Contacts of the helix formed by residues 171 - 179 (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 THR 171 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C SER 4.9 4.5 - - - +
169C GLN* 3.2 13.1 + - - +
170C PHE* 1.3 80.4 - - - +
172C LEU* 1.3 64.9 + - - +
173C SER* 2.9 21.3 + - - -
174C VAL* 3.0 20.9 + - - +
175C LEU* 3.1 13.9 + - - +
198C PHE* 3.7 11.0 - - - -
202C LEU* 5.2 0.7 - - - -
169D GLN* 5.3 1.0 + - - -
171D THR* 6.2 4.0 - - + -
231D GLU* 3.5 15.6 + - - +
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Residues in contact with LEU 172 (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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171C THR* 1.3 73.9 - - - +
173C SER* 1.3 57.7 + - - +
175C LEU* 3.3 2.7 + - - +
176C SER* 3.0 28.4 + - - -
183C SER* 4.0 21.1 - - - +
186C LEU* 3.7 31.6 - - + -
187C SER* 4.2 8.7 - - - +
198C PHE* 3.3 44.9 - - + -
199C GLN* 3.8 13.7 - - - +
231D GLU* 3.9 14.4 + - + +
232D ASP* 3.3 35.4 - - + +
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Residues in contact with SER 173 (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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171C THR* 2.9 17.3 + - - -
172C LEU* 1.3 76.7 - - - +
174C VAL* 1.3 65.8 + - - +
176C SER* 2.8 20.4 + - - -
177C GLU* 3.0 15.2 + - - +
183C SER* 3.4 11.7 - - - -
169D GLN* 3.9 23.3 + - - -
231D GLU* 3.0 19.5 + - - -
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Residues in contact with VAL 174 (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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169C GLN 3.5 19.1 - - - +
170C PHE* 4.0 18.4 - - + -
171C THR* 3.0 24.8 + - - +
173C SER* 1.3 76.9 + - - +
175C LEU* 1.3 67.4 + - - +
177C GLU* 3.2 8.5 + - - +
178C LYS* 3.0 44.4 + - + +
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Residues in contact with LEU 175 (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* 4.5 11.7 - - + -
160C ILE* 3.9 37.0 - - + -
161C ILE* 4.4 9.6 - - + -
170C PHE* 4.2 17.7 - - + -
171C THR 3.1 7.4 + - - +
172C LEU 3.7 7.0 - - - +
174C VAL* 1.3 83.0 - - - +
176C SER* 1.3 64.0 + - - +
178C LYS* 3.1 11.9 + - + +
179C LEU* 3.0 36.9 + - + +
186C LEU* 3.8 17.7 - - + -
190C PHE* 5.7 0.2 - - + -
198C PHE* 3.6 28.5 - - + -
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Residues in contact with SER 176 (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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172C LEU 3.0 10.7 + - - -
173C SER 2.8 17.7 + - - -
175C LEU* 1.3 74.5 - - - +
177C GLU* 1.3 60.7 + - - +
179C LEU* 3.2 2.7 + - - +
180C ASP 3.0 4.2 + - - -
181C LEU* 2.8 46.7 + - - +
182C SER 3.8 3.1 - - - -
183C SER* 3.0 34.8 + - - -
186C LEU* 3.4 17.4 - - - +
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Residues in contact with GLU 177 (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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173C SER 3.0 15.6 + - - +
174C VAL* 3.2 11.8 - - - +
176C SER* 1.3 75.8 + - - +
178C LYS* 1.3 84.6 + - - +
180C ASP* 2.9 22.0 + - - +
181C LEU 4.7 1.8 - - - -
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Residues in contact with LYS 178 (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* 4.7 21.4 - - + +
164C SER* 4.4 15.0 + - - -
170C PHE* 5.2 4.0 - - - -
174C VAL* 3.0 37.2 + - + +
175C LEU* 3.1 14.6 + - + +
177C GLU* 1.3 85.5 - - - +
179C LEU* 1.3 62.1 + - + +
180C ASP* 3.4 8.1 + - - +
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Residues in contact with LEU 179 (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* 5.4 8.7 - - + -
160C ILE* 6.0 5.4 - - + -
175C LEU* 3.0 43.2 + - + +
176C SER 3.2 2.7 + - - +
178C LYS* 1.3 78.5 - - + +
180C ASP* 1.3 70.6 + - - +
181C LEU* 3.2 24.4 + - + +
186C LEU* 4.3 19.3 - - + -
189C MSE 5.0 6.1 - - + -
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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