Contacts of the helix formed by residues 172 - 188 (chain C) in PDB entry 5EKV
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASP* 3.5 23.0 + - - +
168C THR* 5.0 0.6 - - - +
169C GLU* 3.4 33.4 - - - +
170C CYS 3.3 2.6 - - - +
171C GLU* 1.3 77.2 - - - +
173C ARG* 1.3 62.4 + - - +
174C GLU 3.6 0.9 - - - +
175C ALA* 3.9 18.6 - - + +
176C VAL* 3.3 24.1 + - - +
215C PHE* 4.5 0.2 - - - -
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Residues in contact with ARG 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PRO* 5.1 4.2 - - - +
191A PRO* 3.8 32.0 - - + +
192A LYS* 4.4 21.2 - - - +
171C GLU* 3.0 13.8 + - - +
172C ASN* 1.3 71.5 - - - +
174C GLU* 1.3 62.8 + - - +
175C ALA 3.3 0.4 - - - -
176C VAL* 3.8 0.5 + - - -
177C THR* 2.6 32.9 + - - -
215C PHE* 3.6 31.2 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 2.8 46.7 + - + +
185A GLU* 5.4 9.0 - - + +
189A LEU 3.8 6.2 - - - +
191A PRO* 3.4 28.4 - - + +
217A VAL* 4.4 7.9 - - + +
145C TYR* 3.3 27.7 - - + +
173C ARG* 1.3 78.9 - - - +
175C ALA* 1.3 59.0 + - - +
177C THR* 5.3 0.5 - - - -
178C HIS* 3.1 33.3 + - - +
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.5 29.0 - - + +
148C ASP* 2.9 32.3 - - + +
172C ASN* 3.9 15.8 + - + +
173C ARG 3.3 0.6 - - - -
174C GLU* 1.3 77.8 - - - +
176C VAL* 1.3 66.7 + - + +
178C HIS* 3.4 1.7 + - - +
179C ILE* 3.1 30.7 + - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TRP* 2.8 50.6 + - + +
148C ASP* 6.5 0.2 - - + -
167C THR* 4.2 10.3 - - + +
169C GLU 3.5 19.1 - - - +
170C CYS* 4.3 2.9 - - - +
172C ASN 3.3 21.3 + - - +
173C ARG 4.4 0.7 - - - +
174C GLU 3.5 0.2 - - - -
175C ALA* 1.3 76.5 - - + +
177C THR* 1.3 62.8 + - - +
179C ILE* 3.3 5.8 + - - +
180C GLY 3.1 7.3 + - - -
197C TYR* 3.6 33.0 - - + +
215C PHE* 3.7 18.2 - - + -
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Residues in contact with THR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 3.7 34.1 - - + +
113C TRP* 4.4 7.2 - - + -
173C ARG 2.6 24.3 + - - -
174C GLU* 4.2 2.2 - - - -
176C VAL* 1.3 77.9 - - - +
178C HIS* 1.3 62.3 + - - +
180C GLY* 3.6 0.9 + - - -
181C ARG* 3.1 28.0 + - + +
215C PHE* 3.8 20.8 - - + -
216C VAL 5.6 3.8 - - - +
217C VAL* 4.6 9.7 - - + +
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Residues in contact with HIS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 5.6 0.4 - - + -
216A VAL 4.1 8.0 + - - -
217A VAL* 4.5 17.1 - - + +
142C PHE* 3.5 30.7 + - + -
143C ASP* 3.8 17.6 + - + +
145C TYR* 3.6 28.8 - + + -
174C GLU* 3.1 24.8 + - - +
175C ALA 3.9 0.4 - - - +
177C THR* 1.3 76.3 - - - +
179C ILE* 1.3 64.4 + - - +
181C ARG* 3.2 36.2 + - - +
182C VAL* 3.1 38.6 + - + +
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TRP* 4.0 16.2 - - + +
142C PHE* 3.4 45.0 - - + -
145C TYR* 3.4 26.5 - - + +
148C ASP* 4.5 5.2 - - + -
149C VAL* 3.7 13.2 - - + -
165C ILE* 4.4 13.9 - - + -
167C THR* 3.8 18.8 - - + -
175C ALA 3.1 26.3 + - - +
176C VAL 3.7 3.8 - - - +
177C THR 3.3 0.2 - - - -
178C HIS* 1.3 77.0 - - - +
180C GLY* 1.3 58.0 + - - +
182C VAL 3.4 0.9 + - - -
183C TYR* 2.9 30.1 + - + +
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TRP* 3.4 32.1 - - - +
176C VAL 3.1 11.3 + - - -
177C THR 4.0 1.1 - - - -
179C ILE* 1.3 76.2 - - - +
181C ARG* 1.3 56.7 + - - +
183C TYR* 3.9 5.8 - - - -
184C LYS* 3.2 26.2 + - - +
195C ILE* 4.0 6.8 - - - +
217C VAL* 3.7 13.4 - - - +
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Residues in contact with ARG 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 4.0 25.1 - - - +
