Contacts of the helix formed by residues 172 - 188 (chain C) in PDB entry 1APL
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C SER 4.1 1.4 + - - -
171C LEU* 1.3 68.4 - - - +
173C ARG* 1.3 53.2 + - - +
174C ILE* 3.2 7.3 + - - +
175C GLN* 2.6 66.6 + - - +
176C ILE 3.5 1.1 + - - -
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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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22B T 4.4 3.0 + - - -
23B G 2.9 12.1 + - - -
162C LEU* 3.7 23.3 - - + +
166C MET* 3.2 39.0 - - - +
171C LEU 3.0 7.6 + - - -
172C SER* 1.3 65.3 - - - +
174C ILE* 1.4 88.0 + - - +
176C ILE* 3.0 19.2 + - - +
177C LYS* 2.3 55.4 + - - +
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Residues in contact with ILE 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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17A C 5.3 8.3 - - - +
23B G 5.9 1.1 - - - +
172C SER* 2.8 12.0 + - - +
173C ARG* 1.4 89.5 - - - +
175C GLN* 1.3 58.1 + - + +
177C LYS* 3.7 11.7 - - + +
178C ASN* 2.8 44.9 + - - +
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Residues in contact with GLN 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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16A A 2.7 43.1 + - - +
132C ARG* 5.5 2.0 - - - +
136C PHE* 4.3 7.9 - - + -
170C SER 4.5 1.0 - - - +
171C LEU* 3.2 32.6 - - + +
172C SER* 2.6 54.7 + - - +
174C ILE* 1.3 71.4 - - + +
176C ILE* 1.3 58.2 + - - +
178C ASN* 3.3 4.0 + - - +
179C TRP* 2.9 28.4 + - - +
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Residues in contact with ILE 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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144C LEU* 3.9 25.1 - - + -
157C LEU* 4.4 6.5 - - + -
162C LEU* 4.0 16.6 - - + -
165C LEU* 3.5 39.5 - - + -
166C MET* 3.8 17.9 - - + +
169C THR* 3.9 11.9 - - - +
171C LEU* 4.2 23.6 - - + +
172C SER 3.5 0.2 + - - -
173C ARG* 3.0 9.6 + - - +
175C GLN* 1.3 73.7 - - - +
177C LYS* 1.3 68.3 + - - +
179C TRP* 2.9 14.2 + - - -
180C VAL* 3.1 21.3 + - + +
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Residues in contact with LYS 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B G 2.1 61.8 + - - +
24B C 5.3 10.4 + - - +
157C LEU* 3.9 16.7 - - + +
162C LEU* 3.7 23.5 - - + +
173C ARG* 2.3 49.2 + - - +
174C ILE* 3.7 15.7 - - + +
176C ILE* 1.3 76.9 - - - +
178C ASN* 1.3 65.7 + - - +
180C VAL* 4.4 1.4 - - - +
181C SER* 3.4 20.3 + - - -
184C ARG* 5.7 0.3 + - - -
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Residues in contact with ASN 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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15A T 6.4 0.2 - - + -
16A A 4.9 18.8 - - + +
17A C 4.3 26.9 - - - +
174C ILE* 2.8 39.3 + - - +
175C GLN* 3.9 5.3 - - - +
176C ILE 3.1 0.2 - - - -
177C LYS* 1.3 81.2 + - - +
179C TRP* 1.3 65.2 + - - +
181C SER* 4.0 6.6 + - - -
182C ASN* 3.1 33.7 + - - +
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Residues in contact with TRP 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A T 3.6 27.3 + - - -
136C PHE* 4.2 12.6 - + + -
141C VAL* 4.5 12.6 - - + +
144C LEU* 3.2 69.3 - - + +
145C GLU* 3.4 21.1 - - + -
148C PHE* 4.3 6.1 - - + -
175C GLN 2.9 20.0 + - - +
176C ILE* 2.9 5.1 + - - +
178C ASN* 1.3 71.4 - - - +
180C VAL* 1.3 86.0 + - + +
182C ASN* 2.9 11.0 + - + +
183C ARG* 2.8 67.0 + - + +
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Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.1 2.0 - - + -
