Contacts of the helix formed by residues 181 - 196 (chain C) in PDB entry 2W4T
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 181 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLY 3.8 1.0 - - - -
180C ALA* 1.3 78.9 - - - +
182C LYS* 1.3 69.5 + - - +
183C THR* 3.3 3.1 - - - -
184C GLU* 4.1 13.9 - - - -
185C ASN* 2.4 44.5 + - - -
670C CYS* 4.4 2.5 - - - -
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 2.4 50.4 - - + +
175C THR* 3.9 19.3 - - - -
176C GLY 3.6 13.2 + - - +
177C GLU 4.3 6.5 + - - +
178C SER* 5.5 0.7 - - - +
180C ALA* 4.6 0.2 - - - +
181C GLY* 1.3 76.5 - - - +
183C THR* 1.3 58.4 + - + +
185C ASN* 3.9 0.2 - - - +
186C THR* 2.4 40.1 + - + +
460C ASP* 5.0 3.6 - - + -
461C ILE 2.2 41.2 + - - +
462C ALA* 4.8 1.3 - - - +
463C GLY* 2.6 40.9 - - - +
481C ASN* 3.7 1.2 - - - +
670C CYS* 4.0 6.9 - - - +
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Residues in contact with THR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLY* 4.9 1.4 - - - -
182C LYS* 1.3 77.3 - - + +
184C GLU* 1.3 86.6 + - - +
186C THR* 2.5 28.2 + - - -
187C LYS* 2.9 9.3 + - - +
227C GLU* 5.1 11.0 - - - +
239C ASN 5.6 4.2 + - - +
241C SER* 4.3 24.9 - - - +
245C LYS* 6.0 4.3 - - - -
460C ASP* 5.2 10.1 - - + +
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Residues in contact with GLU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLY* 3.5 15.0 + - - +
183C THR* 1.3 90.9 + - - +
185C ASN* 1.3 59.8 + - - +
187C LYS* 3.5 10.5 + - - +
188C LYS* 3.1 27.1 + - - +
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Residues in contact with ASN 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ALA* 4.2 19.8 - - - +
152C LEU* 3.0 32.4 - - + +
174C ILE* 5.1 8.9 - - + +
181C GLY* 2.4 39.1 + - - +
182C LYS* 3.9 4.2 - - - +
184C GLU* 1.3 77.4 - - - +
186C THR* 1.3 63.2 + - - +
188C LYS* 3.8 5.9 - - - +
189C VAL* 2.8 32.8 + - + +
668C VAL* 5.7 5.2 - - + +
670C CYS* 4.9 4.4 - - - +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 3.3 27.1 - - + -
182C LYS 2.4 32.5 - - - +
183C THR* 2.5 22.3 + - - -
185C ASN* 1.3 77.4 - - - +
187C LYS* 1.3 64.6 + - - +
189C VAL* 3.2 10.5 + - - +
190C ILE* 2.8 26.0 + - - +
245C LYS* 5.9 1.9 + - - -
247C ILE* 5.4 2.2 - - - -
458C VAL* 3.9 19.3 - - + +
460C ASP* 3.6 23.4 - - + +
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Residues in contact with LYS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C THR 2.9 7.2 + - - +
184C GLU* 3.6 16.8 - - - +
186C THR* 1.3 84.7 + - - +
188C LYS* 1.3 54.4 + - - +
190C ILE* 2.8 9.5 - - + +
191C MET* 2.6 68.6 + - + +
220C ILE* 3.5 15.0 + - - +
223C ASN* 3.1 43.3 - - + +
224C PRO* 4.9 2.0 - - - +
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Residues in contact with LYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TYR* 4.4 1.8 + - - -
129C LEU* 5.6 0.6 - - - +
131C ILE* 3.8 13.3 + - - +
132C TYR* 3.3 24.7 - - + +
151C HIS* 2.9 28.5 + - + -
152C LEU* 4.9 16.2 - - + +
153C PHE* 2.6 36.6 - - + -
184C GLU 3.1 17.5 + - - +
185C ASN* 3.8 9.9 - - - +
186C THR 3.3 0.4 - - - -
187C LYS* 1.3 77.1 - - - +
189C VAL* 1.3 57.6 + - + +
191C MET* 3.8 9.0 - - + +
192C TYR* 2.9 26.7 + - - +