216A VAL* 2.8 50.4 + - - +
217A VAL* 4.1 3.2 - - - +
177C THR* 3.1 21.1 + - + +
178C HIS* 3.2 33.9 + - - +
179C ILE 3.2 0.2 - - - -
180C GLY* 1.3 75.5 - - - +
182C VAL* 1.3 71.2 + - - +
184C LYS* 3.6 3.3 + - - +
185C GLU* 3.2 44.5 + - + +
217C VAL* 4.1 20.2 - - + +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C CYS* 5.0 2.5 - - - -
141C SER* 3.5 30.7 - - - +
142C PHE* 4.1 11.7 - - + -
143C ASP* 5.9 0.4 - - - +
178C HIS* 3.1 43.1 + - + +
179C ILE 4.0 2.5 - - - +
181C ARG* 1.3 85.5 - - - +
183C TYR* 1.3 61.3 + - - +
185C GLU* 3.2 8.4 + - + +
186C ARG* 2.9 32.3 + - + +
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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
----------------------------------------------------------
113C TRP* 4.9 17.9 - + + -
115C ILE* 3.9 18.0 - - + +
129C PHE* 6.0 0.2 - - - +
132C GLU 5.5 0.2 - - - -
133C THR* 2.9 32.5 + - + +
136C CYS* 4.9 10.5 - - + -
142C PHE* 4.2 7.6 - - + -
163C ILE* 3.4 19.7 + - - +
165C ILE* 3.5 33.5 - - + +
179C ILE* 2.9 20.3 + - + +
180C GLY* 4.1 5.4 - - - +
182C VAL* 1.3 78.1 - - - +
184C LYS* 1.3 60.8 + - - +
186C ARG* 4.0 4.0 - - + +
187C LEU* 3.2 63.6 + - + +
195C ILE* 4.4 15.5 - - + -
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Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C GLY 3.2 17.6 + - - +
181C ARG* 3.8 5.8 - - - +
182C VAL 3.2 0.2 - - - -
183C TYR* 1.3 79.9 - - - +
185C GLU* 1.3 62.4 + - + +
187C LEU* 4.3 0.2 - - - -
188C GLY 3.2 16.8 + - - -
189C LEU* 3.2 46.6 + - + +
190C PRO 3.4 20.0 - - - -
191C PRO* 3.5 20.8 + - - +
193C ILE* 3.2 20.8 + - - +
195C ILE* 4.8 10.3 - - + +
217C VAL* 3.2 36.8 + - + +
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Residues in contact with GLU 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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216A VAL* 5.1 2.6 - - - +
181C ARG* 3.2 42.6 + - + +
182C VAL* 3.2 10.1 + - + +
184C LYS* 1.3 79.2 - - + +
186C ARG* 1.3 61.0 + - - +
188C GLY* 3.6 10.4 + - - +
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Residues in contact with ARG 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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132C GLU* 3.5 35.5 + - + +
135C LEU* 4.1 13.3 + - - +
136C CYS* 3.5 34.9 - - - +
141C SER* 2.9 29.3 + - - -
182C VAL* 2.9 21.0 + - + +
183C TYR* 4.2 5.8 - - + +
185C GLU* 1.3 75.5 - - - +
187C LEU* 1.3 65.1 + - + +
188C GLY* 4.8 0.2 - - - -
54D TYR 4.6 2.2 + - - -
55D ASP* 4.3 4.9 + - - +
56D ARG* 3.3 44.5 - - - +
59D LEU* 4.4 3.2 - - - +
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Residues in contact with LEU 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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115C ILE* 3.9 17.5 - - + -
128C ARG* 5.2 2.6 + - - -
129C PHE* 3.6 50.2 - - + +
132C GLU* 4.0 24.0 - - + +
133C THR 4.8 0.2 - - - +
183C TYR* 3.2 62.5 + - + +
184C LYS 4.3 0.2 - - - +
186C ARG* 1.3 78.3 - - + +
188C GLY* 1.3 60.7 + - - +
189C LEU* 4.0 23.3 - - + -
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Residues in contact with GLY 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PHE* 5.9 0.3 - - - -
184C LYS 3.2 6.7 + - - -
185C GLU 3.6 8.4 + - - -
186C ARG 3.3 2.8 - - - -
187C LEU* 1.3 81.4 - - - +
189C LEU* 1.3 64.5 + - - +
190C PRO* 4.0 5.2 - - - +
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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
------------------------------------------------------------
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