Contacts of the helix formed by residues 178 - 190 (chain C) in PDB entry 4BPU
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 SER 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C LYS 3.5 4.0 + - - -
177C LEU* 1.3 77.7 - - - +
179C SER* 1.3 64.6 + - - +
180C ALA* 3.2 9.9 + - - +
181C VAL* 3.2 29.6 + - - +
182C ARG* 3.1 20.1 + - - +
313C ILE* 4.6 5.4 - - - -
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Residues in contact with SER 179 (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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177C LEU 3.9 0.4 + - - -
178C SER* 1.3 73.9 - - - +
180C ALA* 1.3 57.6 - - - +
182C ARG* 3.4 5.7 + - - +
183C SER* 2.8 29.3 + - - -
311C LYS* 2.7 49.8 + - - +
312C GLY* 4.4 2.3 - - - -
313C ILE* 4.1 18.5 - - - +
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Residues in contact with ALA 180 (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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178C SER* 3.1 9.7 + - - +
179C SER* 1.3 77.6 - - - +
181C VAL* 1.3 61.1 + - + +
183C SER* 3.2 8.2 + - - -
184C GLY 2.8 23.2 + - - -
311C LYS* 5.1 2.7 - - - +
192D LEU* 3.3 27.2 - - + +
196D ARG* 5.7 0.2 - - - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.8 23.3 - - + -
178C SER* 3.2 24.0 + - - +
180C ALA* 1.3 74.4 - - + +
182C ARG* 1.3 55.2 + - - +
184C GLY* 3.0 1.9 + - - -
185C ILE* 2.8 37.0 + - + +
188D PHE* 3.7 29.6 - - + -
189D ALA* 4.2 27.6 - - + +
192D LEU* 3.9 13.5 - - + -
195D PHE* 4.3 4.3 - - + -
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Residues in contact with ARG 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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104C LYS* 3.1 37.6 + - - +
105C GLU 3.3 16.4 + - - -
106C LEU* 3.8 23.5 - - + +
174C VAL 3.6 10.4 + - - -
175C ARG 3.3 15.8 + - - -
177C LEU* 2.8 35.7 + - + -
178C SER 3.1 10.0 + - - +
179C SER* 3.5 7.6 - - - +
181C VAL* 1.3 75.8 - - - +
183C SER* 1.3 57.0 + - - +
185C ILE* 3.0 11.3 + - - +
186C VAL* 2.9 34.0 + - - +
310C SER 3.3 25.5 + - - +
311C LYS 3.7 12.8 - - - +
312C GLY 5.1 1.0 + - - -
313C ILE* 4.1 19.8 - - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C SER 2.8 18.1 + - - -
180C ALA* 3.5 7.2 - - - -
181C VAL 3.2 0.2 - - - -
182C ARG* 1.3 76.0 - - - +
184C GLY* 1.3 57.7 + - - +
186C VAL* 3.4 4.0 + - - +
187C GLU* 3.1 41.0 + - - +
307C ILE* 3.3 27.0 - - - +
311C LYS* 4.2 24.6 + - - +
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Residues in contact with GLY 184 (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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180C ALA 2.8 14.7 + - - -
181C VAL 3.0 4.0 + - - -
183C SER* 1.3 76.3 - - - +
185C ILE* 1.3 58.4 + - - +
187C GLU* 3.2 5.5 + - - +
188C TYR* 2.9 29.3 + - - +
192D LEU* 3.8 8.5 - - - -
195D PHE* 3.6 9.4 - - - -
196D ARG* 3.6 24.4 - - - -
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Residues in contact with ILE 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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106C LEU* 3.8 13.9 - - + -
108C PHE* 4.3 14.6 - - + -
146C LEU* 4.5 4.0 - - + -
150C PHE* 3.8 28.9 - - + -
152C PHE* 3.6 33.0 - - + -
177C LEU* 4.0 13.5 - - + -
181C VAL* 2.8 22.9 + - + +
182C ARG* 3.0 9.2 + - - +
184C GLY* 1.3 72.3 - - - +
186C VAL* 1.3 63.3 + - - +
188C TYR* 3.3 2.4 + - - +
189C LEU* 3.2 37.3 + - + +
188D PHE* 4.0 12.6 - - + -
195D PHE* 4.0 5.4 - - + -
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Residues in contact with VAL 186 (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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106C LEU* 6.0 0.4 - - + -
108C PHE* 4.4 11.7 - - + -
182C ARG 2.9 15.8 + - - +
183C SER 3.7 7.2 - - - +
184C GLY 3.2 0.2 - - - -
185C ILE* 1.3 78.3 - - + +
187C GLU* 1.3 61.7 + - - +
189C LEU* 3.3 8.2 + - - +
190C SER* 3.0 38.6 + - - +
305C LEU* 4.6 13.2 - - + +
306C ASP 5.3 0.4 - - - +
307C ILE* 3.7 41.1 - - + +
310C SER* 3.6 31.9 - - - +
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Residues in contact with GLU 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 SER* 3.1 28.5 + - - +
184C GLY 3.2 4.9 + - - +
186C VAL* 1.3 73.4 - - - +
188C TYR* 1.3 65.7 + - - +
190C SER* 3.4 17.1 + - - +
307C ILE* 4.5 9.3 - - + +
196D ARG* 2.7 65.4 + - - +
198D ARG* 3.5 9.2 + - - -
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Residues in contact with TYR 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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145C ALA* 4.7 0.2 - - + -
149C ASP* 2.6 34.8 + - + +
150C PHE* 3.2 35.4 - + + -
184C GLY 2.9 14.8 + - - +
185C ILE 3.6 3.1 - - - +
187C GLU* 1.3 76.5 - - - +
189C LEU* 1.3 65.0 + - + +
209C HIS* 3.9 27.4 - + - -
211C PHE* 3.5 31.9 + + + +
195D PHE* 3.3 32.5 - - + +
196D ARG 4.0 1.0 + - - -
198D ARG* 2.9 39.6 + - + +
200D VAL 5.1 0.9 - - - -
202D LEU* 4.0 24.3 + - + +
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Residues in contact with LEU 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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108C PHE* 3.8 34.3 - - + -
142C ILE* 4.4 20.7 - - + +
145C ALA* 3.5 32.1 - - + -
146C LEU* 4.5 3.6 - - + -
150C PHE* 4.5 3.6 - - + -
185C ILE* 3.2 24.3 + - + +
186C VAL 3.3 4.5 + - - +
187C GLU 3.3 0.2 - - - -
188C TYR* 1.3 84.4 - - + +
190C SER* 1.3 59.4 + - - +
211C PHE* 3.6 17.0 - - + -
302C PHE* 3.2 27.0 - - - -
303C PRO* 5.1 0.7 - - - +
305C LEU* 3.8 20.1 - - + +
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Residues in contact with SER 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 VAL* 3.0 29.9 + - - +
187C GLU* 3.4 9.5 + - - +
188C TYR 3.3 2.8 - - - -
189C LEU* 1.3 76.8 - - - +
191C LEU* 1.3 60.3 + - - +
192C VAL 5.2 3.8 - - - -
302C PHE* 4.5 1.3 - - - -
303C PRO 5.6 2.0 - - - -
305C LEU* 4.1 19.3 + - - +
198D ARG* 3.0 21.2 + - - -
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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