Contacts of the helix formed by residues 170 - 186 (chain A) in PDB entry 4WLE
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 THR 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A VAL* 4.9 1.1 - - + -
168A GLY 3.0 12.6 + - - +
169A VAL* 1.3 74.3 - - - +
171A THR* 1.3 64.1 + - - +
172A LEU* 3.2 3.6 - - - -
173A ASP* 2.9 33.7 + - - +
174A ILE* 3.5 9.6 - - - +
196A VAL* 5.9 0.9 - - - -
199A GLY 4.7 5.6 - - - +
200A HIS* 4.2 24.2 - - + -
275A CYS 3.4 20.3 + - - -
276A SER* 3.6 1.7 - - - -
277A PHE* 3.9 20.6 - - + +
289A SER* 3.5 18.8 + - - +
401A CIT 6.2 0.2 - - - -
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.4 8.9 - - - +
170A THR* 1.3 78.2 + - - +
172A LEU* 1.3 58.2 + - - +
174A ILE* 3.1 12.8 + - + +
175A VAL* 2.9 26.0 + - + +
254A ALA* 3.5 30.5 - - + +
257A ARG* 3.9 34.3 - - + +
258A PHE* 3.4 31.0 - - - +
274A GLU* 4.5 5.9 + - - +
275A CYS 4.4 5.2 + - - -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR 3.1 1.4 + - - -
171A THR* 1.3 77.6 - - - +
173A ASP* 1.3 57.0 + - - +
175A VAL* 4.2 11.4 - - + -
176A ARG* 2.9 79.4 + - + +
200A HIS* 5.3 0.2 - - + -
247A ALA* 4.2 2.9 - - + -
250A SER* 3.5 42.2 - - - +
251A MET* 3.9 31.4 - - + +
254A ALA* 3.5 14.9 - - + +
401A CIT 3.8 15.9 - - - +
70B HIS* 5.0 1.1 - - + -
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 2.9 19.6 + - - +
172A LEU* 1.3 76.6 - - - +
174A ILE* 1.3 57.4 + - + +
176A ARG* 3.7 14.7 + - - +
177A ALA* 3.0 28.2 + - - +
196A VAL* 3.8 23.1 - - + +
199A GLY 4.0 6.1 - - - +
200A HIS* 2.8 40.6 + - - -
205A ILE* 3.8 30.2 - - + +
230A ILE* 4.1 7.9 - - + +
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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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170A THR* 3.5 24.2 - - - +
171A THR* 3.1 11.7 + - + +
173A ASP* 1.3 74.1 - - + +
175A VAL* 1.3 62.6 + - - +
177A ALA* 3.3 1.2 + - - +
178A ASN* 2.9 50.8 + - - +
193A ASN* 5.8 1.6 - - - +
194A VAL 3.6 24.2 - - - +
196A VAL* 3.8 27.4 - - + +
257A ARG* 4.0 20.9 - - - +
274A GLU* 5.5 1.8 - - - +
275A CYS* 3.7 31.6 - - + +
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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
----------------------------------------------------------
171A THR* 2.9 34.1 + - + +
172A LEU* 3.7 15.0 - - + +
174A ILE* 1.3 76.3 - - - +
176A ARG* 1.3 61.1 + - - +
178A ASN* 3.4 2.4 + - - +
179A THR* 3.0 26.5 + - - -
253A TYR* 3.8 20.0 - - + -
254A ALA* 4.3 3.1 - - + -
257A ARG* 4.1 3.4 - - - +
70B HIS 3.4 17.9 - - - +
71B ILE* 3.9 5.4 - - + -
72B GLU* 3.6 46.3 - - + +
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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
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110A ARG* 4.6 0.8 - - - +
172A LEU* 2.9 47.0 + - + +
173A ASP* 3.7 19.3 + - - +
175A VAL* 1.3 76.6 - - - +
177A ALA* 1.3 57.4 + - - +
179A THR* 3.1 3.6 + - - -
180A PHE* 2.8 47.7 + - + -
200A HIS* 4.4 1.0 - - - -
205A ILE* 6.0 0.4 - - - +
230A ILE* 5.0 7.0 + - + -
233A ALA* 3.5 15.6 + - + +
234A GLY* 3.5 25.9 - - - +
237A VAL* 4.3 1.8 - - - +
247A ALA* 3.9 10.1 - - - +
250A SER* 4.8 0.4 + - - -
401A CIT 2.7 42.4 + - - -
70B HIS* 3.2 43.6 + - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 3.0 18.7 + - - +
174A ILE 3.3 4.7 + - - +
176A ARG* 1.3 75.3 - - - +
178A ASN* 1.3 62.5 + - - +
180A PHE* 4.1 0.6 - - - +
181A VAL* 3.0 30.8 + - - +
194A VAL* 3.7 27.4 - - + -
196A VAL* 4.0 8.1 - - + -
230A ILE* 3.8 30.2 - - + +
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Residues in contact with ASN 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* 2.9 34.1 + - - +
