Contacts of the helix formed by residues 185 - 204 (chain C) in PDB entry 6DWM
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 ASN 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C PHE* 1.3 75.2 - - - +
186C PRO* 1.3 72.6 - - - +
187C TYR* 3.1 19.3 + - - +
188C ARG* 3.2 27.1 + - + +
189C TYR* 3.2 18.2 - - + -
500C HIS* 6.2 0.3 - - - -
502C CYS* 3.8 24.1 - - - +
503C CYS 3.3 16.1 + - - +
504C GLU* 3.9 21.7 + - + +
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Residues in contact with PRO 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 5.7 0.4 - - + -
184C PHE* 3.7 22.8 - - + +
185C ASN* 1.3 88.4 - - - +
187C TYR* 1.3 52.9 + - - +
189C TYR* 3.1 4.8 + - + +
190C VAL* 2.7 40.8 + - + +
327C SER* 5.4 6.7 - - - +
330C LEU* 4.0 26.0 - - + -
331C MET* 5.7 1.3 - - - -
480C PHE* 6.1 0.2 - - + -
500C HIS* 6.1 3.1 - - + -
503C CYS* 3.4 4.5 - - + +
506C PHE* 3.4 48.0 - - + -
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Residues in contact with TYR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASN* 3.1 13.1 + - - +
186C PRO* 1.3 80.2 - - - +
188C ARG* 1.3 63.7 + - - +
190C VAL* 4.4 5.8 - - - +
191C VAL* 3.1 38.1 + - + +
218C VAL 3.8 12.7 + - - -
219C ASN* 3.3 30.7 - - - -
222C ASN* 5.7 3.1 - - - +
319C PHE* 5.0 1.9 - - - -
320C ASP* 4.4 13.6 + - - -
323C THR* 3.5 30.6 - - + +
324C THR* 5.0 8.6 + - - -
327C SER* 4.2 24.1 + - - +
499C LYS* 5.0 18.7 - - + +
500C HIS* 5.3 7.4 - + + -
502C CYS* 6.3 1.8 - - + -
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Residues in contact with ARG 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASN* 3.2 28.7 + - + +
186C PRO 3.2 0.6 - - - -
187C TYR* 1.3 80.0 - - - +
189C TYR* 1.3 94.0 + - + +
191C VAL* 3.4 13.3 - - - +
192C VAL* 3.9 4.7 - - - +
209C HIS 2.7 21.4 + - - -
210C ASN* 3.0 27.5 + - - +
215C LEU* 3.4 30.9 - - - +
219C ASN* 3.7 25.8 - - - +
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Residues in contact with TYR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 3.8 10.5 - - + +
173C THR* 4.0 12.6 - - + -
174C LEU* 4.6 11.2 - - + -
177C LEU* 3.4 44.6 - - + +
184C PHE* 4.1 8.7 - + + -
185C ASN* 3.2 21.3 - - + -
186C PRO 3.1 3.4 + - - +
188C ARG* 1.3 122.5 + - + +
190C VAL* 1.3 63.1 + - + +
191C VAL 3.3 1.6 - - - -
192C VAL* 3.5 2.7 + - - +
193C SER* 3.4 9.7 + - - -
209C HIS* 3.1 44.9 - - + +
210C ASN* 5.4 4.5 - - - -
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 4.5 21.1 - - + -
174C LEU* 6.4 1.3 - - + -
186C PRO* 2.7 28.5 + - + +
187C TYR* 4.4 2.9 - - - +
189C TYR* 1.3 69.7 - - - +
191C VAL* 1.3 66.6 + - - +
192C VAL 3.1 0.4 - - - -
193C SER* 3.2 6.3 + - - +
194C VAL* 2.9 39.2 + - + +
323C THR* 4.3 13.7 - - + +
326C ILE* 4.0 23.1 - - + -
327C SER* 5.0 3.4 - - - +
330C LEU* 4.0 25.1 - - + -
474C LEU* 6.2 0.9 - - + -
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Residues in contact with VAL 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TYR* 3.1 28.7 + - + +
188C ARG 3.4 13.7 - - - +
190C VAL* 1.3 76.3 - - - +
192C VAL* 1.3 63.3 + - + +
195C THR* 2.5 37.2 + - - -
