Contacts of the helix formed by residues 136 - 148 (chain C) in PDB entry 1L0N
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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C PHE* 4.7 3.8 - - - -
134C PRO* 3.4 3.6 - - - +
135C TRP* 1.3 79.5 - - - +
137C GLN* 1.3 66.4 + - - +
138C MET 3.2 3.1 - - - -
139C SER* 2.9 7.3 + - - -
140C PHE* 2.9 22.9 + - - +
255C ASN* 3.3 25.8 - - - -
257C THR 4.0 6.1 - - - -
259C ALA* 4.4 4.0 - - - -
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Residues in contact with GLN 137 (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 GLY* 1.3 70.6 - - - +
138C MET* 1.3 66.7 + - + +
140C PHE* 3.4 0.5 + - - +
141C TRP* 3.1 55.2 + - - +
254C ASP 5.4 2.5 - - - +
255C ASN* 3.4 4.8 + - - +
256C TYR 4.6 4.0 - - - +
257C THR* 3.5 21.9 + - - +
258C PRO 3.0 15.5 + - - +
259C ALA* 3.4 1.2 - - - +
260C ASN* 2.9 37.0 + - - +
263C ASN* 3.9 15.5 - - - +
265C PRO* 3.3 23.4 - - + +
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Residues in contact with MET 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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131C TYR* 3.6 25.1 - - + +
137C GLN* 1.3 81.4 - - + +
139C SER* 1.3 61.1 + - - +
141C TRP* 5.0 0.9 - - + -
142C GLY* 2.8 37.1 + - - +
254C ASP* 4.3 19.3 - - + +
255C ASN* 3.0 14.6 + - + +
265C PRO* 4.7 12.1 - - - -
267C HIS* 3.6 28.0 - - + +
268C ILE* 3.6 19.3 - - + -
269C LYS 3.4 42.8 - - - +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 2.6 34.3 + - - -
132C VAL* 3.4 26.8 + - - +
134C PRO* 3.9 1.2 - - - +
135C TRP* 3.8 3.4 + - - -
136C GLY 2.9 27.4 + - - -
138C MET* 1.3 77.8 - - - +
140C PHE* 1.3 56.1 + - - +
143C ALA* 3.0 27.5 + - - +
255C ASN* 3.3 16.4 + - - -
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Residues in contact with PHE 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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135C TRP* 3.8 22.9 - + + -
136C GLY 2.9 14.2 + - - +
137C GLN 3.9 2.0 - - - +
139C SER* 1.3 77.4 - - - +
141C TRP* 1.3 101.9 + + - +
143C ALA* 3.3 6.2 + - - +
144C THR* 2.7 48.3 + - + -
169C SER* 5.5 4.9 - - - -
170C VAL* 3.2 41.0 - - + +
259C ALA* 3.9 17.7 - - + -
260C ASN 4.6 1.6 - - - -
261C PRO* 3.7 32.1 - - + -
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Residues in contact with TRP 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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137C GLN* 3.1 44.6 + - - +
138C MET* 4.6 3.6 - - + +
140C PHE* 1.3 99.5 - + - +
142C GLY* 1.3 58.8 + - - +
143C ALA 3.1 1.1 - - - -
144C THR* 4.0 18.2 - - + -
145C VAL* 2.7 41.0 + - + +
260C ASN 3.4 22.2 + - - -
261C PRO 3.7 17.5 - - - -
262C LEU 4.9 0.4 - - - -
263C ASN 4.7 0.2 - - - -
264C THR* 3.4 42.7 - - + +
265C PRO* 3.4 20.8 - - + +
268C ILE* 4.3 22.4 - - + -
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PHE* 3.9 2.6 - - - -
131C TYR* 6.1 2.0 - - - -
132C VAL* 5.6 0.2 - - - -
138C MET* 2.8 28.1 + - - +
141C TRP* 1.3 76.7 - - - +
143C ALA* 1.3 61.3 + - - +
145C VAL* 4.8 3.8 - - - -
146C ILE* 3.2 42.4 + - - +
268C ILE* 5.2 2.0 - - - -
269C LYS 5.7 1.6 - - - -
270C PRO* 5.8 4.5 - - - -
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Residues in contact with ALA 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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128C PHE* 4.3 11.0 - - - -
132C VAL* 3.7 23.9 - - + +
139C SER 3.0 23.6 + - - +
140C PHE 3.3 6.7 - - - +
141C TRP 3.1 0.2 - - - -
142C GLY* 1.3 77.9 - - - +
144C THR* 1.3 57.6 + - - +
147C THR* 2.6 32.7 + - - -
170C VAL* 3.9 19.3 - - + +
178C PHE* 4.7 5.4 - - + -
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Residues in contact with THR 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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140C PHE* 2.7 38.7 + - + -
141C TRP* 3.5 25.6 - - + -
143C ALA* 1.3 77.1 - - - +
145C VAL* 1.3 69.3 + - + +
146C ILE 3.2 0.5 + - - -
147C THR* 4.0 0.3 - - - -
148C ASN* 3.0 43.8 + - - +
165C TRP* 4.5 7.9 - - + -
170C VAL* 3.5 17.0 - - + +
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Residues in contact with VAL 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 TRP* 2.7 24.2 + - + +
142C GLY* 4.4 2.5 - - - +
144C THR* 1.3 77.1 - - + +
146C ILE* 1.3 70.9 + - + +
148C ASN* 3.6 13.0 + - - +
149C LEU* 3.8 12.1 + - + +
268C ILE* 3.5 35.2 - - + -
270C PRO* 6.2 0.9 - - + -
278C TYR* 4.8 18.2 - - + +
281C LEU* 6.2 2.2 - - + -
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Residues in contact with ILE 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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128C PHE* 3.6 35.4 - - + -
142C GLY* 3.2 24.6 + - - +
145C VAL* 1.3 80.2 - - + +
147C THR* 1.3 68.4 + - - +
149C LEU* 3.2 37.0 + - + +
150C LEU* 4.6 1.2 + - - +
270C PRO* 3.8 35.9 - - + -
274C PHE* 5.3 15.0 - - + -
278C TYR* 6.2 0.7 - - + -
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Residues in contact with THR 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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128C PHE* 3.7 16.1 - - - -
143C ALA 2.6 24.6 + - - -
144C THR 3.3 1.6 + - - -
146C ILE* 1.3 76.5 - - - +
148C ASN* 1.3 57.6 + - - +
149C LEU 3.0 6.1 + - - -
150C LEU* 3.3 24.5 + - + +
161C VAL* 3.9 7.3 - - + +
164C ILE* 3.6 32.8 - - + -
165C TRP* 3.4 29.2 + - + +
178C PHE* 4.1 9.7 - - + -
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Residues in contact with ASN 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 THR* 3.0 27.9 + - - +
145C VAL* 3.8 7.2 - - - +
146C ILE 3.2 0.4 - - - -
147C THR* 1.3 73.4 - - - +
149C LEU* 1.3 60.0 + - - +
150C LEU 3.2 0.7 - - - -
151C SER* 2.7 38.4 + - - -
161C VAL* 3.9 10.5 - - - +
165C TRP* 3.3 35.3 - - - -
287C LYS* 4.6 1.6 + - - -
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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