Contacts of the helix formed by residues 207 - 214 (chain F) 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 ASP 207 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239E GLY* 5.3 4.0 - - - -
206F ARG* 1.3 78.1 - - - +
208F TRP* 1.3 58.6 + - - +
209F VAL* 2.7 38.1 + - + +
210F SER* 2.9 23.2 + - - -
211F TYR* 3.0 26.7 + - - -
312F THR* 4.1 1.6 - - - -
313F PRO* 5.9 0.2 - - - -
314F GLU* 3.3 22.4 - - + +
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Residues in contact with TRP 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F ASP* 1.3 72.5 - - - +
209F VAL* 1.3 68.8 + - + +
211F TYR* 2.6 26.1 + - + +
212F ARG* 2.9 18.4 + - + +
230F ASN* 5.6 0.4 - - - -
268F GLU* 2.5 35.5 + - + -
271F GLU* 4.1 11.9 - - + -
272F TYR* 3.7 43.1 - + - -
310F PHE* 3.2 42.2 - + + -
311F SER* 4.6 0.7 - - - -
312F THR* 3.6 24.4 + - + +
314F GLU* 2.9 21.9 + - - +
315F ARG* 3.0 49.0 - - + +
317F ASN* 4.8 0.4 - - - -
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ARG 3.5 24.5 - - - +
238E ASN* 4.2 11.0 - - - +
239E GLY* 4.6 1.3 - - - +
207F ASP* 2.7 17.0 - - + +
208F TRP* 1.3 79.4 - - + +
210F SER* 1.3 65.8 + - - +
212F ARG* 3.0 30.6 + - - +
213F GLU* 3.0 31.6 + - + +
314F GLU* 5.7 0.2 - - - +
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Residues in contact with SER 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ASN 4.2 9.4 - - - -
239E GLY* 4.7 8.7 - - - -
206F ARG* 3.4 36.6 + - - +
207F ASP* 2.9 35.1 + - - -
208F TRP 3.0 0.2 - - - -
209F VAL* 1.3 82.4 - - - +
211F TYR* 1.3 57.0 + - - +
214F GLY 2.9 26.3 + - - +
215F PHE* 3.3 16.4 - - - +
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Residues in contact with TYR 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F PHE* 2.8 41.3 + - - -
206F ARG* 3.4 18.6 - - + -
207F ASP 3.0 21.0 + - - +
208F TRP* 2.6 15.4 + - + +
210F SER* 1.3 73.8 - - - +
212F ARG* 1.3 56.5 + - - +
213F GLU 3.3 0.2 - - - -
215F PHE* 3.5 21.8 - + - -
227F TRP* 3.2 38.1 + + - -
229F GLY* 3.5 1.4 - - - -
230F ASN* 2.9 23.2 + - - +
310F PHE* 3.6 24.5 - + + -
312F THR* 4.2 8.3 - - + -
331F GLY 3.5 28.1 + - - -
343F ASN* 3.5 25.3 + - - +
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Residues in contact with ARG 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ASN* 5.4 3.8 - - - +
208F TRP* 2.9 17.2 + - + +
209F VAL* 3.0 42.2 - - - +
211F TYR* 1.3 76.9 - - - +
213F GLU* 1.3 85.1 + - - +
229F GLY* 3.7 1.6 - - - -
230F ASN* 3.5 11.2 + - - +
231F GLU* 3.2 29.8 + - + +
232F LYS* 4.5 1.9 + - - +
268F GLU* 3.5 35.9 + - - -
272F TYR* 3.8 25.4 - - + +
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Residues in contact with GLU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E VAL* 4.6 1.0 - - - +
227E VAL* 4.6 7.3 - - + -
228E SER 5.2 0.9 - - - +
238E ASN* 3.6 56.8 - - + +
209F VAL* 3.0 21.3 + - + +
210F SER 4.1 0.2 - - - +
212F ARG* 1.3 113.9 + - + +
214F GLY* 1.3 60.5 + - - +
228F LEU 3.4 10.4 - - - +
229F GLY* 4.0 0.2 - - - -
231F GLU* 5.3 3.3 - - - +
232F LYS* 3.5 17.5 + - - -
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Residues in contact with GLY 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E VAL* 3.9 6.1 - - - -
227E VAL* 3.7 18.0 - - - +
238E ASN 4.5 2.1 - - - +
210F SER* 2.9 15.8 + - - +
211F TYR 4.4 0.7 - - - -
212F ARG 3.5 1.8 - - - -
213F GLU* 1.3 83.0 - - - +
215F PHE* 1.3 66.5 + - - +
227F TRP 3.1 17.5 - - - -
228F LEU 3.2 9.9 - - - -
229F GLY* 3.8 2.0 - - - -
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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