Contacts of the helix formed by residues 202 - 214 (chain K) in PDB entry 1LWU
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 ARG 202 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164J TYR* 4.2 9.6 + - + +
165J ARG* 4.2 38.8 - - - +
168J LYS* 5.4 7.1 - - - +
195K HIS* 4.8 10.3 - - - -
198K ALA* 2.8 22.3 + - - +
199K LYS* 3.0 69.6 - - - +
201K GLN* 1.3 74.5 - - + +
203K MET* 1.3 61.1 + - + +
205K GLU* 2.6 34.0 - - - +
206K ALA* 3.6 5.9 + - - +
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Residues in contact with MET 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ILE* 4.3 7.9 - - + +
143J VAL* 4.6 4.5 - - + -
144J GLU* 3.3 39.3 - - + +
147J ILE* 4.2 15.3 - - + -
164J TYR* 2.7 23.3 - - + +
199K LYS* 3.0 31.8 + - + +
200K MET* 3.3 17.0 + - + +
201K GLN 3.2 0.8 - - - -
202K ARG* 1.3 79.1 - - + +
204K GLU* 1.3 63.4 + - - +
205K GLU 2.8 5.4 + - - -
206K ALA* 3.1 14.0 + - - +
207K ILE* 3.1 18.4 + - - +
123L LEU* 3.4 30.5 - - + -
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Residues in contact with GLU 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K MET 3.0 13.9 + - - +
201K GLN* 4.4 7.1 + - - +
203K MET* 1.3 76.2 - - - +
205K GLU* 1.3 58.2 + - - +
208K LYS* 3.1 30.7 + - + +
119L PHE* 3.8 7.5 - - + -
122L ARG* 2.7 38.5 + - - -
123L LEU* 3.2 18.5 - - + +
126L GLN* 2.6 36.2 + - - +
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Residues in contact with GLU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J LEU* 5.1 3.5 - - - +
164J TYR* 5.5 0.3 - - - -
201K GLN 3.6 15.9 + - - +
202K ARG* 2.6 29.9 - - - +
203K MET 2.8 0.4 - - - -
204K GLU* 1.3 78.8 - - - +
206K ALA* 1.3 79.3 + - - +
208K LYS* 3.1 4.8 + - - +
209K THR* 2.7 52.4 + - - +
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Residues in contact with ALA 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ILE* 5.3 0.2 - - + -
151J LEU* 3.9 11.7 - - + -
162J LEU* 3.4 16.9 - - + +
164J TYR* 3.5 38.6 - - + -
202K ARG 3.6 2.6 + - - +
203K MET 3.1 7.5 + - - +
205K GLU* 1.3 94.9 + - - +
207K ILE* 1.3 63.1 + - + +
209K THR 3.1 1.4 + - - -
210K GLN* 3.0 22.2 + - - +
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Residues in contact with ILE 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ILE* 3.2 50.7 - - + -
151J LEU* 4.3 12.3 - - + -
203K MET 3.1 13.1 + - - +
206K ALA* 1.3 76.2 - - - +
208K LYS* 1.3 57.5 + - - +
210K GLN* 4.3 0.5 - - - +
211K LYS* 3.0 32.4 + - + +
123L LEU* 4.3 6.3 - - + +
126L GLN* 3.4 48.5 - - + +
127L LEU* 4.2 9.9 - - - +
130L ILE* 3.8 17.4 - - + +
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Residues in contact with LYS 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K GLU* 3.1 22.0 + - + +
205K GLU* 3.1 6.0 + - - +
207K ILE* 1.3 77.7 - - - +
209K THR* 1.3 60.2 + - - +
211K LYS* 3.6 33.4 - - + +
212K GLU* 3.1 27.0 - - - +
126L GLN* 4.4 20.9 + - - +
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Residues in contact with THR 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J LEU* 3.6 24.9 - - + -
205K GLU* 2.7 29.3 + - - +
206K ALA 3.1 3.1 + - - -
208K LYS* 1.3 75.5 - - - +
210K GLN* 1.3 60.4 + - - +
211K LYS 3.0 1.1 - - - -
212K GLU* 2.7 35.2 + - - +
213K LEU* 3.0 15.5 + - + +
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Residues in contact with GLN 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J LEU* 4.0 16.0 + - + +
154J CYS* 3.7 35.8 - - + +
160J ARG 3.2 8.5 - - - +
161J TYR* 3.6 15.8 - - - +
162J LEU* 2.9 49.1 - - + +
206K ALA 3.0 9.7 + - - +
207K ILE 4.3 1.3 - - - +
209K THR* 1.3 74.5 - - - +
211K LYS* 1.3 67.9 + - - +
213K LEU* 3.1 25.8 + - - +
214K CYS* 2.8 32.5 + - - -
130L ILE* 4.5 2.2 - - + -
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Residues in contact with LYS 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K ILE* 3.0 23.2 + - + +
208K LYS* 3.6 33.7 - - + +
210K GLN* 1.3 76.9 - - - +
212K GLU* 1.3 74.1 + - - +
214K CYS* 3.3 13.2 + - - +
215K SER* 3.7 4.0 + - - -
129L ASP* 4.9 16.2 + - + +
130L ILE* 4.1 20.8 - - + +
133L THR* 4.6 16.8 - - + +
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Residues in contact with GLU 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K LYS* 3.1 26.8 - - + +
209K THR* 2.7 11.9 + - - +
211K LYS* 1.3 85.0 - - - +
213K LEU* 1.3 55.5 + - + +
214K CYS 2.6 16.8 + - - -
215K SER* 2.6 27.4 + - - -
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Residues in contact with LEU 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J ALA* 4.0 3.3 + - - +
160J ARG* 3.2 71.2 + - + +
161J TYR 4.6 0.2 - - - +
162J LEU* 4.0 25.4 - - + +
209K THR* 3.0 16.4 + - + +
210K GLN* 3.1 26.0 - - - +
212K GLU* 1.3 79.1 - - + +
214K CYS* 1.4 54.2 + - - +
215K SER* 3.2 3.3 + - - -
216K ALA 3.8 8.5 + - - +
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Residues in contact with CYS 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J CYS* 2.0 49.6 - - - -
210K GLN* 2.8 35.7 + - - +
211K LYS* 3.6 10.8 - - + +
212K GLU 2.6 4.4 + - - -
213K LEU* 1.4 68.8 - - - +
215K SER* 1.3 63.0 + - - +
216K ALA 3.0 7.3 + - - +
217K PRO* 4.6 0.9 - - - +
130L ILE* 4.5 1.1 - - - -
133L THR* 4.0 13.4 + - - +
134L CYS* 3.7 18.6 - - - -
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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