Contacts of the helix formed by residues 151 - 163 (chain D) 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 SER 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ASN* 1.3 60.1 + - - +
153D ALA* 3.3 13.1 + - - +
154D LYS* 2.9 35.7 + - - +
155D GLU* 3.0 32.6 + - - +
193D ASN* 3.4 14.8 + - - -
214E LEU* 6.0 0.9 - - - -
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Residues in contact with ASN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER* 1.3 74.1 - - - +
153D ALA* 1.3 57.8 + - - +
155D GLU* 3.9 19.3 - - - +
156D LEU* 3.0 30.7 + - - +
214E LEU* 3.6 33.5 - - + +
221E ASN* 3.8 25.7 + - - +
236E PHE* 6.0 1.4 - - - -
237E ILE* 5.1 13.1 - - - +
240E PHE* 4.6 16.5 - - - +
241E LYS* 5.1 12.7 + - - +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER* 3.1 10.5 + - - +
152D ASN* 1.3 75.7 - - - +
154D LYS* 1.3 65.1 + - - +
156D LEU* 3.0 26.7 - - - +
157D ILE* 3.2 16.5 + - + +
189D MSE 5.7 0.7 - - - -
193D ASN* 4.6 11.0 - - - +
214E LEU* 3.3 35.8 - - + +
215E LEU* 4.3 10.1 - - + +
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER* 2.9 31.7 + - - +
153D ALA* 1.3 76.2 - - - +
155D GLU* 1.3 59.0 + - + +
157D ILE* 3.4 2.6 + - - +
158D GLN* 2.8 55.5 + - - +
193D ASN* 3.8 29.0 + - + +
194D PHE* 3.7 36.4 - - + +
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER 3.0 18.6 + - - +
152D ASN* 3.6 22.9 - - - +
153D ALA 3.2 0.4 - - - -
154D LYS* 1.3 78.7 - - + +
156D LEU* 1.3 59.5 + - - +
158D GLN* 3.4 17.5 - - - +
159D ASN* 3.0 28.4 + - - +
241E LYS* 4.3 18.5 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 3.0 18.3 + - - +
153D ALA* 3.0 34.5 - - - +
155D GLU* 1.3 77.7 - - - +
157D ILE* 1.3 61.4 + - + +
159D ASN* 3.6 7.2 - - + +
160D ILE* 3.0 42.4 + - + +
179D LEU* 4.9 1.6 - - + -
211E LYS* 4.2 28.5 - - + -
214E LEU* 5.1 3.8 - - + -
215E LEU* 3.8 18.8 - - + -
240E PHE* 4.1 30.7 - - + -
244E TYR* 4.9 13.2 - - + -
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA 3.2 20.6 + - - +
154D LYS* 3.7 3.4 - - - +
156D LEU* 1.3 76.3 - - + +
158D GLN* 1.3 66.0 + - - +
159D ASN 3.1 1.3 - - - -
160D ILE* 3.0 8.2 + - - +
161D ILE* 2.9 30.5 + - + +
175D LEU* 4.3 10.1 - - + -
179D LEU* 4.0 24.7 - - + -
186D LEU* 4.8 3.1 - - + -
189D MSE 3.9 35.2 - - + -
190D PHE* 4.0 16.2 - - + -
193D ASN* 5.5 0.9 - - - +
194D PHE* 3.7 28.5 - - + -
215E LEU* 4.2 4.7 - - + -
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LYS* 2.8 45.2 + - - +
155D GLU* 3.4 28.6 + - - +
157D ILE* 1.3 73.7 - - - +
159D ASN* 1.3 58.0 + - - +
161D ILE* 3.4 5.3 + - - +
162D GLU* 2.9 31.5 + - - +
194D PHE* 3.8 19.5 - - + -
201D TYR* 4.0 17.3 + - - +
205D LYS* 5.3 1.7 + - - -
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLU 3.0 18.0 + - - +
156D LEU* 3.6 9.6 - - + +
158D GLN* 1.3 74.2 - - - +
160D ILE* 1.3 68.3 + - - +
162D GLU* 3.3 5.9 + - - +
163D GLU* 3.1 33.5 + - - +
244E TYR 4.3 6.8 - - - +
245E GLN* 5.6 4.1 + - - -
246E ILE* 3.0 44.4 + - - +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.0 23.4 + - + +
157D ILE 3.0 7.0 + - - +
159D ASN* 1.3 77.7 - - + +
161D ILE* 1.3 63.7 + - - +
163D GLU* 3.2 9.8 + - - +
164D SER* 3.2 27.6 + - - +
170D PHE* 4.5 7.0 - - + -
175D LEU* 3.8 21.1 - - + -
178D LYS* 4.3 29.4 - - + +
179D LEU* 3.4 33.0 - - + -
211E LYS* 5.5 2.9 - - - +
246E ILE* 5.2 6.5 - - + -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ILE* 2.9 28.4 + - + +
158D GLN* 3.7 3.6 - - - +
160D ILE* 1.3 75.9 - - - +
162D GLU* 1.3 64.6 + - - +
164D SER 3.0 0.7 + - - -
165D TYR* 3.0 32.9 + - + +
170D PHE* 4.1 21.5 - - + -
175D LEU* 4.5 4.0 - - + -
190D PHE* 4.0 21.5 - - + -
194D PHE* 5.3 0.2 - - + -
198D PHE* 4.0 15.0 - - + -
201D TYR* 3.7 31.4 - - + -
202D LEU* 4.3 13.2 - - + -
205D LYS* 3.9 21.3 - - + -
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLN 2.9 18.0 + - - +
159D ASN* 3.3 9.4 + - - +
161D ILE* 1.3 76.1 - - - +
163D GLU* 1.3 73.9 + - - +
165D TYR* 3.3 25.3 + - - -
205D LYS* 2.9 38.3 + - - +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASN* 3.1 17.2 + - - +
160D ILE 3.2 3.5 + - - +
161D ILE 3.0 1.0 - - - -
162D GLU* 1.3 94.5 - - - +
164D SER* 1.3 61.6 + - - +
165D TYR* 5.2 0.2 - - - -
166D THR* 5.7 0.8 + - - -
246E ILE* 3.1 57.2 - - + +
247E THR 4.6 10.2 - - - +
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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