Contacts of the helix formed by residues 179 - 194 (chain C) in PDB entry 7CE1
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 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ARG* 4.3 8.4 + - - +
178C PHE* 1.3 72.1 - - - +
180C ASN* 1.3 53.0 + - - +
181C GLU* 3.3 15.0 + - - +
182C ALA* 2.8 39.3 + - + +
183C TYR* 2.7 32.7 + - - +
338C VAL* 3.7 19.5 - - + +
339C SER 3.0 16.0 + - - +
340C ARG* 4.8 1.6 - - - -
341C PRO* 3.7 8.0 - - + +
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Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 4.6 1.4 - - - +
177C ASP* 4.7 5.7 + - - -
178C PHE* 2.6 49.6 + - - +
179C ASP* 1.3 69.7 - - - +
181C GLU* 1.3 59.5 + - - +
183C TYR* 3.7 7.0 - - - +
184C ALA* 2.9 30.7 + - - +
210C PHE* 3.1 44.0 - - - +
213C HIS* 4.0 17.3 - - + -
214C ALA* 3.7 12.3 - - + +
264C ILE* 5.3 6.3 - - + -
292C LYS* 3.6 14.0 + - - +
310C GLU* 5.6 0.2 + - - -
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 5.5 0.2 - - - +
179C ASP* 3.2 9.4 + - - +
180C ASN* 1.3 77.7 - - - +
182C ALA* 1.3 59.6 + - - +
185C TYR* 3.0 31.2 + - - +
213C HIS* 3.2 30.4 + - + +
216C LYS* 3.2 37.6 + - - +
217C GLY* 3.5 18.8 - - - -
220C ARG* 3.4 25.7 + - - +
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP* 2.8 35.0 + - - +
181C GLU* 1.3 77.3 - - - +
183C TYR* 1.3 58.2 + - - +
185C TYR* 3.7 4.6 - - - +
186C GLU* 2.9 44.6 + - - +
220C ARG* 5.3 3.4 - - - +
341C PRO* 3.5 19.3 - - + -
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Residues in contact with TYR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C PHE* 3.6 17.0 - + + -
179C ASP 2.7 19.0 + - - +
180C ASN* 3.7 6.1 - - - +
181C GLU 3.3 0.2 - - - -
182C ALA* 1.3 74.3 - - - +
184C ALA* 1.3 59.1 + - - +
186C GLU* 3.7 3.1 - - - +
187C ALA* 2.9 28.6 + - + +
262C VAL* 4.0 13.7 - - + +
263C SER 2.4 33.3 + - - -
264C ILE* 3.5 25.1 - - + -
290C VAL* 3.4 15.1 + - + -
291C SER* 3.2 8.8 + - - -
292C LYS* 3.0 28.8 + - + -
308C VAL* 3.6 42.8 - - + -
341C PRO* 3.5 10.1 - - + +
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ASN 2.9 16.1 + - - +
181C GLU 4.1 0.2 - - - +
183C TYR* 1.3 83.9 - - + +
185C TYR* 1.3 62.8 + - - +
187C ALA* 3.3 6.4 + - - +
188C VAL* 3.2 29.3 + - - +
201C ILE* 4.6 7.9 - - + -
214C ALA* 3.1 34.5 - - + +
217C GLY 4.0 2.9 - - - -
218C PHE* 3.6 11.6 - - + +
262C VAL* 4.6 2.5 - - - -
264C ILE* 5.2 0.2 - - + -
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Residues in contact with TYR 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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181C GLU 3.0 20.2 + - - +
182C ALA* 3.7 4.3 - - - +
184C ALA* 1.3 78.3 - - - +
186C GLU* 1.3 69.2 + - + +
188C VAL* 3.7 3.1 + - - +
189C GLU* 3.2 25.0 + - + +
217C GLY 3.2 15.0 + - - +
220C ARG* 3.7 52.9 - - + +
221C GLY* 3.6 17.0 - - - -
224C ASP* 3.3 19.4 + - - -
225C PHE* 3.5 29.8 - + - -
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Residues in contact with GLU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ALA* 2.9 31.2 + - - +
183C TYR* 4.0 3.6 - - + +
185C TYR* 1.3 87.2 - - + +
187C ALA* 1.3 56.8 + - - +
188C VAL 3.3 0.2 - - - -
189C GLU* 3.6 18.9 - - - +
190C ARG* 2.8 33.3 + - - +
340C ARG* 5.9 1.7 - - - +
341C PRO* 4.5 19.0 - - + +
343C TRP* 4.0 26.8 + - + -
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 2.9 20.1 + - + +
184C ALA 3.3 4.2 + - - +