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LEU* 4.9 20.4 - - + +
156C ALA* 4.0 22.9 - - + -
172C CYS* 4.7 12.3 - - + -
174C ILE* 5.6 3.4 - - + -
185C ASN 2.8 24.2 - - - +
186C THR* 3.4 9.9 - - - +
187C LYS 3.1 0.6 - - - -
188C LYS* 1.3 74.8 - - + +
190C ILE* 1.3 59.9 + - + +
192C TYR* 2.5 43.7 - - + -
193C LEU* 2.8 1.5 + - + +
456C ILE* 5.9 4.9 - - + -
458C VAL* 4.3 19.5 - - + -
668C VAL* 6.0 3.1 - - + -
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C THR 2.8 20.2 - - - +
187C LYS* 2.8 16.6 - - + +
189C VAL* 1.3 72.1 - - + +
191C MET* 1.3 101.5 + - + +
192C TYR 3.0 0.9 - - - -
193C LEU* 3.2 7.5 + - - +
194C ALA* 2.7 27.4 + - + +
219C ILE* 2.6 40.2 - - + -
220C ILE* 4.3 2.7 - - - -
223C ASN* 4.7 6.5 - - - +
247C ILE* 4.6 24.2 - - + -
249C ILE* 5.7 8.5 - - + -
458C VAL* 4.9 5.8 - - + -
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Residues in contact with MET 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE* 6.4 0.2 - - + -
187C LYS* 2.6 65.9 + - + +
188C LYS* 3.8 9.4 - - + +
190C ILE* 1.3 94.6 - - + +
192C TYR* 1.3 62.3 + - - +
194C ALA* 3.6 4.9 - - - +
195C LYS* 3.1 22.9 + - - +
220C ILE* 4.0 22.7 - - + -
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Residues in contact with TYR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ILE* 6.2 1.1 - - - -
140C TYR* 3.1 27.8 - + + -
153C PHE* 3.5 27.3 - + + -
156C ALA* 2.1 63.7 + - + +
157C ASP 3.0 3.8 - - - -
159C ALA* 5.4 0.5 - - - +
160C TYR* 3.9 14.8 + - + +
188C LYS 2.9 19.2 + - - +
189C VAL* 2.5 14.8 - - + -
191C MET* 1.3 72.5 - - - +
193C LEU* 1.3 138.5 + - + +
194C ALA 3.0 1.1 - - - -
195C LYS* 2.9 23.9 + - - +
196C VAL* 3.3 17.2 + - + +
456C ILE* 5.7 4.7 - - + +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TYR* 5.5 1.1 - - + -
189C VAL* 2.8 9.2 + - + +
190C ILE* 3.9 6.5 - - - +
192C TYR* 1.3 137.3 - - + +
194C ALA* 1.3 61.0 + - - +
196C VAL* 3.7 16.5 + - + +
249C ILE* 2.5 50.0 - - + -
251C PHE* 2.8 15.4 - - + -
257C ILE* 3.4 29.5 - - + +
456C ILE* 3.3 9.4 - - + -
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE 2.7 23.1 + - - +
191C MET* 3.6 8.3 - - - +
193C LEU* 1.3 79.6 - - + +
195C LYS* 1.3 61.3 + - - +
196C VAL 3.5 2.1 + - - -
216C GLU* 4.6 21.0 - - + +
219C ILE* 4.5 21.3 - - + -
220C ILE* 4.8 4.7 - - + -
256C LYS* 5.8 1.0 + - - -
257C ILE* 4.7 13.2 - - - +
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ASP* 3.0 29.5 - - + +
137C ILE* 3.0 49.0 - - + +
141C ARG* 4.5 4.7 + - - -
191C MET 3.1 13.9 + - - +
192C TYR* 2.9 11.7 + - - +
194C ALA* 1.3 76.7 - - - +
196C VAL* 1.3 58.9 + - + +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ILE* 3.8 23.6 - - + -
140C TYR* 3.8 27.6 - - + +
141C ARG* 2.4 52.8 + - + +
157C ASP* 5.7 0.2 - - - +
160C TYR* 5.8 12.6 + - + -
192C TYR* 3.5 17.0 - - + +
193C LEU* 3.9 18.8 - - + +
194C ALA 3.3 4.2 - - - -
195C LYS* 1.3 85.8 - - + +
251C PHE* 6.5 1.1 - - - -
255C GLY 5.4 4.5 - - - +
256C LYS* 6.0 7.6 - - - -
257C ILE* 5.9 3.8 - - - -
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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
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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