.9 - - + -
170A GLN 3.1 23.7 + - - +
171A MET* 3.7 22.2 - - + +
172A VAL 3.3 0.2 - - - -
173A THR* 1.3 75.6 - - - +
175A VAL* 1.3 61.6 + - + +
177A SER* 3.3 1.7 + - - -
178A VAL* 3.0 36.7 + - + +
232A ILE* 3.5 9.1 - - + +
233A GLY* 3.6 41.1 - - - +
234A HIS 3.8 3.1 - - - +
235A LEU* 3.6 32.8 - - + -
244A MET* 4.1 26.2 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.3 6.1 - - + +
49A ALA* 5.6 0.7 - - - +
52A ALA* 4.7 7.4 - - + +
70A ILE* 3.3 29.4 - - + -
74A LEU* 3.8 21.5 - - + -
76A CYS* 4.0 14.8 - - + -
171A MET* 3.2 34.1 + - + +
173A THR 3.3 0.2 - - - -
174A ILE* 1.3 75.1 - - + +
176A ARG* 1.3 64.8 + - - +
178A VAL* 3.4 7.5 + - - +
179A GLN* 3.1 40.8 + - + +
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.7 29.5 + - - +
74A LEU* 4.0 27.7 - - + +
172A VAL* 3.0 46.4 + - - +
173A THR* 3.9 4.9 - - - +
175A VAL* 1.3 75.4 - - - +
177A SER* 1.3 56.7 + - - +
179A GLN* 3.3 14.0 + - - +
180A PHE* 2.8 28.5 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A THR* 2.8 20.0 + - - -
174A ILE 3.5 3.6 - - - -
176A ARG* 1.3 74.3 - - - +
178A VAL* 1.3 60.1 + - - +
180A PHE* 3.2 9.6 + - - +
181A LEU* 2.8 36.6 + - - +
231A THR 4.1 3.8 + - - -
232A ILE* 3.2 40.4 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 4.6 5.8 - - - +
52A ALA* 3.7 15.9 - - + +
53A VAL* 3.7 48.2 - - + +
56A ASN* 4.6 1.1 - - + -
125A PHE* 5.3 1.8 - - + -
174A ILE* 3.0 28.9 + - + +
175A VAL 3.7 4.9 - - - +
177A SER* 1.3 75.2 - - - +
179A GLN* 1.3 62.9 + - - +
181A LEU* 3.9 4.5 - - - +
182A CYS* 3.2 32.1 + - - -
232A ILE* 3.7 22.9 - - + -
244A MET* 4.6 2.0 - - + -
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 5.7 0.7 - - + -
56A ASN* 3.8 33.2 - - - +
74A LEU* 4.5 10.7 - - - +
75A LYS 3.8 20.6 + - - -
76A CYS* 5.0 4.2 - - - +
175A VAL* 3.1 28.1 + - + +
176A ARG* 3.5 16.6 - - - +
177A SER 3.2 0.2 - - - -
178A VAL* 1.3 78.3 - - + +
180A PHE* 1.3 61.6 + - - +
182A CYS* 3.5 1.0 + - - +
183A THR* 3.1 31.1 + - - +
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG 2.8 17.4 + - - +
177A SER* 3.2 10.5 + - - +
179A GLN* 1.3 76.8 - - - +
181A LEU* 1.3 74.9 + - + +
183A THR* 4.9 2.2 - - - -
184A LYS* 3.0 58.1 + - + +
185A VAL* 3.7 25.8 + - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 5.0 2.0 - - + -
177A SER* 2.8 23.9 + - - +
178A VAL* 3.9 5.2 - - - +
180A PHE* 1.3 82.7 - - + +
182A CYS* 1.3 58.5 + - - +
185A VAL* 3.1 33.9 + - + -
186A LEU* 2.7 43.1 + - + +
230A ALA* 4.1 23.1 - - + -
231A THR 5.4 0.7 - - - +
232A ILE* 3.9 23.1 - - + -
246A CYS* 3.6 34.8 - - + -
251A MET* 5.5 1.6 - - + -
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Residues in contact with CYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL 4.7 1.3 - - - -
56A ASN* 3.3 45.4 - - + +
57A ARG* 3.8 26.7 + - - +
125A PHE* 4.8 7.0 - - - -
178A VAL* 3.2 28.1 + - - +
179A GLN 4.1 1.1 - - - +
181A LEU* 1.3 82.2 - - - +
183A THR* 1.3 63.1 + - - +
186A LEU* 4.1 23.0 - - - +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 4.9 6.6 + - - -
179A GLN* 3.1 19.7 + - - +
180A PHE* 4.8 0.7 - - - -
182A CYS* 1.3 80.2 - - - +
184A LYS* 1.3 74.8 - - + +
186A LEU 5.7 0.7 - - - -
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.0 43.1 + - + +
183A THR* 1.3 96.1 - - + +
185A VAL* 1.3 62.6 + - + +
186A LEU 4.0 1.1 - - - -
252A SER 5.5 3.1 - - - -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.7 34.7 + - + -
181A LEU* 3.1 28.2 + - + +
184A LYS* 1.3 81.3 - - + +
186A LEU* 1.3 68.5 + - + +
187A GLU 3.5 1.7 + - - -
251A MET* 4.3 20.4 - - + -
252A SER* 3.1 44.8 + - - +
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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
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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) + - + + + + + -
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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