Contacts of the helix formed by residues 207 - 218 (chain B) in PDB entry 1L1E
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.6 1.8 - - - -
171B ARG* 3.4 35.2 - - - +
173B THR* 4.1 6.3 - - - -
206B PRO* 1.3 75.0 - - - +
208B ILE* 1.3 67.5 + - - +
209B PRO* 3.3 12.0 - - - +
210B THR* 2.7 39.2 + - - -
211B VAL* 3.3 10.0 + - - +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.1 35.4 - - + +
171B ARG 3.6 8.4 + - - +
172B PRO* 4.3 12.3 - - + -
173B THR 5.0 1.6 - - - +
207B SER* 1.3 71.1 - - - +
209B PRO* 1.3 68.6 - - + +
211B VAL* 3.2 7.4 + - - +
212B HIS* 2.9 49.4 + - + -
225B VAL* 5.7 2.2 - - + -
279B ASP* 5.7 0.4 - - - +
281B ASP* 3.1 28.3 - - - +
283B PHE* 4.3 7.4 - - + -
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Residues in contact with PRO 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B THR* 4.3 20.2 - - + +
174B PHE* 5.3 11.0 - - + -
207B SER* 3.3 15.7 - - - +
208B ILE* 1.3 92.9 - - + +
210B THR* 1.3 58.2 + - - +
212B HIS* 3.1 10.1 + - + +
213B GLU* 2.8 32.9 + - - +
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B HIS* 4.1 10.2 - - + +
147B TYR* 3.8 25.6 - - + -
171B ARG* 5.5 0.9 + - - -
204B TRP* 6.2 0.7 - - - +
206B PRO* 4.7 2.2 - - + -
207B SER* 2.7 33.6 + - - -
209B PRO* 1.3 78.0 - - - +
211B VAL* 1.3 64.1 + - - +
213B GLU* 3.3 7.5 + - - -
214B TYR* 3.0 55.6 + - + +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE* 4.7 9.6 - - + -
147B TYR* 6.2 0.4 - - - -
151B PHE* 4.2 21.7 - - + -
166B LEU* 4.6 7.0 - - + -
168B THR* 5.3 1.6 - - + -
170B VAL* 5.3 0.9 - - + -
206B PRO* 4.1 23.1 - - + -
207B SER 3.7 12.6 - - - +
208B ILE 3.2 7.8 + - - +
209B PRO 3.2 0.4 - - - -
210B THR* 1.3 77.3 - - - +
212B HIS* 1.3 64.3 + - - +
215B ALA* 3.1 27.1 + - + +
222B VAL* 5.8 0.9 - - + -
283B PHE* 3.9 48.0 - - + -
285B LEU* 5.7 2.7 - - + -
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Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 6.0 2.9 - - - -
208B ILE* 2.9 43.5 + - + +
209B PRO* 3.1 11.3 + - + +
211B VAL* 1.3 77.7 - - - +
213B GLU* 1.3 62.4 + - - +
215B ALA 4.0 0.2 - - - -
216B GLU* 3.0 53.4 + - - +
222B VAL* 4.2 26.9 - - + +
225B VAL* 4.4 10.3 - - + +
283B PHE* 4.1 16.9 - + - -
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B PRO 2.8 19.4 + - - +
210B THR* 3.7 8.2 + - - +
212B HIS* 1.3 73.9 - - - +
214B TYR* 1.3 79.0 + - - +
216B GLU* 3.3 7.2 + - - +
217B LYS* 2.7 66.1 + - + +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B HIS* 3.0 29.7 + + - -
147B TYR* 3.4 12.6 - - + -
148B HIS* 3.3 45.1 + - + -
151B PHE* 3.7 22.1 - - + +
210B THR* 3.0 46.4 + - + +
213B GLU* 1.3 99.0 - - + +
215B ALA* 1.3 62.8 + - - +
217B LYS* 3.4 19.7 + - + +
218B VAL* 3.4 23.4 + - - +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 3.4 32.7 - - + -
211B VAL* 3.1 20.2 + - + +
212B HIS 4.2 1.6 - - - +
214B TYR* 1.3 77.9 - - - +
216B GLU* 1.3 59.1 + - - +
218B VAL* 3.6 5.0 + - - +
220B PHE* 2.8 34.9 + - + +
222B VAL* 4.6 4.0 - - + -
285B LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 4.6 14.5 + - - -
212B HIS* 3.0 48.9 + - - +
213B GLU* 3.9 5.3 + - - +
215B ALA* 1.3 77.6 - - - +
217B LYS* 1.3 62.5 + - + +
218B VAL 3.2 0.7 - - - -
219B GLY* 3.2 12.8 + - - -
220B PHE 3.8 17.8 - - - +
221B ARG* 5.4 0.8 + - - -
222B VAL* 4.4 15.2 + - + +
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Residues in contact with LYS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B HIS* 4.8 20.8 - - + +
213B GLU* 2.7 61.5 + - + +
214B TYR* 3.8 18.2 - - + +
215B ALA 3.4 0.6 - - - -
216B GLU* 1.3 80.6 - - + +
218B VAL* 1.3 60.4 + - - +
219B GLY 3.2 1.1 + - - -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B HIS* 4.2 20.9 - - + +
151B PHE* 3.6 10.1 - - + +
152B GLU* 3.4 37.9 - - + +
155B HIS* 2.7 63.4 + - + -
214B TYR 3.4 17.8 + - - +
215B ALA 3.6 5.1 + - - +
216B GLU 3.2 0.4 - - - -
217B LYS* 1.3 78.2 - - - +
219B GLY* 1.3 53.9 + - - +
220B PHE* 3.6 0.9 - - + -
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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