147C TRP* 3.5 22.9 - - + -
148C PHE* 4.2 2.2 - - + -
155C PRO 3.5 14.6 - - - +
157C LEU* 3.6 35.2 - - + -
176C ILE* 3.1 18.2 + - + +
177C LYS 4.4 0.7 - - - +
179C TRP* 1.3 94.6 - - + +
181C SER* 1.3 61.7 + - - +
183C ARG* 3.6 3.8 - - - +
184C ARG* 3.3 40.8 + - - +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A C 5.8 0.3 + - - -
24B C 5.6 5.4 - - - -
25B G 4.8 7.8 + - - -
26B T 3.9 30.0 + - - +
177C LYS 3.4 17.2 + - - -
178C ASN* 4.0 9.6 + - - -
179C TRP 3.2 0.8 - - - -
180C VAL* 1.3 71.4 - - - +
182C ASN* 1.3 69.6 + - - +
184C ARG* 2.8 35.4 + - - +
185C ARG* 3.1 8.5 + - - +
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Residues in contact with ASN 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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15A T 3.6 31.4 - - + +
16A A 3.0 48.5 + - - +
17A C 4.4 4.1 + - - +
26B T 5.2 0.9 - - - +
178C ASN* 3.1 22.9 + - - +
179C TRP* 2.9 8.8 + - + +
181C SER* 1.3 76.1 + - - +
183C ARG* 1.3 53.7 + - - +
185C ARG* 2.8 51.2 + - - +
186C LYS* 3.0 10.9 + - - +
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Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLU* 2.9 39.0 + - - -
148C PHE* 3.1 41.7 - - + -
179C TRP* 2.8 50.4 + - + +
180C VAL 3.6 6.1 - - - +
182C ASN* 1.3 70.8 - - - +
184C ARG* 1.3 56.5 + - - +
186C LYS* 3.2 27.9 + - - +
187C GLU* 3.0 52.1 + - - +
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Residues in contact with ARG 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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24B C 4.3 13.3 + - - -
25B G 2.4 34.4 + - - +
148C PHE* 3.4 20.0 - - + -
155C PRO* 2.8 38.5 + - + +
156C TYR* 3.3 33.2 - - - +
157C LEU* 4.8 2.6 - - - +
177C LYS 5.7 0.2 + - - -
180C VAL* 3.3 33.8 + - - +
181C SER* 2.8 29.3 + - - +
183C ARG* 1.3 69.3 - - - +
185C ARG* 1.3 64.5 + - - +
187C GLU* 3.4 3.7 + - - +
188C LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 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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15A T 5.4 2.4 + - - +
16A A 3.4 5.3 - - - +
26B T 3.7 39.3 + - + +
27B G 2.9 45.9 + - - -
28B T 3.0 25.7 + - - +
181C SER 3.1 6.1 + - - +
182C ASN* 2.8 44.9 + - - +
184C ARG* 1.3 69.5 - - - +
186C LYS* 1.3 58.8 + - - +
188C LYS* 2.8 33.6 + - + +
189C THR* 3.3 7.6 + - - -
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Residues in contact with LYS 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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13A T 4.5 14.5 + - - -
14A T 2.9 31.7 + - - +
145C GLU* 5.9 0.2 - - - +
182C ASN 3.0 10.8 + - - +
183C ARG* 3.4 32.8 - - - +
184C ARG 3.1 0.2 - - - -
185C ARG* 1.3 71.2 - - - +
187C GLU* 1.3 68.0 + - - +
189C THR* 2.7 33.6 + - - +
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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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148C PHE* 4.0 20.0 - - + -
152C ILE* 4.6 18.6 - - + +
183C ARG* 3.0 26.9 + - - +
184C ARG* 3.4 8.3 + - - +
186C LYS* 1.3 78.0 - - - +
188C LYS* 1.3 56.1 + - - +
189C THR 2.9 11.7 + - - -
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Residues in contact with LYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B G 4.1 18.0 + - - -
26B T 3.1 39.7 + - - +
184C ARG* 3.0 16.6 + - - +
185C ARG* 2.8 22.3 + - + +
186C LYS 2.8 3.4 + - - -
187C GLU* 1.3 70.6 - - - +
189C THR* 1.3 61.1 + - - +
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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