218C VAL* 3.7 35.0 - - + +
219C ASN* 4.3 18.4 - - + -
319C PHE* 4.1 9.0 - - + -
323C THR* 3.6 30.4 + - + +
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Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ARG 3.9 11.0 - - - +
189C TYR 3.5 7.3 + - - +
190C VAL 3.1 0.8 - - - -
191C VAL* 1.3 78.0 - - + +
193C SER* 1.3 58.7 + - - +
195C THR* 3.2 4.4 + - - -
196C ASN* 2.9 44.7 + - - +
207C TYR 4.3 1.3 - - - +
208C ASP 4.0 8.1 - - - +
209C HIS* 3.9 36.6 - - + +
214C LEU* 4.0 19.7 - - + -
215C LEU* 3.6 31.4 - - + -
218C VAL* 5.3 0.7 - - + -
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Residues in contact with SER 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU* 3.7 20.2 + - - +
170C LEU* 3.5 22.7 - - - +
189C TYR 3.4 2.3 + - - -
190C VAL* 3.2 7.0 + - - -
192C VAL* 1.3 80.2 - - - +
194C VAL* 1.3 62.6 + - - +
196C ASN* 3.3 10.4 + - - +
197C VAL* 3.4 17.8 + - - +
209C HIS* 3.3 26.1 + - - -
470C PHE* 4.2 22.0 - - - -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C VAL* 2.9 26.7 + - + +
193C SER* 1.3 76.1 - - - +
195C THR* 1.3 62.7 + - - +
197C VAL* 3.3 12.5 + - - +
198C ILE* 3.4 12.1 + - - +
318C GLY 3.9 9.4 - - - +
319C PHE* 4.0 2.2 - - - +
322C VAL* 3.7 28.5 - - + -
323C THR* 3.4 25.1 - - - +
326C ILE* 3.5 30.3 - - + -
466C GLU* 3.7 9.8 - - - +
470C PHE* 4.3 9.4 - - + -
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 2.5 26.9 + - - +
192C VAL* 3.2 6.5 + - - -
194C VAL* 1.3 78.1 - - - +
196C ASN* 1.3 52.1 + - - +
198C ILE* 3.3 8.0 - - - +
199C CYS* 2.6 43.2 + - + +
207C TYR* 6.1 0.2 - - + -
214C LEU* 3.8 25.1 - - + -
218C VAL* 4.1 4.7 - - + +
315C PHE* 3.7 31.0 - - + -
319C PHE* 3.4 23.2 - - + +
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Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU* 3.1 42.7 + - - +
192C VAL* 2.9 30.2 + - - +
193C SER* 3.6 1.3 - - - +
194C VAL 3.3 0.4 - - - -
195C THR* 1.3 75.3 - - - +
197C VAL* 1.3 57.8 + - - +
199C CYS* 4.1 4.8 - - - +
200C ALA* 2.9 30.8 + - - +
205C ARG 4.1 2.6 - - - +
206C ARG* 3.7 10.0 - - + +
207C TYR* 3.0 52.1 + - - +
209C HIS* 5.2 2.0 - - - -
214C LEU* 4.6 2.6 - - - +
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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
----------------------------------------------------------
159C LEU* 3.9 15.0 - - + -
162C HIS* 4.1 14.9 - - + +
163C VAL* 3.9 24.2 - - + -
166C GLU* 3.8 15.0 - - + -
193C SER 3.4 15.3 - - - +
194C VAL 3.3 2.0 + - - +
195C THR 3.1 0.4 - - - -
196C ASN* 1.3 79.0 - - - +
198C ILE* 1.3 62.9 + - - +
200C ALA* 3.4 2.8 + - - +
201C ILE* 3.2 29.1 + - + +
466C GLU* 3.3 33.4 - - - +
470C PHE* 4.0 13.7 - - + -
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Residues in contact with ILE 198 (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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142C LEU* 4.8 4.0 - - + -
194C VAL 3.4 10.0 + - - +
195C THR* 3.3 15.5 - - - +
197C VAL* 1.3 80.9 - - + +
199C CYS* 1.3 60.2 + - - +
200C ALA 3.3 0.2 - - - -
201C ILE* 3.4 18.8 + - + -
202C CYS* 3.1 42.9 + - - -
314C LEU 3.9 15.5 - - - +
