Contacts of the helix formed by residues 158 - 175 (chain A) in PDB entry 3APO
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A SER* 3.7 21.1 - - - +
156A PRO 3.2 4.8 + - - -
157A GLY* 1.3 70.9 - - - +
159A SER* 1.3 58.1 + - - +
160A HIS* 3.1 11.8 + - - +
161A SER* 2.8 49.6 + - - -
162A HIS* 3.2 8.5 + - - -
202A PRO* 4.2 14.6 - - - +
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Residues in contact with SER 159 (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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157A GLY 2.8 13.3 + - - -
158A SER* 1.3 67.9 - - - +
160A HIS* 1.3 63.1 + - - +
161A SER 3.2 0.7 - - - -
162A HIS* 3.6 19.8 - - - +
163A ASP* 2.7 31.9 + - - +
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Residues in contact with HIS 160 (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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158A SER* 3.1 9.5 + - - +
159A SER* 1.3 82.9 + - - +
161A SER* 1.3 60.3 + - - +
163A ASP* 3.6 15.5 - - + +
164A LEU* 3.6 21.7 + - - +
202A PRO* 4.6 19.7 - - + +
220A ARG* 5.2 6.5 + - - +
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Residues in contact with SER 161 (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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124A ILE* 5.7 0.5 - - - +
125A TYR* 4.2 5.4 + - - -
152A ASN* 6.0 0.9 - - - +
154A TYR* 3.4 23.4 - - - +
155A SER 3.3 24.4 + - - -
158A SER* 2.8 33.9 + - - -
160A HIS* 1.3 76.6 - - - +
162A HIS* 1.3 62.5 + - - +
163A ASP 3.3 0.2 - - - -
164A LEU* 3.4 6.1 + - - +
165A ALA* 3.2 22.9 + - - +
202A PRO* 4.5 7.6 - - - +
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Residues in contact with HIS 162 (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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120A TYR* 3.2 38.1 + + + +
121A ASP* 3.0 32.6 + - - -
124A ILE* 4.4 16.5 - - + +
155A SER 5.6 2.0 - - - -
157A GLY* 4.4 8.7 + - - -
158A SER 3.2 14.4 + - - -
159A SER* 3.7 24.5 - - - +
161A SER* 1.3 73.8 - - - +
163A ASP* 1.3 65.6 - - - +
164A LEU 3.2 1.0 + - - -
165A ALA* 3.6 6.8 + - - +
166A PRO* 3.5 18.0 - - - +
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Residues in contact with ASP 163 (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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159A SER 2.7 23.4 + - - +
160A HIS* 3.6 20.7 - - + +
162A HIS* 1.3 75.4 - - - +
164A LEU* 1.3 58.3 + - + +
166A PRO* 4.0 7.1 - - - +
167A THR* 4.0 6.8 + - - -
220A ARG* 6.0 1.6 - - - +
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Residues in contact with LEU 164 (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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152A ASN* 3.9 18.2 - - - +
160A HIS 3.6 14.3 + - - +
161A SER* 3.4 6.1 + - - +
162A HIS 3.2 0.4 - - - -
163A ASP* 1.3 78.8 - - + +
165A ALA* 1.3 65.0 + - - +
166A PRO* 3.3 3.4 - - - -
167A THR* 2.8 26.0 + - + +
168A TRP* 2.9 31.0 + - + +
202A PRO 6.1 1.3 - - - +
204A LEU* 3.9 28.7 - - + -
220A ARG* 3.7 55.2 - - + +
225A LEU* 4.8 2.2 - - + -
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Residues in contact with ALA 165 (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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124A ILE* 3.7 29.4 - - + -
125A TYR* 3.5 15.6 - - + +
161A SER 3.2 12.1 + - - +
162A HIS* 4.0 8.3 - - - +
164A LEU* 1.3 75.5 - - - +
166A PRO* 1.4 69.8 - - + +
168A TRP* 3.4 2.5 + - - +
169A ARG* 3.1 39.4 + - - +
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Residues in contact with PRO 166 (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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162A HIS 3.5 12.8 - - - +
163A ASP 4.0 6.3 - - - +
164A LEU 3.5 4.0 - - - -
165A ALA* 1.4 93.9 - - + +
167A THR* 1.3 61.2 + - - +
169A ARG* 3.4 18.1 + - - +
170A GLU* 3.2 29.2 + - + +
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Residues in contact with THR 167 (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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163A ASP 4.0 5.7 + - - -
164A LEU* 2.8 30.0 + - + +
