Contacts of the helix formed by residues 169 - 182 (chain C) in PDB entry 5A31
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 GLY 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C ASP* 1.3 78.3 + - - +
170C PHE* 1.3 65.7 + - - -
172C LEU* 3.2 25.1 + - - +
173C TYR* 3.2 9.7 + - - +
195C ALA* 4.4 6.7 - - - +
198C VAL* 3.9 5.6 - - - +
199C LEU* 3.8 31.9 - - - -
202C HIS* 5.8 0.2 - - - -
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Residues in contact with PHE 170 (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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39C ILE* 5.1 2.7 - - + -
42C LEU* 4.1 26.7 - - + -
43C THR* 3.9 18.8 - - + -
46C ARG* 3.2 49.4 - - + -
48C LEU* 4.1 6.5 - - + -
116C PHE* 3.7 27.4 - + + -
168C ASP 3.1 3.9 + - - +
169C GLY* 1.3 67.2 - - - -
171C GLY* 1.3 59.6 + - - +
173C TYR* 2.6 29.9 + - - +
174C LEU 2.7 11.3 + - - -
199C LEU* 3.9 23.8 - - + -
202C HIS* 3.5 31.2 - + + -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 6.4 0.2 - - - -
116C PHE* 3.8 17.3 - - - +
158C LEU* 4.8 1.7 - - - +
167C LEU* 3.4 29.7 - - - +
168C ASP 3.1 9.4 + - - -
170C PHE* 1.3 77.3 - - - +
172C LEU* 1.3 50.9 + - - +
174C LEU* 3.1 5.6 + - - +
175C TYR* 2.8 34.3 + - - +
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Residues in contact with LEU 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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162C HIS* 3.7 26.9 - - + +
167C LEU* 3.4 37.8 - - + +
168C ASP* 4.3 1.3 + - - -
169C GLY 3.2 28.7 + - - +
170C PHE 3.2 0.4 - - - -
171C GLY* 1.3 74.0 - - - +
173C TYR* 1.3 59.1 + - - +
175C TYR* 3.2 3.6 + - + +
176C GLY* 2.8 24.8 + - - -
191C VAL* 3.4 19.8 - - + +
192C PHE* 4.9 0.2 - - - -
194C GLU* 4.4 12.1 - - + -
195C ALA* 3.8 22.7 - - + +
198C VAL* 4.3 21.5 - - + -
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Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 4.1 13.7 - - - +
48C LEU* 4.3 18.8 - - + -
116C PHE* 5.0 2.5 - + - -
120C TYR* 5.4 9.6 - + - -
169C GLY 3.2 3.7 + - - +
170C PHE* 2.6 21.5 + - - +
172C LEU* 1.3 74.8 - - - +
174C LEU* 1.3 67.8 + - + -
176C GLY* 3.1 1.7 + - - -
177C VAL* 2.9 39.9 + - + +
192C PHE* 3.8 10.8 - + - -
195C ALA* 4.2 4.5 - - + +
202C HIS* 3.6 27.1 - + + +
204C GLY* 3.4 27.9 - - - -
205C ALA* 3.6 25.4 - - + -
208C GLU* 3.2 24.3 + - + -
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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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116C PHE* 3.6 25.8 - - + -
119C MET* 4.0 24.0 - - + +
120C TYR* 3.7 36.6 - - + +
123C TYR* 4.3 15.3 - - + -
154C LEU* 4.6 3.8 - - + -
158C LEU* 3.3 33.2 - - + -
170C PHE 2.7 9.7 + - - -
171C GLY* 3.4 8.5 - - - +
173C TYR* 1.3 78.4 - - + +
175C TYR* 1.3 63.0 - - - +
177C VAL* 3.3 11.8 + - + +
178C VAL* 3.1 27.1 + - + +
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Residues in contact with TYR 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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155C ARG* 4.1 15.5 - - + +
158C LEU* 3.6 26.7 - - + -
159C SER* 3.6 31.6 - - - -
162C HIS* 3.5 40.3 + + + -
167C LEU* 4.2 9.2 - - + -
171C GLY 2.8 13.4 + - - +
172C LEU* 3.4 9.2 - - + +
174C LEU* 1.3 77.5 - - - +
176C GLY* 1.3 60.7 - - - +
178C VAL* 3.1 4.4 + - + +
179C LEU* 3.0 48.3 + - + +
191C VAL* 3.8 27.8 - - + -
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Residues in contact with GLY 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 LEU 2.8 14.9 + - - -
