Contacts of the helix formed by residues 165 - 183 (chain A) in PDB entry 3PJA
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASP* 2.8 11.8 + - - -
164A TYR* 1.3 77.1 - - - +
166A ARG* 1.3 68.9 + - - +
167A PRO 3.3 1.3 - - - -
168A LEU* 3.0 21.0 + - - +
169A HIS* 3.5 29.7 + - - -
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Residues in contact with ARG 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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54A ILE* 3.6 26.5 - - - +
107A TYR* 4.6 6.7 + - - -
108A LEU* 4.1 31.1 + - - +
111A GLU* 3.9 29.3 + - - +
154A LEU* 4.7 17.4 - - - +
158A SER* 3.5 15.9 - - - +
163A ASP* 3.0 29.1 + - - +
165A SER* 1.3 74.3 - - - +
167A PRO* 1.3 71.4 - - + +
169A HIS* 2.7 25.4 + - - +
170A ILE* 2.9 23.5 + - + +
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 3.5 25.8 - - - +
158A SER* 3.5 2.9 - - - +
159A VAL* 3.3 29.2 - - + -
163A ASP 3.3 15.5 - - - +
165A SER 3.3 4.7 - - - +
166A ARG* 1.3 94.1 - - + +
168A LEU* 1.3 57.8 + - + +
170A ILE* 3.6 3.1 + - + -
171A SER* 3.0 27.7 + - - -
205A VAL* 3.5 7.1 - - - +
208A VAL* 3.9 7.9 - - + -
209A VAL* 3.5 4.9 - - + +
212A LEU* 3.8 21.8 - - + -
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Residues in contact with LEU 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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164A TYR 2.9 29.4 - - - +
165A SER* 3.0 12.2 + - - +
166A ARG 2.8 4.0 + - - -
167A PRO* 1.3 72.1 - - - +
169A HIS* 1.3 70.0 + - + +
171A SER* 3.1 3.3 + - - -
172A THR* 3.0 26.6 + - - -
209A VAL* 3.9 25.4 - - + -
212A LEU* 4.4 11.4 - - + -
213A SER* 6.0 0.9 - - - +
217A PHE 5.4 3.6 - - - +
218A ASN* 4.1 31.2 - - + +
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Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.7 7.6 + - - +
111A GLU* 3.0 41.5 + - + +
165A SER* 3.8 27.8 + - - -
166A ARG* 2.7 14.1 + - - +
168A LEU* 1.3 78.3 - - + +
170A ILE* 1.3 56.3 + - - +
172A THR* 3.4 7.0 + - - -
173A PHE* 3.0 30.1 + - - +
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Residues in contact with ILE 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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107A TYR* 3.4 24.0 - - + +
151A LEU* 3.2 37.5 - - + +
154A LEU* 4.2 20.0 - - + -
155A SER* 3.6 20.2 - - - +
166A ARG* 2.9 27.6 + - + +
167A PRO* 3.8 4.9 - - + +
169A HIS* 1.3 72.5 - - + +
171A SER* 1.3 66.1 + - - +
173A PHE* 3.7 2.5 - - - +
174A ILE* 3.0 33.6 + - + +
205A VAL* 3.7 21.1 - - + -
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Residues in contact with SER 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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167A PRO 3.0 15.8 + - - -
168A LEU* 3.1 9.1 + - - -
170A ILE* 1.3 75.0 - - - +
172A THR* 1.3 68.6 + - - +
173A PHE 3.1 0.3 + - - -
174A ILE* 3.2 1.7 + - - +
175A ASN* 2.8 38.4 + - - +
205A VAL* 3.3 17.9 - - - +
206A GLU* 4.0 16.1 - - - +
209A VAL* 3.8 16.3 - - - +
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Residues in contact with THR 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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168A LEU 3.0 11.1 + - - -
169A HIS* 3.7 9.8 - - - -
171A SER* 1.3 78.7 + - - +
173A PHE* 1.3 58.4 + - - +
175A ASN* 3.2 7.7 + - - +
176A GLU* 3.0 49.2 + - + +
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Residues in contact with PHE 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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107A TYR* 3.5 35.7 - + + +
111A GLU 4.1 7.9 - - - +
112A THR* 3.8 4.9 - - - -
113A LEU* 3.7 43.3 - - + -
147A LEU* 4.3 10.5 - - + -
151A LEU* 3.8 21.1 - - + -
169A HIS 3.0 18.0 + - - +
170A ILE 3.7 3.6 - - - +
172A THR* 1.3 77.5 - - - +
174A ILE* 1.3 64.3 + - + +
176A GLU* 3.1 22.0 + - - +
177A LEU* 3.0 49.0 + - + +
3E VAL* 4.2 8.5 - - + +
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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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148A ALA* 3.6 39.5 - - + +
151A LEU* 4.1 5.8 - - + -
152A SER 4.2 1.1 - - - +
170A ILE* 3.0 25.5 + - + +
171A SER 4.1 2.2 - - - +
173A PHE* 1.3 88.9 - - + +
175A ASN* 1.3 59.1 + - - +
177A LEU* 3.3 9.4 + - + +
178A ASP* 3.0 24.6 + - - +
198A LEU* 4.5 8.6 - - + +
201A ASP* 4.5 5.4 - - + +
202A VAL* 3.7 36.6 - - + +