166A PRO* 1.3 73.0 - - - +
168A TRP* 1.3 56.1 + - - +
170A GLU* 3.2 9.7 + - + +
171A PHE* 2.7 36.8 + - - +
220A ARG* 3.4 22.3 + - - +
221A SER* 4.3 2.0 - - - -
222A LYS* 3.9 24.4 - - + +
225A LEU* 4.9 2.7 - - + -
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Residues in contact with TRP 168 (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 TYR* 4.2 21.8 - + + +
131A ILE* 3.9 10.0 - - + +
150A PHE* 3.3 51.6 - + - -
152A ASN* 3.4 39.1 - - + +
164A LEU* 2.9 28.5 + - + +
165A ALA 3.8 4.5 - - - +
167A THR* 1.3 76.5 - - - +
169A ARG* 1.3 61.3 + - - +
171A PHE* 3.7 21.9 - + - +
172A ALA* 3.3 23.6 + - - +
181A ILE* 3.2 22.4 - - + +
182A GLY 3.4 8.5 + - - -
183A ALA* 5.2 0.2 - - + -
204A LEU* 4.2 12.8 - - + -
225A LEU* 3.8 28.5 - - + -
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Residues in contact with ARG 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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124A ILE* 3.0 38.9 + - - +
125A TYR* 4.2 2.7 - - + -
128A ASP* 3.2 41.9 + - + +
130A GLU* 4.9 2.9 - - - +
131A ILE* 4.0 13.0 - - + -
165A ALA* 3.1 29.7 + - - +
166A PRO* 3.6 14.2 - - - +
167A THR 3.1 0.6 - - - -
168A TRP* 1.3 75.3 - - - +
170A GLU* 1.3 68.4 + - - +
172A ALA* 3.5 3.5 + - - +
173A LYS* 3.1 22.5 + - - +
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Residues in contact with GLU 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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166A PRO* 3.2 18.3 - - + +
167A THR* 3.4 9.4 - - + +
169A ARG* 1.3 77.8 - - - +
171A PHE* 1.3 53.1 + - - +
173A LYS* 2.8 34.6 + - - +
174A GLU* 2.8 34.0 + - - +
222A LYS* 3.8 27.6 - - + -
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Residues in contact with PHE 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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150A PHE* 3.6 22.0 - + - -
167A THR 2.7 20.5 + - - +
168A TRP* 3.7 31.9 - + - +
170A GLU* 1.3 73.0 - - - +
172A ALA* 1.3 56.0 + - - +
174A GLU* 3.2 2.3 + - - +
175A VAL* 3.1 46.0 + - + +
179A LEU* 5.0 0.2 - - + -
181A ILE* 3.6 26.0 - - + -
222A LYS* 3.8 16.8 - - + +
225A LEU* 3.5 32.8 - - + -
226A VAL* 3.4 42.2 - - + -
229A ALA* 4.5 5.8 - - + -
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Residues in contact with ALA 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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130A GLU* 3.6 21.4 - - + +
131A ILE* 3.9 14.6 - - + -
168A TRP 3.3 17.0 + - - +
169A ARG 3.8 4.3 - - - +
170A GLU 3.2 0.8 - - - -
171A PHE* 1.3 76.4 - - - +
173A LYS* 1.3 64.6 - - - +
175A VAL* 4.0 1.1 - - - +
176A ASP* 3.3 19.8 + - - -
179A LEU 5.8 0.2 - - - +
181A ILE* 3.6 36.0 - - + +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.0 21.5 - - + +
169A ARG 3.1 13.1 + - - +
170A GLU* 2.8 38.0 + - - +
172A ALA* 1.3 76.3 - - - +
174A GLU* 1.3 63.4 + - - +
175A VAL 3.4 0.7 + - - -
176A ASP* 3.6 15.0 + - - +
337A LYS* 3.8 11.4 - - + +
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Residues in contact with GLU 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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170A GLU 2.8 11.3 + - - +
171A PHE* 3.2 9.8 + - - +
173A LYS* 1.3 78.6 - - - +
175A VAL* 1.3 57.1 + - + +
222A LYS* 3.9 29.5 + - + -
226A VAL* 4.1 22.2 - - + -
278A ARG* 2.4 57.5 + - - +
282A MET* 6.1 0.2 - - - +
337A LYS* 3.4 31.7 + - - +
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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
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171A PHE* 3.1 34.8 - - + +
172A ALA* 4.2 0.7 - - - -
174A GLU* 1.3 81.7 - - + +
176A ASP* 1.3 57.4 + - - +
177A GLY 3.0 0.2 + - - -
178A LEU* 2.7 51.9 + - + -
179A LEU* 3.3 34.2 + - + +
181A ILE* 4.0 25.6 - - + -
226A VAL* 4.2 16.2 - - + -
229A ALA* 5.7 0.2 - - + -
278A ARG* 4.4 4.5 - - - +
282A MET* 6.1 0.2 - - - -
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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
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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