315C PHE* 4.2 12.7 - - + -
318C GLY* 4.0 9.9 - - - -
319C PHE* 3.9 20.9 - - + +
462C ILE* 6.1 2.2 - - + -
466C GLU* 5.6 3.4 - - - +
601C HEM 3.9 26.9 - - + -
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Residues in contact with CYS 199 (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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195C THR* 2.6 30.3 + - + +
196C ASN* 4.0 4.9 - - - +
198C ILE* 1.3 72.5 - - - +
200C ALA* 1.3 60.0 + - - +
203C PHE* 2.8 48.9 + - - +
204C GLY 3.3 4.0 + - - -
205C ARG* 3.6 17.6 - - - +
207C TYR* 3.9 26.0 - - + -
214C LEU* 5.9 0.4 - - - -
261C PHE* 5.1 2.9 - - - -
265C MET* 5.2 0.4 - - - -
315C PHE* 4.1 18.8 - - + -
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Residues in contact with ALA 200 (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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162C HIS* 3.5 35.9 + - + +
196C ASN 2.9 18.8 + - - +
197C VAL 3.7 2.0 - - - +
198C ILE 3.3 0.2 - - - -
199C CYS* 1.3 74.5 - - - +
201C ILE* 1.3 64.5 + - - +
204C GLY* 3.2 22.5 + - - +
205C ARG 3.5 14.3 + - - +
206C ARG* 5.8 2.0 - - + -
279C ARG 5.1 1.4 - - - +
280C ASP* 4.2 4.0 - - - +
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 4.4 11.0 - - + +
145C PHE* 3.6 33.4 - - + +
146C SER* 4.4 10.5 - - - -
159C LEU* 4.1 24.9 - - + -
162C HIS* 4.2 15.0 - - + +
197C VAL* 3.2 20.5 + - + +
198C ILE* 3.8 17.9 - - + +
199C CYS 3.3 0.2 - - - -
200C ALA* 1.3 77.6 - - - +
202C CYS* 1.3 59.0 + - - +
280C ASP* 3.6 4.4 - - - +
281C ILE* 3.2 44.3 + - + +
462C ILE* 5.2 7.4 - - + -
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Residues in contact with CYS 202 (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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198C ILE* 3.1 42.7 + - - +
199C CYS* 4.6 0.2 - - - -
201C ILE* 1.3 82.3 - - - +
203C PHE* 1.3 69.0 + - + +
280C ASP* 3.4 3.7 - - - -
281C ILE* 4.3 10.5 - - - -
282C THR* 2.5 38.6 + - - -
311C VAL* 3.5 35.9 - - + -
314C LEU* 4.4 6.7 - - - -
315C PHE* 4.4 7.2 - - + -
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Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C CYS* 2.8 31.4 + - - +
202C CYS* 1.3 83.0 - - + +
204C GLY* 1.3 66.9 + - - +
205C ARG* 3.3 8.5 + - - +
261C PHE* 3.9 24.2 - + - -
262C MET* 5.4 7.2 - - + -
265C MET* 3.2 47.8 - - + -
266C VAL* 5.7 2.0 - - + -
269C HIS* 3.1 19.7 + + + -
280C ASP* 2.9 11.6 - - - +
282C THR* 3.1 30.7 - - + -
311C VAL* 3.9 26.2 - - + -
312C LEU* 5.9 2.7 - - + -
315C PHE* 4.1 20.4 - + + -
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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
----------------------------------------------------------
199C CYS 3.3 0.6 + - - -
200C ALA* 3.2 22.9 + - - -
203C PHE* 1.3 77.2 - - - +
205C ARG* 1.3 61.6 + - - +
279C ARG* 5.5 4.9 - - - -
280C ASP* 3.3 9.1 + - - -
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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
------------------------------------------------------------
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