205A VAL* 3.9 24.2 - - + -
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Residues in contact with ASN 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 SER* 2.8 38.4 + - - +
172A THR* 3.4 10.5 - - - +
173A PHE 3.1 0.2 - - - -
174A ILE* 1.3 77.2 - - - +
176A GLU* 1.3 63.5 + - + +
178A ASP* 3.1 7.8 + - - +
179A SER* 3.0 25.5 + - - -
202A VAL* 4.0 7.6 + - - +
206A GLU* 3.2 29.1 + - - +
46C HIS* 5.8 4.2 - - - +
153C ARG* 3.2 15.1 + - - -
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Residues in contact with GLU 176 (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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172A THR* 3.0 34.0 + - + +
173A PHE* 3.4 19.1 - - - +
175A ASN* 1.3 75.5 - - + +
177A LEU* 1.3 62.1 + - - +
179A SER* 3.0 19.6 + - - -
180A GLY* 3.0 8.1 + - - -
3E VAL* 3.2 40.0 + - + +
4E SER* 5.9 0.2 - - - -
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Residues in contact with LEU 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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113A LEU* 3.8 28.9 - - + -
144A VAL* 4.0 26.7 - - + +
147A LEU* 5.2 1.8 - - + -
148A ALA* 4.2 26.5 - - + +
173A PHE* 3.0 41.6 + - + +
174A ILE* 3.4 12.8 - - + +
175A ASN 3.1 0.2 - - - -
176A GLU* 1.3 78.1 - - - +
178A ASP* 1.3 62.3 + - - +
180A GLY* 3.2 2.4 + - - -
181A PHE* 3.0 32.6 + - + -
198A LEU* 4.7 7.9 - - + -
3E VAL* 3.9 12.6 - - + -
7E PHE* 4.1 5.9 - - + -
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Residues in contact with ASP 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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174A ILE 3.0 13.6 + - - +
175A ASN* 3.1 10.7 + - - +
177A LEU* 1.3 76.8 - - - +
179A SER* 1.3 57.4 + - - +
181A PHE* 3.4 2.9 + - - +
182A ARG* 3.0 38.6 + - - +
195A TYR* 3.5 18.4 + - - -
198A LEU* 3.7 22.5 - - + +
199A LYS* 5.5 3.4 + - - +
202A VAL* 4.0 21.1 - - + +
153C ARG* 4.5 14.0 + - - -
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Residues in contact with SER 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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175A ASN 3.0 12.3 + - - -
176A GLU* 3.0 18.4 + - - -
178A ASP* 1.3 73.7 - - - +
180A GLY* 1.3 65.6 + - - +
182A ARG* 3.1 35.8 + - - +
183A LEU* 3.1 16.4 + - - +
40C THR* 6.2 2.0 - - - -
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Residues in contact with GLY 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 GLU 3.0 15.8 + - - -
177A LEU 3.2 2.7 + - - -
179A SER* 1.3 76.2 + - - +
181A PHE* 1.3 57.8 + - - +
183A LEU* 2.9 32.3 + - - +
184A LEU* 3.7 1.7 + - - +
3E VAL* 4.9 0.9 - - - -
4E SER* 5.6 2.7 - - - -
7E PHE* 3.1 39.3 - - - -
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Residues in contact with PHE 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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141A LEU* 3.9 38.8 - - + -
144A VAL* 4.3 12.6 - - + -
145A LEU* 3.6 41.5 - - + -
177A LEU* 3.0 24.7 + - + +
178A ASP 3.5 5.6 - - - +
180A GLY* 1.3 72.2 - - - +
182A ARG* 1.3 67.0 + - - +
183A LEU 3.0 1.3 - - - -
184A LEU* 2.9 27.5 + - + +
186A LEU* 4.2 20.9 - - + +
191A LEU* 5.5 1.3 - - + -
195A TYR* 3.5 35.3 + + + -
198A LEU* 4.1 11.0 - - + -
7E PHE* 3.5 20.8 - + - -
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Residues in contact with ARG 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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178A ASP* 3.0 27.4 + - - +
179A SER* 3.1 29.2 + - - +
181A PHE* 1.3 76.1 - - - +
183A LEU* 1.3 62.2 + - + +
184A LEU 3.2 1.6 + - - +
195A TYR* 4.6 8.2 + - - +
36C ARG* 3.2 50.1 + - + +
39C LEU* 3.6 18.3 - - + +
40C THR* 3.2 42.0 + - - +
43C GLN* 2.7 35.7 - - - +
153C ARG* 5.3 4.0 - - - +
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Residues in contact with LEU 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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179A SER 3.1 12.0 + - - +
180A GLY* 2.9 20.4 + - - +
182A ARG* 1.3 80.2 - - + +
184A LEU* 1.3 66.4 + - + +
185A ASN 4.0 0.7 + - - -
33C GLN* 5.4 0.9 - - - +
36C ARG* 4.8 6.0 + - - -
40C THR* 6.1 1.6 - - - +
4E SER* 4.6 8.7 - - - +
7E PHE* 4.4 6.1 - - + +
8E VAL* 3.6 39.3 - - + +
11E GLN* 3.4 32.6 + - - +
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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