Contacts of the helix formed by residues 194 - 213 (chain C) in PDB entry 3UDB
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 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLU* 4.4 4.0 - - - +
193C TYR* 1.3 77.7 - - - +
195C GLY* 1.3 63.5 + - - +
196C LYS* 2.8 24.9 + - - +
197C VAL* 3.5 24.3 + - + +
198C ALA* 3.2 24.4 + - - +
262C PRO* 6.1 3.6 - - + -
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ASP* 5.8 1.9 - - - +
193C TYR* 3.9 13.6 + - - -
194C ASP* 1.3 72.9 + - - +
196C LYS* 1.3 59.4 - - - +
197C VAL 3.4 0.4 - - - -
198C ALA* 3.9 9.9 - - - +
199C ASP* 3.1 33.4 + - - +
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Residues in contact with LYS 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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132C HIS* 3.2 72.3 + - + +
135C GLN* 4.3 14.5 + - - -
194C ASP* 2.8 15.2 + - - +
195C GLY* 1.3 78.2 - - - +
197C VAL* 1.3 67.5 + - + +
199C ASP* 3.5 14.4 + - - +
200C VAL* 3.5 10.9 + - - +
268C ILE* 5.2 0.5 - - - +
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C GLU* 3.8 4.3 - - - +
194C ASP* 3.5 24.7 + - + +
196C LYS* 1.3 75.9 - - + +
198C ALA* 1.3 67.1 + - - +
199C ASP 3.1 0.2 - - - -
200C VAL* 3.2 17.2 + - - +
201C TRP 3.3 4.5 + - - -
262C PRO* 3.8 31.6 - - + +
265C ARG* 3.1 41.6 + - + +
266C ILE 5.6 1.8 - - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ARG* 5.7 6.4 + - - +
182C TYR 5.2 1.4 - - - +
184C ALA* 4.3 12.9 - - + +
186C GLU* 3.6 15.1 + - - +
187C VAL* 4.6 3.1 - - + -
193C TYR* 4.2 15.9 - - + -
194C ASP 3.2 15.3 + - - +
195C GLY* 3.9 10.3 - - - +
196C LYS 3.3 0.2 - - - -
197C VAL* 1.3 81.0 - - - +
199C ASP* 1.3 63.4 + - - +
201C TRP* 3.4 5.7 + - - +
202C SER* 3.2 19.4 + - - -
265C ARG* 4.2 2.0 - - - +
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 4.7 5.8 - - + +
132C HIS* 3.0 29.1 + - + +
140C ASP* 5.2 7.9 - - - +
141C LEU* 5.0 13.0 - - - +
143C LEU* 3.8 16.9 - - + +
195C GLY 3.1 17.6 + - - +
196C LYS 3.5 10.8 - - - +
197C VAL 3.1 0.4 - - - -
198C ALA* 1.3 78.2 - - - +
200C VAL* 1.3 58.3 + - - +
202C SER* 3.1 10.0 + - - -
203C CYS* 2.8 32.3 + - - -
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LYS 3.5 12.7 + - - +
197C VAL* 3.2 11.5 + - - +
199C ASP* 1.3 72.8 - - - +
201C TRP* 1.3 67.3 + - - +
203C CYS* 2.9 11.0 + - + +
204C GLY 2.8 18.9 + - - -
257C ILE* 3.6 17.9 - - + +
265C ARG* 4.1 8.1 - - + -
266C ILE 3.7 25.4 - - - +
267C SER* 4.7 0.9 - - - -
268C ILE* 3.8 37.0 - - + +
271C ILE* 4.0 18.4 - - + -
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Residues in contact with TRP 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ALA 3.5 18.4 + - - -
182C TYR 3.6 16.6 - - - -
183C ILE 3.8 0.2 - - - -
184C ALA* 3.6 17.3 - - + +
185C PRO* 3.5 35.0 - - + -
197C VAL 3.3 3.2 + - - -
198C ALA 3.5 8.7 - - - +
199C ASP 3.2 0.6 - - - -
200C VAL* 1.3 78.8 - - - +
202C SER* 1.3 56.9 + - - +
204C GLY* 2.8 21.7 + - - -
205C VAL* 3.0 17.3 + - + +
217C PHE* 3.4 36.8 - + - -
233C ILE* 4.0 11.4 - - + -
236C VAL* 4.0 11.9 - - + -
257C ILE* 3.8 19.5 - - - -
