Contacts of the helix formed by residues 137 - 151 (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 THR 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ARG 3.7 2.4 + - - -
136C PHE* 1.3 72.7 - - - +
138C LYS* 1.3 56.5 + - - +
139C GLU* 4.1 14.8 - - + +
140C ASN* 2.7 45.1 + - - +
141C VAL 3.2 7.1 + - - -
170C SER* 5.4 4.3 - - - +
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Residues in contact with LYS 138 (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 PHE 3.4 4.1 + - - -
137C THR* 1.3 68.9 - - - +
139C GLU* 1.4 64.0 + - - +
140C ASN 3.1 0.2 + - - -
141C VAL* 3.3 6.0 + - - +
142C ARG* 2.8 32.9 + - + +
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Residues in contact with GLU 139 (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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137C THR* 3.1 12.8 + - + +
138C LYS* 1.4 77.5 - - - +
140C ASN* 1.3 65.7 + - - +
142C ARG* 3.1 40.4 + - - +
143C ILE* 2.9 43.4 + - + +
168C ASN 4.7 3.6 - - - +
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Residues in contact with ASN 140 (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 PHE* 4.1 12.8 - - + +
137C THR* 2.7 34.9 + - - +
139C GLU* 1.3 73.4 + - - +
141C VAL* 1.3 58.7 + - - +
142C ARG 2.9 0.9 - - - -
143C ILE* 2.7 25.4 + - - +
144C LEU* 2.9 16.0 + - + +
168C ASN 4.2 2.6 + - - -
169C THR* 3.2 33.8 - - + +
170C SER* 3.6 17.2 + - - +
171C LEU* 3.1 32.5 - - + +
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Residues in contact with VAL 141 (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 4.0 29.2 - - - +
136C PHE* 4.0 25.1 - - + +
137C THR 3.2 5.3 + - - +
138C LYS* 3.3 6.0 + - - +
140C ASN* 1.3 75.9 - - - +
142C ARG* 1.3 60.1 + - - +
144C LEU* 4.5 7.0 - - - -
145C GLU* 3.1 33.9 + - + +
179C TRP* 4.5 13.2 - - + +
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Residues in contact with ARG 142 (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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138C LYS* 2.8 23.1 + - + +
139C GLU* 3.1 46.2 + - - +
140C ASN 2.8 0.6 + - - -
141C VAL* 1.3 76.6 - - - +
143C ILE* 1.3 69.9 + - - +
145C GLU* 3.3 6.3 + - - +
146C SER* 2.9 21.7 + - - -
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Residues in contact with ILE 143 (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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139C GLU* 2.9 36.8 + - + +
140C ASN* 2.7 10.9 + - - +
142C ARG* 1.3 79.4 - - - +
144C LEU* 1.3 61.7 + - - +
146C SER* 2.8 33.0 + - - +
147C TRP* 2.9 7.7 + - + +
165C LEU* 4.5 13.5 - - + -
168C ASN* 3.1 45.5 - - + +
169C THR* 3.8 12.6 - - + -
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Residues in contact with LEU 144 (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 PHE* 4.0 26.2 - - + -
140C ASN 2.9 19.2 + - - +
141C VAL* 4.2 2.9 - - - +
143C ILE* 1.3 77.7 - - - +
145C GLU* 1.3 61.1 + - - +
147C TRP* 3.3 3.8 + - - +
148C PHE 3.0 18.2 + - - -
165C LEU* 3.6 26.9 - - + -
169C THR* 4.9 7.6 - - + -
171C LEU* 4.8 8.1 - - + -
176C ILE* 3.9 27.8 - - + -
179C TRP* 3.2 55.8 - - + +
180C VAL* 5.1 1.1 - - + -
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Residues in contact with GLU 145 (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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141C VAL* 3.1 30.8 + - + +
142C ARG* 3.6 5.2 - - - +
144C LEU* 1.3 71.7 - - - +
146C SER* 1.3 67.2 + - - +
147C TRP 3.1 0.2 + - - -
148C PHE* 3.1 4.1 + - - +
149C ALA* 3.0 25.1 + - - +
179C TRP* 3.7 13.5 - - + -
183C ARG* 2.9 40.9 + - - -
186C LYS* 5.9 0.5 - - - +
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Residues in contact with SER 146 (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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142C ARG 2.9 13.0 + - - -
143C ILE* 2.8 30.7 + - - +
145C GLU* 1.3 76.1 - - - +
147C TRP* 1.3 58.2 + - - +
149C ALA* 3.2 4.7 + - - +
150C LYS* 2.9 33.7 + - - +
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Residues in contact with TRP 147 (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 ILE* 2.9 11.3 + - + +
144C LEU* 3.5 9.0 - - + +
146C SER* 1.3 81.5 + - - +
148C PHE* 1.3 88.4 + + + +
150C LYS* 3.3 3.0 + - - -
151C ASN* 2.9 49.8 + - + +
155C PRO* 3.5 32.5 - - + -
156C TYR 3.8 13.5 - - - -
157C LEU* 3.6 25.5 - - + +
158C ASP* 5.3 1.8 - - - -
161C GLY* 5.0 12.1 - - - -
165C LEU* 4.1 25.8 - - + +
180C VAL* 3.5 33.9 - - + -
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Residues in contact with PHE 148 (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 3.0 10.8 + - - +
145C GLU* 3.1 9.2 + - - +
147C TRP* 1.3 94.4 - + + +
149C ALA* 1.3 64.7 + - - +
151C ASN* 3.1 18.8 + - - -
152C ILE* 3.2 25.8 + - + -
155C PRO* 4.1 19.1 - - + -
179C TRP* 4.3 9.0 - + + -
180C VAL* 4.2 3.4 - - + -
183C ARG* 3.1 49.6 - - + -
184C ARG* 3.4 36.3 - - + -
187C GLU* 4.0 20.6 - - + -
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Residues in contact with ALA 149 (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 GLU* 3.0 18.8 + - - +
146C SER* 3.8 5.2 - - - +
148C PHE* 1.3 75.6 - - - +
150C LYS* 1.4 59.2 + - - +
151C ASN 2.9 9.6 + - - -
152C ILE* 3.2 29.7 - - - +
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Residues in contact with LYS 150 (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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146C SER 2.9 20.9 + - - +
147C TRP* 3.8 4.5 - - + +
149C ALA* 1.4 70.2 - - - +
151C ASN* 1.3 68.9 + - - +
152C ILE* 3.9 1.4 + - - +
153C GLU* 4.4 9.5 - - - +
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Residues in contact with ASN 151 (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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147C TRP* 2.9 53.5 + - + +
148C PHE 3.1 6.1 - - - +
149C ALA 2.9 0.6 + - - -
150C LYS* 1.3 90.5 + - - +
152C ILE* 1.4 61.2 + - - -
153C GLU* 3.2 14.3 + - - -
154C ASN 3.5 7.8 + - - +
155C PRO* 3.2 25.1 - - + +
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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