Contacts of the strand formed by residues 238 - 249 (chain F) in PDB entry 1II4
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 GLY 238 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153F ALA* 4.1 2.0 - - - -
154F PRO* 3.5 12.8 - - - +
234F GLU* 3.3 4.3 - - - +
235F ASN* 3.0 32.5 + - - +
236F GLU 3.5 1.4 - - - -
237F TYR* 1.3 81.8 - - - +
239F SER* 1.3 61.5 + - - -
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Residues in contact with SER 239 (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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154F PRO* 4.4 0.6 - - - +
232F VAL* 4.0 7.4 - - - +
233F VAL 3.3 7.0 + - - -
234F GLU* 2.8 30.7 + - - +
238F GLY* 1.3 77.3 - - - -
240F ILE* 1.3 69.1 + - - +
241F ASN* 5.3 1.0 - - - +
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Residues in contact with ILE 240 (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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154F PRO* 3.4 40.4 - - + +
155F TYR* 3.7 11.4 - - - +
156F TRP* 3.5 39.5 - - + +
232F VAL* 3.7 1.7 - - - +
233F VAL* 2.9 36.5 + - + +
239F SER* 1.3 83.1 - - - +
241F ASN* 1.3 65.0 + - - +
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Residues in contact with ASN 241 (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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156F TRP* 3.9 11.0 + - - -
230F THR* 3.9 17.8 - - + +
231F CYS 3.1 15.0 - - - +
232F VAL* 4.0 13.2 - - + -
239F SER 5.3 0.7 - - - +
240F ILE* 1.3 78.1 - - - +
242F HIS* 1.3 65.8 + - - +
243F THR* 4.6 5.1 + - - +
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Residues in contact with HIS 242 (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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156F TRP* 4.0 4.4 + - + +
162F MET* 3.3 63.5 + - + +
165F ARG* 3.4 33.9 + - + -
229F TYR 3.9 0.7 - - - +
230F THR* 3.3 2.7 - - - +
231F CYS* 3.0 36.0 + - - -
241F ASN* 1.3 78.3 + - - +
243F THR* 1.3 70.5 + - - +
244F TYR* 3.4 36.9 - + - -
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Residues in contact with THR 243 (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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165F ARG* 4.4 13.3 + - - +
228F ASN* 3.9 22.7 - - + +
229F TYR 3.4 4.0 - - - +
230F THR* 2.9 30.2 + - - +
241F ASN* 4.6 5.2 + - - +
242F HIS* 1.3 89.7 + - - +
244F TYR* 1.3 77.3 + - - +
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Residues in contact with TYR 244 (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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161F LYS 3.6 5.4 + - - -
162F MET* 3.3 24.7 - - - +
164F LYS 3.4 27.1 - - - -
165F ARG* 3.3 12.6 - - - +
167F HIS* 4.0 12.6 - + - -
177F PHE* 3.6 38.6 - + + -
178F ARG 2.5 42.1 + - - -
179F CYS* 3.9 8.1 - - - -
191F TRP* 4.4 4.7 - + - -
228F ASN* 3.4 4.2 - - - -
229F TYR* 2.7 39.4 + - - +
242F HIS* 3.4 31.0 - + - -
243F THR* 1.3 77.8 - - - +
245F HIS* 1.3 59.6 + - - +
246F LEU 4.1 0.2 + - - -
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Residues in contact with HIS 245 (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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165F ARG 2.9 9.9 + - - +
166F LEU* 3.5 21.6 - - + +
167F HIS* 2.8 31.4 + - - +
177F PHE* 4.8 0.4 - - - -
227F GLY 3.6 4.7 - - - +
228F ASN* 3.7 15.9 - - - +
244F TYR* 1.3 74.8 - - - +
246F LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 246 (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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166F LEU* 4.9 0.2 - - - -
167F HIS 3.4 11.2 - - - +
169F VAL* 4.4 6.3 - - + -
175F VAL* 3.9 28.0 - - + -
177F PHE* 4.0 7.4 - - + -
218F MET* 3.7 27.1 - - + -
221F VAL* 4.5 7.6 - - + -
225F ASP* 3.5 33.7 - - + +
226F LYS* 3.3 8.7 - - - +
227F GLY 2.8 27.0 + - - -
229F TYR* 3.6 17.2 - - + -
244F TYR 4.1 0.4 + - - -
245F HIS* 1.3 74.2 - - - +
247F ASP* 1.3 76.6 + - - +
248F VAL* 4.4 6.7 - - + -
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Residues in contact with ASP 247 (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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151B MET* 3.6 29.4 - - + +
166F LEU* 4.5 10.9 - - + +
167F HIS 2.9 9.8 + - - +
168F ALA* 3.2 5.3 - - + +
169F VAL 3.0 25.6 + - - -
226F LYS* 3.4 40.7 + - - +
246F LEU* 1.3 76.0 - - - +
248F VAL* 1.3 78.2 + - - +
249F VAL* 4.2 2.0 + - - +
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Residues in contact with VAL 248 (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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169F VAL 3.4 3.8 - - - +
170F PRO 4.3 0.2 - - - -
171F ALA* 3.3 38.8 - - + +
221F VAL* 3.8 21.8 - - + -
222F VAL* 3.3 37.2 - - - +
223F PRO* 3.8 16.7 - - + +
225F ASP* 4.6 2.0 - - + -
226F LYS* 4.8 5.1 - - - +
246F LEU* 4.4 15.3 - - + -
247F ASP* 1.3 85.9 + - - +
249F VAL* 1.3 67.3 + - - +
250F GLU 4.3 0.5 + - - -
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Residues in contact with VAL 249 (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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149B LEU* 3.8 30.7 - - + -
150B PRO* 4.0 15.3 - - + +
151B MET* 4.2 27.1 - - + -
169F VAL 3.0 6.1 + - - -
170F PRO* 3.1 6.2 - - - +
171F ALA* 2.6 28.0 + - - -
247F ASP* 5.1 1.3 - - - +
248F VAL* 1.3 78.1 - - - +
250F GLU* 1.3 69.5 - - - +
251F ARG* 3.7 16.1 + - - +
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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