186C GLU* 1.3 78.8 - - - +
188C VAL* 1.3 58.7 + - - +
190C ARG* 3.2 5.2 + - - +
191C LEU* 2.8 31.9 + - - +
262C VAL* 3.5 32.5 - - + -
290C VAL* 3.7 26.8 - - + +
343C TRP* 4.7 1.5 - - - -
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Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA 3.2 16.0 + - - +
185C TYR 4.1 0.4 - - - +
187C ALA* 1.3 71.9 - - - +
189C GLU* 1.3 61.1 + - - +
190C ARG 3.1 1.3 - - - -
191C LEU* 3.8 7.1 - - - +
192C ALA* 2.9 28.4 + - - +
199C ILE* 4.9 6.3 - - + -
218C PHE* 3.4 42.6 - - + +
221C GLY* 3.4 34.1 - - - +
222C ILE* 3.7 15.0 - - + -
225C PHE* 4.3 5.6 - - + -
227C VAL* 5.0 6.1 - - + -
262C VAL* 4.3 5.2 - - + -
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.2 16.8 + - + +
186C GLU* 3.6 22.5 - - - +
187C ALA 3.3 0.2 - - - -
188C VAL* 1.3 79.3 - - - +
190C ARG* 1.3 60.0 + - - +
192C ALA* 3.6 2.6 + - - +
193C GLN* 3.2 42.5 + - + +
225C PHE* 3.4 42.6 - - + -
343C TRP* 5.6 2.8 + - - -
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Residues in contact with ARG 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 GLU 2.8 18.0 + - - +
187C ALA* 3.3 6.5 - - - +
189C GLU* 1.3 78.2 + - - +
191C LEU* 1.3 64.6 + - - +
193C GLN* 3.3 22.1 + - - +
194C CYS* 3.6 20.6 + - - -
290C VAL* 4.2 6.5 - - + -
306C HIS* 3.3 29.2 + - - +
343C TRP* 3.4 57.4 - - + +
347C ALA* 4.1 11.7 - - - +
348C PRO 2.6 30.9 + - - -
349C LYS 3.6 12.7 + - - -
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Residues in contact with LEU 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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187C ALA 2.8 17.7 + - - +
188C VAL* 3.3 6.5 + - - +
190C ARG* 1.3 71.9 - - - +
192C ALA* 1.3 63.2 + - - +
194C CYS* 3.3 8.8 + - + +
196C ARG* 3.0 31.8 + - + +
199C ILE* 3.8 23.6 - - + -
260C GLY* 3.8 9.9 - - - -
261C ILE 3.6 23.3 - - - +
262C VAL* 3.6 28.0 - - + -
288C ASP* 3.8 35.2 - - + +
290C VAL* 3.8 18.4 - - + -
306C HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 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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188C VAL 2.9 17.7 + - - +
189C GLU 3.8 5.2 - - - +
190C ARG 3.3 0.2 - - - -
191C LEU* 1.3 76.4 - - - +
193C GLN* 1.3 53.2 + - - +
195C GLY* 2.7 25.5 + - - -
196C ARG 3.8 10.5 + - - -
197C LYS* 5.8 1.2 - - - -
225C PHE* 4.0 28.9 - - + +
227C VAL* 4.4 10.7 - - + +
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Residues in contact with GLN 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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189C GLU* 3.2 34.7 + - + +
190C ARG* 3.3 33.8 + - - +
191C LEU 3.3 0.2 - - - -
192C ALA* 1.3 77.0 - - + +
194C CYS* 1.3 62.8 + - - +
195C GLY* 3.4 0.7 + - - -
349C LYS* 4.2 23.1 + - - +
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Residues in contact with CYS 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 ARG* 3.6 9.6 + - - -
191C LEU* 3.3 12.4 + - - +
192C ALA 3.1 1.2 - - - -
193C GLN* 1.3 78.3 - - - +
195C GLY* 1.3 57.4 + - - +
196C ARG* 3.2 6.4 + - + +
288C ASP* 3.1 30.5 - - + +
306C HIS* 3.7 27.1 - - - -
349C LYS* 4.5 31.4 + - - +
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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
------------------------------------------------------------
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