Contacts of the helix formed by residues 174 - 190 (chain A) in PDB entry 3SJN
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 ASP 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL 5.1 0.4 + - - -
172A GLY 3.5 0.4 - - - -
173A ASP* 1.3 89.0 - - + +
175A PRO* 1.3 64.9 - - - +
176A ASP* 4.2 3.6 + - + +
177A THR* 2.8 34.9 + - - +
178A ASP* 2.6 41.1 + - - +
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Residues in contact with PRO 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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173A ASP 4.1 5.2 - - - +
174A ASP* 1.3 86.7 - - + +
176A ASP* 1.3 63.0 + - - +
178A ASP* 4.3 1.6 - - + +
179A TYR* 3.1 26.2 + - - +
208A HIS* 3.7 26.7 - - + +
212A MET* 3.7 29.8 - - - +
215A ARG* 6.3 1.6 - - - -
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Residues in contact with ASP 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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174A ASP* 3.1 3.9 + - + +
175A PRO* 1.3 81.1 - - - +
177A THR* 1.3 63.4 + - - +
179A TYR* 3.5 6.8 + - - +
180A ALA* 3.1 28.1 + - - +
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Residues in contact with THR 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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144A ASP 4.7 9.2 - - - +
146A PRO* 5.5 4.5 - - + -
170A VAL* 5.5 10.5 - - + +
173A ASP* 6.2 0.7 - - + -
174A ASP* 2.8 34.3 + - - +
176A ASP* 1.3 75.8 - - - +
178A ASP* 1.3 65.0 + - - +
180A ALA* 3.5 4.2 + - - +
181A ILE* 3.2 41.4 + - + +
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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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170A VAL 4.4 1.9 - - - +
171A MET* 3.8 20.0 - - + +
172A GLY* 2.8 38.1 + - - +
173A ASP 3.8 1.4 + - - -
174A ASP 2.6 24.3 + - - +
175A PRO* 4.5 0.9 - - - +
177A THR* 1.3 73.7 - - - +
179A TYR* 1.3 60.9 + - - +
181A ILE* 3.5 3.3 + - - +
182A VAL* 3.2 30.5 + - - +
203A TRP* 3.0 28.4 + - + -
208A HIS* 5.1 0.5 - - - -
212A MET* 3.6 20.6 - - + +
216A LEU* 4.7 2.5 - - + -
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Residues in contact with TYR 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 PRO 3.1 16.5 + - - +
176A ASP* 3.7 8.7 - - - +
177A THR 3.3 0.2 - - - -
178A ASP* 1.3 81.3 - - - +
180A ALA* 1.3 58.9 + - + +
182A VAL* 3.5 1.7 + - - +
183A LYS* 2.9 60.4 + - - +
212A MET* 4.5 1.7 - - + +
215A ARG* 3.3 33.0 - - + -
216A LEU* 3.8 22.7 - - + -
218A GLU* 2.9 26.1 + - - -
219A PHE* 3.6 15.4 - + - -
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Residues in contact with ALA 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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146A PRO* 3.4 31.9 - - + +
176A ASP 3.1 16.7 + - - +
177A THR* 4.0 5.4 - - - +
178A ASP 3.3 0.4 - - - -
179A TYR* 1.3 78.6 - - + +
181A ILE* 1.3 60.0 + - - +
183A LYS* 3.5 9.1 - - - +
184A ALA* 3.2 21.1 + - - +
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Residues in contact with ILE 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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142A PRO* 3.9 19.5 - - + -
143A ALA 4.2 14.6 - - - +
144A ASP* 4.2 10.1 - - - +
146A PRO* 4.0 26.2 - - + +
149A ASN* 3.8 17.9 - - - +
166A PHE* 4.0 16.2 - - + -
170A VAL* 5.3 10.3 - - + +
171A MET* 4.4 14.1 - - - -
177A THR* 3.2 29.7 + - + +
178A ASP* 4.1 4.3 - - - +
180A ALA* 1.3 73.0 - - - +
182A VAL* 1.3 64.8 + - - +
184A ALA* 3.4 2.1 + - - +
185A VAL* 3.3 25.6 + - + +
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Residues in contact with VAL 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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166A PHE* 3.7 19.5 - - + -
171A MET* 3.9 13.9 - - + -
178A ASP 3.2 17.9 + - - +
179A TYR 4.0 0.4 - - - +