175A VAL 3.6 5.4 - - - +
177A ALA* 1.3 74.5 - - - +
179A THR* 1.3 63.1 + - - +
181A VAL* 4.0 1.2 - - - +
182A ALA* 3.0 26.6 + - - +
189A PRO* 4.3 9.4 - - - +
192A VAL* 3.2 33.2 + - + +
193A ASN* 3.4 6.7 + - - +
194A VAL* 2.7 30.7 + - - +
257A ARG* 3.9 4.4 - - - +
72B GLU* 2.9 27.9 + - + +
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Residues in contact with THR 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 VAL 3.0 8.3 + - - -
176A ARG* 3.1 7.8 + - - -
178A ASN* 1.3 76.1 - - - +
180A PHE* 1.3 63.8 + - + +
182A ALA* 3.3 6.3 + - - +
183A GLU* 2.9 52.3 + - + +
189A PRO* 4.5 7.2 - - + -
45B LYS* 6.0 0.2 - - - +
69B SER 3.5 24.9 - - - +
70B HIS* 2.8 22.6 + - - +
71B ILE 4.2 4.9 - - - +
72B GLU* 3.2 17.3 + - - +
73B THR 5.7 1.6 - - - +
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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
----------------------------------------------------------
176A ARG* 2.8 37.4 + - + +
177A ALA 4.1 1.6 - - - +
179A THR* 1.3 76.6 - - + +
181A VAL* 1.3 66.0 + - - +
183A GLU* 3.4 20.6 + - - +
184A LEU* 3.0 28.1 + - - +
226A LEU* 3.5 18.6 - - + -
229A ARG* 3.6 62.6 - - + +
230A ILE* 3.8 18.4 - - + -
233A ALA* 4.1 3.8 - - + -
69B SER 5.2 0.7 - - - -
70B HIS* 3.6 38.8 - + - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA 3.0 22.4 + - - +
178A ASN 4.0 2.7 - - - +
180A PHE* 1.3 75.8 - - - +
182A ALA* 1.3 64.5 + - - +
184A LEU* 3.2 3.3 + - - +
185A LYS* 3.0 23.6 + - - +
187A LEU* 4.7 4.0 - - + -
192A VAL* 4.0 18.4 - - + -
194A VAL* 3.8 15.5 - - + -
209A ILE* 4.0 10.8 - - + -
212A CYS* 4.2 2.7 - - - -
216A VAL* 4.1 31.9 - - + -
218A PHE* 4.2 11.2 - - + -
226A LEU* 3.9 24.7 - - + -
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Residues in contact with ALA 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 ASN 3.0 18.9 + - - +
179A THR 3.5 4.0 - - - +
181A VAL* 1.3 78.1 - - - +
183A GLU* 1.3 53.9 + - + +
186A GLY* 2.8 30.7 + - - -
187A LEU* 2.8 39.3 + - - +
189A PRO* 3.6 24.9 - - + -
192A VAL* 4.1 5.8 - - + -
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Residues in contact with GLU 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 THR* 2.9 35.7 + - + +
180A PHE* 3.8 25.0 - - - +
182A ALA* 1.3 79.0 - - + +
184A LEU* 1.3 62.3 + - + +
185A LYS 3.5 0.2 + - - -
186A GLY* 3.7 6.9 + - - -
229A ARG* 5.0 5.0 + - - -
69B SER* 4.1 8.5 - - - +
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Residues in contact with LEU 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 13.6 + - - +
181A VAL 3.7 1.6 - - - +
183A GLU* 1.3 78.3 - - + +
185A LYS* 1.3 61.1 + - - +
186A GLY 3.5 0.2 - - - -
218A PHE* 3.6 30.0 - - + -
222A GLN* 4.3 32.1 - - + +
226A LEU* 4.0 38.8 - - + -
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Residues in contact with LYS 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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181A VAL 3.0 11.1 + - - +
184A LEU* 1.3 77.2 - - - +
186A GLY* 1.3 63.4 + - - +
187A LEU* 3.6 24.3 - - + +
216A VAL* 3.9 18.4 - - + +
217A ASP* 2.8 41.1 + - - +
218A PHE* 3.6 33.5 - - + +
219A PRO* 5.5 1.8 - - - +
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Residues in contact with GLY 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 ALA 2.8 10.1 + - - -
183A GLU* 3.7 6.0 + - - -
184A LEU 3.5 2.2 - - - -
185A LYS* 1.3 79.8 - - - +
187A LEU* 1.3 60.9 + - - +
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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