173C TYR 3.5 1.6 - - - -
175C TYR* 1.3 76.0 - - - +
177C VAL* 1.3 61.0 + - - +
178C VAL 3.3 0.2 + - - -
179C LEU* 3.4 7.3 + - - +
180C ARG* 2.9 24.8 + - - +
188C ALA* 4.0 1.9 - - - +
191C VAL* 3.8 16.6 - - - +
192C PHE* 3.3 24.5 - - - -
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Residues in contact with VAL 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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47A GLU* 6.0 2.0 - - + -
120C TYR* 6.3 0.4 - - + -
123C TYR* 3.6 39.3 - - + +
173C TYR* 2.9 49.4 + - + +
174C LEU* 3.4 16.4 - - + +
176C GLY* 1.3 74.1 - - - +
178C VAL* 1.3 59.9 + - + +
180C ARG* 3.3 13.2 + - - +
181C LYS* 3.0 33.1 + - + +
192C PHE* 3.4 8.4 - - + -
208C GLU* 4.4 7.6 - - + +
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Residues in contact with VAL 178 (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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123C TYR* 4.0 15.9 - - + -
151C LEU* 3.6 47.8 - - + +
154C LEU* 4.1 14.1 - - + -
155C ARG* 4.1 23.1 - - + +
158C LEU* 4.6 1.8 - - + -
174C LEU* 3.1 19.9 + - + +
175C TYR* 3.1 11.0 + - + +
177C VAL* 1.3 75.7 - - + +
179C LEU* 1.3 64.7 + - - +
181C LYS* 3.2 5.1 + - - +
182C LEU* 3.1 23.3 + - + +
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Residues in contact with LEU 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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155C ARG* 4.0 13.0 - - + -
175C TYR* 3.0 50.8 + - + +
176C GLY* 3.6 4.7 - - - +
178C VAL* 1.3 76.1 - - - +
180C ARG* 1.3 62.4 + - - +
182C LEU* 3.0 14.0 + - - +
183C ASP 3.1 0.2 + - - -
184C LEU* 3.0 49.6 + - + +
187C GLU* 4.7 8.1 - - + +
188C ALA* 3.9 17.9 - - + +
191C VAL* 3.5 34.8 - - + -
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Residues in contact with ARG 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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44A PRO* 5.2 5.8 - - - +
45A ALA* 2.8 30.8 + - - +
46A SER 5.2 0.4 + - - -
47A GLU* 4.3 8.7 - - - +
176C GLY 2.9 17.4 + - - +
177C VAL* 3.6 15.1 + - - +
179C LEU* 1.3 76.4 - - - +
181C LYS* 1.3 80.5 + - - +
183C ASP* 2.8 23.4 + - - +
184C LEU 4.6 2.9 - - - +
185C VAL* 5.1 4.1 - - + +
188C ALA* 4.0 10.4 - - + +
192C PHE* 4.7 2.9 - - + -
208C GLU* 2.9 39.8 + - - +
211C ASN* 4.9 9.9 - - - +
212C LEU* 3.6 39.7 - - + -
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Residues in contact with LYS 181 (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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44A PRO* 4.0 33.4 + - + +
45A ALA 3.5 12.7 + - - -
46A SER* 4.1 14.5 + - - +
47A GLU* 4.9 2.4 - - - +
123C TYR* 2.5 33.7 + - + +
127C GLU* 2.6 26.9 + - - +
130C LYS* 6.3 0.4 - - - -
151C LEU* 3.5 25.5 - - + +
177C VAL* 3.0 20.1 + - - +
178C VAL* 3.2 5.3 + - - +
180C ARG* 1.3 100.0 - - - +
182C LEU* 1.3 62.2 + - - +
183C ASP* 3.0 12.3 - - - +
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Residues in contact with LEU 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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151C LEU* 3.4 46.4 - - + +
152C ARG* 5.0 3.8 - - - +
155C ARG* 4.0 38.6 - - + +
178C VAL* 3.1 14.2 + - + +
179C LEU* 3.0 8.5 + - - +
181C LYS* 1.3 75.1 - - - +
183C ASP* 1.3 73.1 + - - +
184C LEU* 3.3 21.7 + - + +
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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