Contacts of the helix formed by residues 152 - 165 (chain C) in PDB entry 3LSG
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 ASN 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C ALA* 1.3 67.5 + - - +
154C LYS* 3.2 5.8 + - - +
155C GLU* 3.4 27.3 + - - +
156C LEU* 3.6 27.1 + - - +
193C ASN* 5.7 2.6 - - - +
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Residues in contact with ALA 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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152C ASN* 1.3 76.9 - - - +
154C LYS* 1.3 60.3 + - - +
156C LEU* 3.4 9.3 + - - +
157C ILE* 2.9 46.5 + - + +
189C MSE 5.0 9.9 - - + -
193C ASN* 4.7 11.1 - - - +
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Residues in contact with LYS 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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152C ASN 3.2 2.8 - - - +
153C ALA* 1.3 79.8 - - - +
155C GLU* 1.3 57.0 + - - +
157C ILE 3.3 0.7 + - - -
158C GLN* 2.9 52.6 + - - +
193C ASN* 3.3 42.5 + - + +
194C PHE* 3.6 45.5 + - + +
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Residues in contact with GLU 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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152C ASN* 3.4 21.8 + - - +
154C LYS* 1.3 77.7 - - - +
156C LEU* 1.3 64.5 + - - +
158C GLN* 3.3 18.3 - - - +
159C ASN* 3.1 41.3 + - - +
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Residues in contact with LEU 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 ASN* 3.6 33.8 + - - +
153C ALA* 3.4 9.4 + - - +
154C LYS 3.2 0.6 - - - -
155C GLU* 1.3 83.3 - - + +
157C ILE* 1.3 65.6 + - + +
159C ASN* 3.2 18.8 + - + +
160C ILE* 3.1 22.2 + - - +
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Residues in contact with ILE 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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153C ALA* 2.9 27.9 + - + +
154C LYS 3.9 2.9 - - - +
156C LEU* 1.3 75.0 - - + +
158C GLN* 1.3 68.4 + - - +
160C ILE* 3.2 11.4 - - + +
161C ILE* 3.0 42.4 + - + +
175C LEU* 4.5 10.8 - - + -
179C LEU* 5.4 9.4 - - + -
186C LEU* 4.9 6.7 - - + -
189C MSE 3.6 39.3 - - + -
190C PHE* 4.0 10.8 - - + -
193C ASN* 6.0 0.7 - - + -
194C PHE* 3.9 20.4 - - + -
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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 LYS* 2.9 41.2 + - - +
155C GLU* 3.3 24.7 - - - +
157C ILE* 1.3 77.5 - - - +
159C ASN* 1.3 65.9 + - - +
161C ILE* 3.3 5.2 + - - +
162C GLU* 3.0 23.4 + - - +
194C PHE* 3.7 17.1 - - + -
201C TYR* 3.7 22.7 + - - +
205C LYS* 5.4 1.9 + - - -
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Residues in contact with ASN 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 GLU* 3.1 29.7 + - - +
156C LEU* 3.5 23.6 - - + +
157C ILE 3.2 0.6 - - - -
158C GLN* 1.3 83.5 - - - +
160C ILE* 1.3 64.3 + - - +
162C GLU* 3.1 9.5 + - - +
163C GLU* 3.1 31.0 + - - +
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Residues in contact with ILE 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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156C LEU 3.1 5.8 + - - +
157C ILE* 3.2 22.7 - - + +
159C ASN* 1.3 78.9 - - - +
161C ILE* 1.3 68.0 + - + +
163C GLU* 3.2 16.7 + - - +
164C SER* 2.7 38.3 + - - +
170C PHE* 5.3 0.4 - - + -
175C LEU* 3.9 34.1 - - + -
178C LYS* 4.7 19.1 - - + +
179C LEU* 6.0 5.8 - - + -
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Residues in contact with ILE 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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157C ILE* 3.0 36.9 + - + +
158C GLN 3.7 3.6 - - - +
160C ILE* 1.3 81.1 - - + +
162C GLU* 1.3 57.6 + - - +
164C SER 2.9 16.8 + - - -
165C TYR* 2.9 18.4 + - + +
170C PHE* 4.1 22.7 - - + -
175C LEU* 4.4 0.4 - - + -
190C PHE* 3.8 18.4 - - + -
194C PHE* 5.2 0.2 - - + -
198C PHE* 3.9 13.5 - - + -
201C TYR* 3.9 28.9 - - + -
202C LEU* 4.1 25.4 - - + -
205C LYS* 5.0 6.7 - - + +
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Residues in contact with GLU 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 3.0 13.2 + - - +
159C ASN* 3.4 11.9 - - - +
161C ILE* 1.3 76.6 - - - +
163C GLU* 1.3 62.3 + - + +
165C TYR* 3.1 40.3 + - - -
166C THR* 5.4 0.3 - - - +
205C LYS* 3.0 28.6 + - - +
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Residues in contact with GLU 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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159C ASN* 3.1 21.3 + - - +
160C ILE* 3.6 21.0 - - + +
161C ILE 3.1 0.4 - - - -
162C GLU* 1.3 79.5 - - + +
164C SER* 1.3 61.1 + - - +
165C TYR 3.8 0.2 - - - -
166C THR* 5.4 4.5 + - - +
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Residues in contact with SER 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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160C ILE* 2.7 29.4 + - - +
161C ILE 2.9 1.4 + - - -
163C GLU* 1.3 83.8 - - - +
165C TYR* 1.3 63.3 + - - +
166C THR* 3.3 3.6 - - - -
167C ASP* 3.1 18.5 + - - +
170C PHE* 3.4 49.2 - - - +
178C LYS* 4.4 9.6 + - - -
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Residues in contact with TYR 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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161C ILE* 2.9 14.7 + - + +
162C GLU* 3.1 49.5 + - - -
164C SER* 1.3 76.7 - - - +
166C THR* 1.3 79.6 + - + +
167C ASP 3.1 1.6 - - - -
170C PHE* 4.3 2.9 - - - -
202C LEU* 3.7 28.0 - - + -
205C LYS* 4.7 12.6 - - + -
206C ARG* 2.9 40.8 + - + -
209C LYS* 3.3 52.8 + - + +
228C VAL* 3.2 21.0 - - + +
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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