258C PHE* 3.8 27.4 - + - -
259C VAL 4.0 8.3 - - - -
265C ARG* 3.8 28.0 - - - +
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Residues in contact with SER 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ARG* 4.6 6.9 + - - -
143C LEU* 4.0 20.5 - - - +
144C GLU* 5.0 2.3 + - - -
182C TYR* 3.3 34.1 + - - +
198C ALA 3.2 10.0 + - - -
199C ASP* 3.1 13.8 + - - -
201C TRP* 1.3 83.7 - - - +
203C CYS* 1.3 62.0 + - - +
205C VAL* 3.2 3.9 + - - +
206C THR* 3.1 28.5 + - - +
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Residues in contact with CYS 203 (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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121C PHE* 3.5 17.2 - - + -
124C LEU* 3.9 28.9 - - + -
125C ILE* 4.1 25.1 - - + -
128C VAL* 4.1 12.6 - - - -
143C LEU* 3.5 20.4 - - - -
199C ASP 2.8 20.2 + - - -
200C VAL* 2.9 11.4 + - + +
202C SER* 1.3 75.9 - - - +
204C GLY* 1.3 61.7 + - - +
206C THR* 3.4 3.0 + - - -
207C LEU 3.1 16.8 + - - -
257C ILE* 5.8 0.9 - - + -
268C ILE* 5.4 0.4 - - - -
271C ILE* 6.0 0.2 - - + -
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Residues in contact with GLY 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL 2.8 5.9 + - - -
201C TRP 2.8 9.7 + - - -
203C CYS* 1.3 74.7 - - - +
205C VAL* 1.3 59.8 + - - +
207C LEU* 3.1 7.1 + - - +
208C TYR* 2.9 28.4 + - - +
254C ILE* 5.8 2.0 - - - +
257C ILE* 3.7 30.2 - - - +
258C PHE* 3.6 10.5 - - - -
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Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ALA* 3.7 25.4 - - + +
182C TYR* 3.8 31.4 - - + -
201C TRP* 3.0 31.1 + - + +
202C SER 3.2 6.5 + - - +
204C GLY* 1.3 74.4 - - - +
206C THR* 1.3 59.1 + - - +
208C TYR* 3.3 3.0 + - - +
209C VAL* 3.0 31.2 + - + +
215C TYR* 4.6 0.9 - - + -
216C PRO* 3.6 26.7 - - + -
217C PHE* 4.7 0.4 - - + -
258C PHE* 3.7 14.8 - - + -
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Residues in contact with THR 206 (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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102C LEU* 4.6 16.1 - - - +
106C ILE* 5.0 0.2 - - - +
124C LEU* 3.6 21.7 - - + +
143C LEU* 3.4 21.0 + - + +
182C TYR* 3.4 26.0 - - + +
202C SER 3.1 18.5 + - - +
203C CYS* 3.4 3.8 + - - +
204C GLY 3.2 0.2 - - - -
205C VAL* 1.3 78.0 - - - +
207C LEU* 1.3 61.4 + - - +
209C VAL* 3.9 7.3 - - - +
210C MET* 3.0 31.1 + - - +
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Residues in contact with LEU 207 (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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117C ALA* 4.4 9.0 - - + -
121C PHE* 3.8 34.5 - - + -
203C CYS 3.1 13.1 + - - +
204C GLY* 3.1 9.2 + - - +
206C THR* 1.3 74.8 + - - +
208C TYR* 1.3 66.7 + - - +
210C MET* 3.4 7.9 + - + +
211C LEU* 3.1 43.5 + - + +
250C CYS* 5.4 1.8 - - - -
253C LEU* 4.2 17.0 - - + -
254C ILE* 4.2 20.6 - - + -
257C ILE* 4.9 5.2 - - + -
276C TRP* 3.7 24.5 - - + -
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLY 2.9 15.2 + - - +
205C VAL 3.6 5.2 - - - +
207C LEU* 1.3 78.4 - - - +
