Contacts of the helix formed by residues 159 - 179 (chain C) in PDB entry 4AD7
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 LEU 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 6.3 0.2 - - + -
147C GLU* 4.8 5.2 - - + +
148C LEU* 3.8 20.4 - - + -
151C TYR* 3.6 60.3 - - + +
156C ASN* 4.9 2.0 - - - +
158C HIS* 1.3 70.5 - - - +
160C GLU* 1.3 61.0 + - - +
161C GLU 3.3 0.7 - - - -
162C THR* 2.3 37.6 + - - +
163C LEU* 3.0 35.4 + - + +
210C ARG* 4.9 2.0 - - + +
213C ALA* 3.9 21.1 - - + -
214C THR* 4.1 12.8 - - - +
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C HIS* 3.6 3.4 - - + +
159C LEU* 1.3 78.7 - - - +
161C GLU* 1.3 57.3 + - - +
163C LEU* 3.4 8.0 + - + +
164C ALA* 2.9 33.4 + - + +
210C ARG* 3.8 35.8 + - + +
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Residues in contact with GLU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C HIS* 4.5 13.4 + - + +
159C LEU 3.3 0.6 - - - -
160C GLU* 1.3 78.0 - - - +
162C THR* 1.3 60.2 + - + +
164C ALA* 3.9 4.8 - - - +
165C GLU* 2.9 43.4 + - + +
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Residues in contact with THR 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.8 2.5 - - - +
147C GLU* 3.7 29.3 - - - +
156C ASN* 3.6 25.5 + - - +
158C HIS 3.9 6.7 - - - +
159C LEU* 2.3 40.9 + - - +
161C GLU* 1.3 79.1 - - + +
163C LEU* 1.3 57.7 + - - +
165C GLU* 3.4 8.4 + - - +
166C PHE* 2.9 29.5 + - - +
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 3.7 28.5 - - + -
148C LEU* 5.3 4.3 - - + -
159C LEU* 3.0 42.4 + - + +
160C GLU* 3.8 4.7 - - - +
162C THR* 1.3 83.7 + - - +
164C ALA* 1.3 56.6 + - - +
166C PHE* 3.2 5.6 + - + +
167C TRP* 2.9 47.6 + - + +
209C LEU* 4.0 24.2 - - + +
210C ARG* 4.0 36.1 - - + +
213C ALA* 4.9 2.7 - - + -
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Residues in contact with ALA 164 (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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160C GLU* 2.9 21.9 + - + +
161C GLU* 3.9 6.1 - - - +
163C LEU* 1.3 75.1 - - - +
165C GLU* 1.3 57.9 + - - +
167C TRP* 3.3 9.1 + - - +
168C ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLU* 2.9 31.4 + - - +
162C THR* 3.6 7.3 - - - +
164C ALA* 1.3 76.6 - - - +
166C PHE* 1.3 63.2 + - - +
168C ALA* 3.3 5.9 + - + +
169C ARG* 2.8 66.9 + - - +
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ALA* 3.7 41.5 - - + -
141C PHE* 4.3 16.4 - + - -
143C ASP* 6.2 0.4 - - + -
144C LEU* 3.5 44.9 - - + -
162C THR 2.9 14.7 + - - +
163C LEU* 3.2 11.2 + - + +
165C GLU* 1.3 76.2 - - - +
167C TRP* 1.3 100.3 + + - +
169C ARG* 4.3 2.1 - - - +
170C LEU* 2.9 52.7 + - + +
321C LEU* 4.5 1.1 - - + -
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Residues in contact with TRP 167 (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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163C LEU* 2.9 46.2 + - + +
164C ALA* 3.9 6.5 - - - +
166C PHE* 1.3 98.0 - + - +
168C ALA* 1.3 58.6 + - - +
170C LEU* 3.8 16.1 - - + +
171C LEU* 2.9 31.0 + - - +
202C PHE* 4.0 32.1 - + + -
205C ALA* 4.9 1.1 - - + -
206C PRO* 4.2 37.7 + - + +
209C LEU* 3.6 25.0 - - + +
320C TRP 5.1 0.9 - - - -
321C LEU* 3.8 15.5 - - + -
324C ALA* 3.5 33.2 - - + -
325C ILE* 6.4 0.4 - - + -
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Residues in contact with ALA 168 (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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164C ALA 2.9 17.9 + - - +
165C GLU* 3.6 7.2 - - - +
167C TRP* 1.3 76.8 - - - +
169C ARG* 1.3 60.2 + - + +
171C LEU* 3.1 8.5 + - - +
172C GLU* 3.0 39.2 + - - +
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Residues in contact with ARG 169 (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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143C ASP* 5.9 0.8 + - - -
165C GLU* 2.8 59.3 + - - +
166C PHE* 4.3 1.8 - - - +
168C ALA* 1.3 76.5 - - + +
170C LEU* 1.3 57.5 + - - +
172C GLU* 3.2 21.3 + - + +
173C ARG* 2.9 41.4 + - + +