181A ILE* 1.3 71.7 - - - +
183A LYS* 1.3 66.7 + - - +
185A VAL* 3.3 18.1 - - + +
186A ARG* 3.3 11.1 + - + +
197A ILE* 4.2 7.6 - - + -
216A LEU* 3.8 24.9 - - + -
219A PHE* 3.7 29.7 - - + -
221A LEU* 4.4 19.3 - - + -
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Residues in contact with LYS 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 TYR* 2.9 50.7 + - - +
180A ALA* 3.5 11.4 - - - +
182A VAL* 1.3 78.4 - - - +
184A ALA* 1.3 60.7 + - + +
185A VAL 3.1 5.1 + - - -
186A ARG* 4.0 1.4 - - - +
187A GLU* 3.2 51.8 + - - +
218A GLU* 5.1 2.4 + - - -
219A PHE* 3.7 24.6 - - + -
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Residues in contact with ALA 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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146A PRO* 3.3 31.2 - - + +
147A GLU* 4.1 16.2 - - + -
150A VAL* 3.8 12.0 + - + +
180A ALA 3.2 14.0 + - - +
181A ILE 3.4 3.1 + - - +
183A LYS* 1.3 78.7 - - + +
185A VAL* 1.3 59.4 + - - +
187A GLU* 4.1 9.9 - - - +
188A ALA* 3.3 24.2 + - - +
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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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140A PHE* 4.1 13.2 - - + -
149A ASN* 3.8 28.9 - - + -
153A VAL* 3.9 21.9 - - + +
164A ILE* 5.0 3.4 - - + +
166A PHE* 3.4 33.0 - - + -
181A ILE* 3.4 16.6 - - + +
182A VAL* 3.3 13.7 - - + +
184A ALA* 1.3 78.1 - - - +
186A ARG* 1.3 62.9 + - + +
187A GLU 3.4 0.4 - - - -
188A ALA* 3.5 1.8 + - - +
189A ALA* 3.0 30.1 + - - +
195A VAL* 4.4 8.0 - - + +
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Residues in contact with ARG 186 (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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182A VAL 3.3 14.4 + - - +
183A LYS 4.1 0.2 - - - +
185A VAL* 1.3 79.1 - - + +
187A GLU* 1.3 61.8 + - + +
189A ALA* 4.5 2.5 - - - -
190A GLY* 2.8 49.4 + - - +
191A PRO* 3.7 17.9 + - - +
193A MET 3.0 28.5 + - - -
194A GLU* 4.8 0.4 - - - +
195A VAL* 3.6 30.1 - - + +
219A PHE* 2.8 45.7 + - + +
220A ASN* 3.0 33.0 + - - +
221A LEU* 5.9 0.6 - - + +
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Residues in contact with GLU 187 (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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183A LYS* 3.2 47.5 + - + +
184A ALA* 4.1 7.4 - - - +
186A ARG* 1.3 77.6 - - + +
188A ALA* 1.3 62.0 + - - +
189A ALA 3.5 0.5 + - - -
190A GLY* 3.8 7.6 + - - -
219A PHE* 5.5 3.6 - - + -
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Residues in contact with ALA 188 (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 VAL* 3.8 34.7 - - + +
153A VAL* 3.8 19.5 - - + +
154A GLN* 4.8 9.8 + - - +
157A LYS* 4.3 8.1 - - - +
184A ALA 3.3 20.9 + - - +
185A VAL 3.5 5.7 + - - +
186A ARG 3.3 0.2 - - - -
187A GLU* 1.3 79.5 - - - +
189A ALA* 1.3 59.2 + - - +
190A GLY 3.6 0.2 - - - -
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Residues in contact with ALA 189 (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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153A VAL* 3.9 8.7 - - + -
157A LYS* 3.3 23.7 - - - +
164A ILE* 4.7 1.3 - - + -
185A VAL 3.0 17.5 + - - +
186A ARG 3.3 2.9 + - - +
188A ALA* 1.3 79.0 - - - +
190A GLY* 1.3 62.3 + - - +
192A GLU* 5.9 0.3 - - - +
193A MET* 3.5 42.7 + - + +
195A VAL* 4.4 9.4 - - + -
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Residues in contact with GLY 190 (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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186A ARG* 2.8 38.0 + - - -
187A GLU* 3.8 6.0 + - - -
188A ALA 3.6 1.6 - - - -
189A ALA* 1.3 83.8 - - - +
191A PRO* 1.3 70.5 - - - +
192A GLU* 3.4 3.0 + - - -
193A MET 4.0 2.6 + - - -
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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