Contacts of the helix formed by residues 150 - 164 (chain C) in PDB entry 1L9W
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 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C PRO* 1.3 78.2 - - - +
151C ALA* 1.3 66.4 + - - +
152C GLU* 3.5 10.8 + - - +
153C GLU* 3.0 20.6 + - - +
154C MET* 2.9 19.9 + - - +
183C THR* 4.3 3.4 - - - -
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Residues in contact with ALA 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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150C SER* 1.3 74.3 - - - +
152C GLU* 1.3 54.9 + - - +
154C MET* 3.3 8.7 + - - +
155C VAL* 2.9 36.5 + - - +
183C THR* 3.8 30.7 - - + +
186C THR* 4.7 11.0 - - + -
187C ALA* 4.0 11.4 - - + +
190C GLU* 4.8 8.3 - - - +
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Residues in contact with GLU 152 (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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150C SER* 3.6 9.6 + - - +
151C ALA* 1.3 73.7 - - - +
153C GLU* 1.3 62.6 + - - +
155C VAL* 3.4 6.4 + - - +
156C SER* 2.9 28.2 + - - -
190C GLU* 5.6 2.2 - - - -
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Residues in contact with GLU 153 (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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118C PHE* 5.3 1.2 - - - -
149C PRO* 3.8 19.3 - - + -
150C SER* 3.0 16.9 + - - +
152C GLU* 1.3 80.2 + - - +
154C MET* 1.4 62.7 + - - +
156C SER* 3.3 11.6 + - - -
157C ARG* 2.8 69.2 + - - +
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Residues in contact with MET 154 (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 THR* 3.9 4.3 - - + -
149C PRO* 3.6 22.9 - - + +
150C SER 2.9 11.0 + - - +
151C ALA* 3.8 7.0 - - - +
153C GLU* 1.4 74.6 - - - +
155C VAL* 1.3 58.8 + - - +
157C ARG* 3.3 4.1 + - - +
158C LEU* 2.9 36.0 + - + +
171C ILE* 3.9 25.9 - - + +
173C VAL* 3.9 20.9 - - - -
183C THR* 3.6 35.0 - - + +
184C LEU* 3.7 40.4 - - - +
187C ALA* 4.0 11.9 - - + -
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Residues in contact with VAL 155 (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 ALA 2.9 21.7 + - - +
152C GLU* 3.8 6.1 - - - +
154C MET* 1.3 77.9 - - - +
156C SER* 1.3 62.6 + - - +
158C LEU* 3.3 7.2 + - + +
159C ARG* 2.9 50.5 + - + +
187C ALA* 3.7 32.3 - - + +
190C GLU* 4.2 20.4 - - + +
191C MET* 4.6 6.1 - - + +
195C TYR* 3.9 22.4 - - + -
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Residues in contact with SER 156 (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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152C GLU 2.9 17.5 + - - -
153C GLU* 3.3 15.2 + - - -
155C VAL* 1.3 75.8 - - - +
157C ARG* 1.3 51.7 + - - +
159C ARG* 3.2 15.2 + - - +
160C LYS* 2.7 40.9 + - - +
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Residues in contact with ARG 157 (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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117C LEU* 4.3 11.2 - - + +
118C PHE* 3.8 27.7 - - + -
142C ASN* 2.9 42.4 + - - +
143C HIS 5.1 1.0 + - - -
144C ASP* 4.9 13.1 + - - +
149C PRO* 4.1 20.3 - - - +
153C GLU* 2.8 49.1 + - - +
154C MET* 3.4 9.9 - - - +
156C SER* 1.3 75.3 - - - +
158C LEU* 1.4 58.5 + - - +
160C LYS* 3.2 8.7 + - + +
161C MET* 2.9 41.1 + - + +
171C ILE* 4.5 9.4 - - + +