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN* 4.1 31.9 - - + +
140C ALA* 4.8 10.1 - - + -
141C PHE* 4.5 19.5 - - + -
166C PHE* 2.9 51.2 + - + +
167C TRP* 3.8 20.6 - - + +
169C ARG* 1.3 77.7 - - - +
171C LEU* 1.3 58.3 + - - +
173C ARG* 3.9 5.1 - - + +
174C LEU* 2.9 40.7 + - + +
202C PHE* 4.5 12.1 - - + -
325C ILE* 5.6 5.6 - - + -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TRP 2.9 19.1 + - - +
168C ALA* 3.5 6.3 - - - +
170C LEU* 1.3 73.1 - - - +
172C GLU* 1.3 67.1 - - - +
174C LEU* 4.3 2.0 - - - -
175C PHE* 2.9 37.5 + - + +
197C GLU* 5.8 5.6 - - - +
201C PRO* 4.5 14.8 - - + -
202C PHE* 4.0 17.7 - - + -
328C LEU* 3.7 33.9 - - + -
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Residues in contact with GLU 172 (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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168C ALA* 3.0 27.7 + - - +
169C ARG* 3.2 25.6 + - + +
171C LEU* 1.3 77.3 - - + +
173C ARG* 1.3 64.8 + - + +
175C PHE* 3.9 2.3 - - - +
176C LYS* 3.0 30.9 + - - +
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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
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136C GLN 3.5 12.5 + - - -
137C ASN* 2.4 51.4 + - - +
139C ARG* 6.2 2.5 - - - +
140C ALA* 5.3 11.0 - - - -
169C ARG* 2.9 27.7 + - + +
170C LEU* 4.0 4.9 - - - +
172C GLU* 1.3 76.5 - - + +
174C LEU* 1.3 57.0 + - - +
176C LYS* 3.2 14.2 + - - +
177C GLN* 2.9 51.8 + - - +
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Residues in contact with LEU 174 (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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133C LEU* 3.7 42.6 - - + +
137C ASN* 3.3 27.0 + - - +
170C LEU* 2.9 29.4 + - + +
171C LEU* 3.9 5.4 - - - +
172C GLU 3.3 0.2 - - - -
173C ARG* 1.3 77.6 - - - +
175C PHE* 1.3 57.5 + - - +
177C GLN* 3.4 5.8 + - - +
178C LEU* 2.9 44.4 + - + +
202C PHE* 5.9 0.4 - - + -
325C ILE* 5.9 7.6 - - + -
328C LEU* 3.8 31.2 - - + -
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Residues in contact with PHE 175 (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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171C LEU* 2.9 28.7 + - + +
172C GLU* 4.1 2.5 - - - +
174C LEU* 1.3 76.6 - - - +
176C LYS* 1.3 66.4 + - - +
178C LEU* 3.4 12.7 - - + +
179C HIS* 3.0 53.6 + + + +
328C LEU* 6.4 0.9 - - + -
335C LEU* 3.6 40.4 - - + -
336C THR* 6.2 2.0 - - - -
337C ALA* 6.0 7.4 - - + -
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Residues in contact with LYS 176 (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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172C GLU* 3.0 24.1 + - - +
173C ARG* 3.6 13.7 - - - +
175C PHE* 1.3 78.6 - - - +
177C GLN* 1.3 59.8 + - + +
179C HIS 3.0 20.7 - - - +
180C PRO* 3.8 9.4 - - - +
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Residues in contact with GLN 177 (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 4.4 2.1 - - - +
133C LEU* 4.8 6.5 - - + +
136C GLN* 3.4 33.0 - - + +
137C ASN* 2.8 42.3 + - - -
173C ARG* 2.9 39.8 + - - +
174C LEU* 3.7 6.6 - - - +
176C LYS* 1.3 79.5 - - + +
178C LEU* 1.3 67.0 + - - +
179C HIS 3.4 0.2 + - - -
180C PRO* 3.9 14.1 - - - +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 5.1 13.9 - - + +
174C LEU* 2.9 37.9 + - + +
175C PHE* 3.1 19.9 + - + +
177C GLN* 1.3 77.6 - - - +
179C HIS* 1.3 89.3 + - + +
180C PRO* 3.5 6.4 - - - +
328C LEU* 5.1 9.6 - - + +
332C ARG* 3.8 44.3 + - + +
335C LEU* 5.5 4.5 - - + -
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Residues in contact with HIS 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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175C PHE* 3.0 42.8 + + + +
176C LYS* 3.0 16.0 - - - +
178C LEU* 1.3 103.4 + - + +
180C PRO* 1.3 70.5 - - + +
332C ARG* 4.6 17.9 + - - -
335C LEU* 6.1 1.0 - - - +
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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