Contacts of the helix formed by residues 153 - 169 (chain C) in PDB entry 1LUA
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 LYS 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C GLY* 3.2 2.9 - - - -
152C ARG* 1.3 89.6 - - + +
154C LEU* 1.3 66.8 + - - +
155C ASP* 3.4 18.3 + - - +
156C LYS* 3.5 12.0 + - + +
157C ALA* 3.1 21.7 + - - +
176C GLU* 3.5 9.4 - - - +
2456C NAP 4.9 2.2 + - - -
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Residues in contact with LEU 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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153C LYS* 1.3 73.6 - - - +
155C ASP* 1.3 59.1 + - - +
157C ALA* 3.3 2.8 + - - -
158C GLN* 2.8 38.5 + - + +
174C ALA* 4.3 12.6 - - + +
175C ALA* 4.2 12.6 - - - +
176C GLU* 2.7 45.4 + - + +
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Residues in contact with ASP 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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153C LYS* 3.4 20.7 - - - +
154C LEU* 1.3 75.4 + - - +
156C LYS* 1.3 63.9 + - - +
158C GLN* 3.4 5.1 + - - +
159C ALA* 2.9 29.3 + - - +
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Residues in contact with LYS 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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129C THR* 3.8 16.8 - - + -
152C ARG* 4.8 1.6 - - - +
153C LYS* 3.5 13.7 + - + +
154C LEU 3.3 0.2 - - - -
155C ASP* 1.3 86.1 + - - +
157C ALA* 1.3 63.6 + - - +
159C ALA* 3.3 7.4 + - + +
160C ALA* 3.0 22.3 + - - +
2456C NAP 2.8 51.9 + - - +
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Residues in contact with ALA 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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129C THR* 3.6 14.6 - - + +
149C LEU* 4.0 15.6 - - - +
151C GLY* 4.1 10.8 - - - +
153C LYS 3.1 17.7 + - - +
154C LEU* 3.7 4.5 - - - +
156C LYS* 1.3 77.3 - - - +
158C GLN* 1.3 62.5 + - - +
160C ALA* 3.3 4.3 + - - +
161C ALA* 3.1 18.0 + - - +
174C ALA* 3.6 11.9 - - + +
175C ALA 3.9 21.3 - - - +
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Residues in contact with GLN 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 LEU* 2.8 27.0 + - + +
155C ASP* 3.8 4.5 - - - +
157C ALA* 1.3 75.3 - - - +
159C ALA* 1.3 61.4 + - - +
161C ALA* 3.3 9.5 + - - +
162C ASP* 2.9 62.8 + - - +
165C ASN* 5.5 1.8 - - - +
172C VAL 5.3 2.6 + - - -
173C THR* 5.9 0.4 - - - +
174C ALA* 3.5 25.0 + - + +
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Residues in contact with ALA 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 ASP 2.9 17.7 + - - +
156C LYS* 3.6 8.7 - - - +
158C GLN* 1.3 77.5 - - - +
160C ALA* 1.3 57.2 + - - +
162C ASP* 3.3 10.3 + - - +
163C SER* 2.9 29.9 + - - -
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Residues in contact with ALA 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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129C THR* 4.1 9.6 - - + +
134C MET* 3.6 29.6 - - + +
149C LEU* 4.0 18.4 - - + -
156C LYS 3.0 12.6 + - - +
157C ALA 3.4 9.6 - - - +
158C GLN 3.1 0.2 - - - -
159C ALA* 1.3 77.3 - - - +
161C ALA* 1.3 62.7 + - - +
163C SER* 3.2 3.7 + - - -
164C VAL* 3.0 29.1 + - - +
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Residues in contact with ALA 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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149C LEU* 4.2 8.2 - - + +
157C ALA 3.1 14.7 + - - +
158C GLN* 3.3 10.1 + - - +
160C ALA* 1.3 73.2 - - - +
162C ASP* 1.3 59.9 + - - +
164C VAL* 3.3 6.1 + - - +
165C ASN* 2.8 38.7 + - - +
172C VAL* 3.8 31.6 - - + +
174C ALA* 4.2 15.5 - - + -
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Residues in contact with ASP 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 GLN* 2.9 54.4 + - - +
159C ALA* 3.5 9.3 - - - +
161C ALA* 1.3 75.9 - - - +
163C SER* 1.3 63.5 + - - +
165C ASN* 3.8 8.9 + - - +
166C LYS* 3.0 27.6 + - - +
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Residues in contact with SER 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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134C MET* 3.7 18.2 - - - +
159C ALA 2.9 13.6 + - - -
160C ALA* 3.2 8.5 + - - -
162C ASP* 1.3 76.7 - - - +
164C VAL* 1.3 57.3 + - - +
166C LYS* 3.8 5.5 - - - +
167C ARG* 2.9 32.7 + - - +
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Residues in contact with VAL 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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134C MET* 3.6 41.3 - - + +
137C ALA* 4.7 0.7 - - + -
138C ALA* 3.7 37.2 - - + +
149C LEU* 4.6 5.8 - - + -
160C ALA 3.0 21.7 + - - +
161C ALA* 3.7 5.8 - - - +
163C SER* 1.3 74.1 - - - +
165C ASN* 1.3 59.9 + - - +
167C ARG* 4.7 0.7 - - - -
168C PHE* 2.9 39.6 + - + +
170C VAL* 4.0 10.3 - - + +
172C VAL* 4.2 10.5 - - + -
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Residues in contact with ASN 165 (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 GLN* 5.5 1.6 - - - +
161C ALA* 2.8 32.3 + - - +
162C ASP* 3.9 10.5 + - - +
164C VAL* 1.3 72.5 - - - +
166C LYS* 1.3 57.4 + - - +
169C LYS* 2.9 28.6 + - - -
170C VAL* 3.1 27.5 + - - +
171C ASN* 4.0 7.0 + - - +
172C VAL* 2.7 48.1 + - - +
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Residues in contact with LYS 166 (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 ASP 3.0 17.7 + - - +
163C SER* 3.8 5.4 - - - +
165C ASN* 1.3 78.2 - - - +
167C ARG* 1.3 64.0 + - - +
168C PHE 3.6 0.2 + - - -
169C LYS* 3.9 14.2 + - - +
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Residues in contact with ARG 167 (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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74C GLU* 5.5 4.1 + - - +
78C GLU* 5.7 2.8 + - - -
81C LYS* 5.7 3.8 - - - +
135C ARG* 5.3 6.3 - - - +
163C SER* 2.9 19.7 + - - +
164C VAL* 4.7 0.2 - - - -
166C LYS* 1.3 82.1 - - - +
168C PHE* 1.3 91.2 + - + +
169C LYS* 4.8 2.9 - - - +
276C ASP* 3.1 30.3 + - - +
278C GLU* 3.0 38.4 + - - -
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Residues in contact with PHE 168 (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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134C MET 5.3 0.7 - - - -
135C ARG* 3.9 37.0 - - - -
138C ALA* 3.4 32.3 - - + +
139C LEU* 5.8 2.7 - - + -
164C VAL* 2.9 29.0 + - + +
167C ARG* 1.3 113.8 - - + +
169C LYS* 1.3 76.2 + - - +
170C VAL* 3.5 18.0 - - + +
277C ALA* 4.0 11.0 - - + -
278C GLU* 3.6 29.4 - - + -
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Residues in contact with LYS 169 (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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165C ASN 2.9 13.0 + - - -
166C LYS* 4.2 13.0 - - - +
167C ARG 3.5 3.1 - - - +
168C PHE* 1.3 82.5 - - - +
170C VAL* 1.3 62.6 + - - +
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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