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Residues in contact with LEU 158 (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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154C MET* 2.9 25.8 + - + +
155C VAL* 3.6 5.8 - - + +
157C ARG* 1.4 76.1 - - + +
159C ARG* 1.3 62.7 + - - +
161C MET* 3.2 9.4 + - + +
162C GLN* 3.1 21.1 + - - +
169C PRO* 3.9 29.0 - - + +
170C LYS 4.3 8.3 - - - +
171C ILE* 4.1 27.6 - - + +
187C ALA* 4.7 7.2 - - + +
191C MET* 3.6 41.3 - - + +
200C VAL* 4.3 13.0 - - + -
202C THR* 4.4 10.5 - - + -
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Residues in contact with ARG 159 (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 VAL* 2.9 39.5 + - - +
156C SER* 3.6 9.7 - - - +
158C LEU* 1.3 71.9 - - - +
160C LYS* 1.3 61.2 + - - +
162C GLN* 3.2 13.5 - - - +
163C ALA* 2.9 29.2 + - - +
191C MET* 4.0 15.3 - - + -
195C TYR* 3.6 47.3 + - + -
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Residues in contact with LYS 160 (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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117C LEU* 3.6 32.4 + - + +
118C PHE* 5.0 7.5 - - - -
121C ASP* 3.0 39.1 + - - -
156C SER* 2.7 24.2 + - - +
157C ARG* 3.5 7.4 - - + +
159C ARG* 1.3 71.5 - - - +
161C MET* 1.3 62.1 + - - +
163C ALA* 3.2 8.9 + - - +
164C LEU* 3.2 26.9 + - + +
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Residues in contact with MET 161 (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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117C LEU* 3.8 17.0 - - + -
140C MET* 3.3 51.1 - - - +
141C SER 4.1 1.3 - - - -
142C ASN* 3.4 26.7 - - + +
157C ARG* 2.9 28.5 + - + +
158C LEU* 3.2 12.5 + - + +
160C LYS* 1.3 76.1 - - - +
162C GLN* 1.3 64.4 + - - +
164C LEU* 3.3 9.1 + - - +
165C GLY 3.4 0.2 + - - -
166C ALA* 3.0 27.3 + - + +
169C PRO* 3.8 12.3 - - + -
170C LYS 3.4 29.6 - - - +
171C ILE* 5.0 1.1 - - + -
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Residues in contact with GLN 162 (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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158C LEU 3.1 9.9 + - - +
159C ARG* 3.2 13.5 - - - +
161C MET* 1.3 80.5 - - - +
163C ALA* 1.3 63.0 + - - +
165C GLY* 3.1 12.0 + - - -
166C ALA 4.5 0.7 - - - +
169C PRO* 4.3 9.4 - - + +
191C MET* 3.8 12.4 - - - +
195C TYR* 3.3 16.8 - - - +
196C ALA* 3.6 9.3 - - - +
197C ASP* 3.2 37.1 + - - +
198C ARG* 3.5 45.1 + - - +
200C VAL* 5.5 0.2 - - - +
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Residues in contact with ALA 163 (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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125C LYS* 5.3 4.0 - - - -
159C ARG 2.9 18.9 + - - +
160C LYS* 3.2 8.0 + - - +
162C GLN* 1.3 75.5 - - - +
164C LEU* 1.3 61.0 + - + +
165C GLY* 3.3 1.2 + - - -
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Residues in contact with LEU 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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117C LEU* 3.7 30.1 - - + -
121C ASP* 4.3 34.5 - - + +
124C VAL* 4.0 17.7 - - + -
125C LYS* 3.9 37.7 - - + +
128C VAL* 3.9 14.6 - - - +
129C ASP* 5.4 0.3 - - - +
140C MET* 3.9 13.5 - - + -
160C LYS* 3.2 19.0 + - + +
161C MET 3.3 7.5 + - - +
163C ALA* 1.3 74.9 - - + +
165C GLY* 1.3 58.4 + - - +
166C ALA 3.5 0.6 + - - -
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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