209C VAL* 1.3 57.6 + - - +
211C LEU* 2.9 8.7 + - - +
212C VAL* 2.8 62.2 + - + +
214C ALA 3.4 20.2 - - - -
215C TYR 3.7 2.6 + - - -
216C PRO* 3.2 46.3 + - + +
238C TYR* 4.2 21.3 - + + -
239C ALA 3.4 23.2 + - - -
240C ILE* 4.4 17.0 - - + -
241C PRO* 4.2 1.2 - - - +
254C ILE* 5.0 9.4 - - + +
258C PHE* 4.3 14.1 - + + -
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Residues in contact with VAL 209 (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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103C PHE* 4.4 19.7 - - + -
106C ILE* 3.7 27.0 - - + +
182C TYR* 4.8 3.1 - - - +
205C VAL* 3.0 23.5 + - + +
206C THR* 3.9 7.2 - - - +
208C TYR* 1.3 75.9 - - - +
210C MET* 1.3 59.5 + - - +
213C GLY* 2.8 28.5 + - - +
214C ALA 3.9 20.6 - - - +
215C TYR* 3.2 38.4 - - + -
216C PRO* 4.3 1.6 - - + -
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Residues in contact with MET 210 (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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102C LEU* 4.2 11.4 - - + -
106C ILE* 3.5 25.3 - - + +
111C ARG* 3.6 1.9 - - - -
112C PHE* 2.7 55.8 + - + +
117C ALA* 3.4 36.1 - - + +
120C PHE* 3.6 28.9 - - + -
121C PHE* 4.0 11.0 - - + +
124C LEU* 6.1 1.1 - - + -
206C THR* 3.0 29.6 + - - +
207C LEU* 3.7 12.6 - - + +
208C TYR 3.3 0.2 - - - -
209C VAL* 1.3 78.9 - - - +
211C LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 211 (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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111C ARG* 3.1 24.1 + - - +
112C PHE 4.2 5.3 - - - +
113C SER 4.5 1.1 - - - +
114C GLU* 3.9 24.2 - - + +
117C ALA* 3.7 21.8 - - + -
207C LEU* 3.1 35.9 + - + +
208C TYR* 2.9 5.4 + - - +
210C MET* 1.3 76.6 - - - +
212C VAL* 1.3 66.3 + - + +
244C VAL* 3.9 10.2 - - + +
246C ILE* 4.1 21.3 - - + -
250C CYS* 3.6 27.8 - - - -
254C ILE* 4.1 12.3 - - + -
276C TRP* 5.2 0.4 - - + -
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Residues in contact with VAL 212 (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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111C ARG* 3.8 14.9 - - - +
208C TYR* 2.8 48.5 + - + +
211C LEU* 1.3 87.2 - - + +
213C GLY* 1.3 58.3 + - - +
214C ALA* 3.9 13.5 - - + +
240C ILE* 3.9 28.3 - - + -
241C PRO* 4.0 24.9 - - + -
243C TYR* 5.3 4.8 + - - +
244C VAL* 4.5 6.0 - - + +
24D VAL 4.9 1.7 - - - +
25D LYS* 4.8 6.1 - - - +
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Residues in contact with GLY 213 (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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103C PHE* 5.9 2.5 - - - -
106C ILE* 4.5 6.9 - - - +
107C CYS* 5.5 2.6 - - - +
110C GLY 3.3 23.2 - - - +
111C ARG* 3.9 2.1 - - - +
209C VAL* 2.8 27.2 + - - -
212C VAL* 1.3 72.5 - - - +
214C ALA* 1.3 60.5 - - - +
25D LYS* 3.7 24.4 + - - +
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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
------------------------------------------------------------
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