Contacts of the helix formed by residues 251 - 263 (chain F) in PDB entry 4ILW
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 251 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230F ASN* 4.6 6.3 - - - -
232F GLU* 3.8 23.5 + - - -
233F ALA* 3.5 6.2 - - - +
234F LEU 5.0 0.4 - - - +
249F ARG* 3.5 3.8 + - - -
250F LEU* 1.3 77.6 - - - +
252F GLN* 1.3 60.5 + - - +
253F ASP* 3.3 10.4 + - - +
254F ASP* 2.9 49.4 + - - +
255F VAL* 3.0 14.3 + - - +
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Residues in contact with GLN 252 (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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251F SER* 1.3 72.0 - - - +
253F ASP* 1.3 61.4 + - - +
255F VAL* 3.3 21.8 + - - +
256F ASN* 2.7 66.7 + - - +
259F GLN* 5.6 0.3 + - - -
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Residues in contact with ASP 253 (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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228F SER* 4.2 12.8 + - - +
230F ASN* 3.3 33.2 - - - +
233F ALA* 4.6 1.8 - - + -
251F SER* 3.3 10.0 + - - +
252F GLN* 1.3 80.6 - - - +
254F ASP* 1.3 59.2 + - - +
256F ASN* 3.5 13.1 + - - +
257F GLY* 3.2 19.4 + - - -
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Residues in contact with ASP 254 (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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140F TRP* 4.2 9.6 - - + -
225F LEU* 4.5 4.6 - - - +
228F SER* 5.0 1.0 - - - -
233F ALA* 3.6 5.9 - - - +
234F LEU* 2.8 32.6 + - - +
235F MET* 3.2 32.4 + - - +
250F LEU* 3.8 17.6 - - + +
251F SER* 2.9 32.6 + - - +
253F ASP* 1.3 74.4 - - - +
255F VAL* 1.3 65.6 + - - +
257F GLY* 3.3 1.7 + - - -
258F ILE* 3.0 26.7 + - - +
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Residues in contact with VAL 255 (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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143F VAL* 4.4 13.7 - - + -
250F LEU* 4.0 24.0 - - + +
251F SER 3.0 14.6 + - - +
252F GLN* 3.3 27.3 + - - +
254F ASP* 1.3 76.8 - - - +
256F ASN* 1.3 57.1 + - - +
258F ILE* 3.4 6.9 - - - +
259F GLN* 2.9 61.7 + - + +
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Residues in contact with ASN 256 (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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252F GLN* 2.7 57.9 + - - +
253F ASP* 3.7 15.0 + - - +
255F VAL* 1.3 74.5 - - - +
257F GLY* 1.3 59.3 + - - +
259F GLN* 3.8 4.9 + - - +
260F SER* 2.9 32.3 + - - -
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Residues in contact with GLY 257 (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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225F LEU* 3.6 18.9 - - - +
253F ASP 3.2 11.8 + - - -
254F ASP* 3.8 2.9 - - - -
255F VAL 3.3 0.2 - - - -
256F ASN* 1.3 79.2 - - - +
258F ILE* 1.3 60.8 + - - +
260F SER* 2.4 26.4 + - - -
261F LEU* 3.5 5.2 + - - +
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Residues in contact with ILE 258 (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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140F TRP* 3.8 20.6 - - + -
143F VAL* 3.7 27.1 - - + -
144F THR* 3.7 19.1 - - + -
223F LEU* 4.0 26.2 - - + -
225F LEU* 3.7 22.0 - - + +
254F ASP 3.0 16.9 + - - +
255F VAL* 3.4 11.2 - - - +
257F GLY* 1.3 77.2 - - - +
259F GLN* 1.3 62.8 + - + +
261F LEU* 3.3 3.5 + - + -
262F TYR* 3.0 52.0 + - + +
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Residues in contact with GLN 259 (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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143F VAL* 3.0 34.9 - - - +
144F THR* 5.2 0.7 - - - -
252F GLN* 5.6 0.2 + - - -
255F VAL* 2.9 42.6 + - + +
256F ASN* 4.3 4.2 + - - +
258F ILE* 1.3 77.4 - - + +
260F SER* 1.3 60.9 + - - +
261F LEU 3.2 0.2 - - - -
262F TYR 4.8 0.2 - - - -
263F GLY* 2.9 43.6 + - - +
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Residues in contact with SER 260 (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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256F ASN 2.9 15.4 + - - -
257F GLY* 2.4 24.4 + - - -
259F GLN* 1.3 78.1 - - - +
261F LEU* 1.3 64.8 + - - +
263F GLY 4.8 0.2 - - - -
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Residues in contact with LEU 261 (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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106F PRO* 3.8 24.7 - - + +
107F LYS* 2.8 44.5 + - + +
223F LEU 3.7 21.8 - - - +
224F GLY 3.9 21.1 - - - +
225F LEU* 4.0 17.3 - - + -
257F GLY 4.0 5.4 - - - +
258F ILE* 3.3 3.5 + - + +
259F GLN 3.2 0.4 - - - -
260F SER* 1.3 84.6 + - - +
262F TYR* 1.3 74.2 + - + +
263F GLY 3.6 1.1 + - - -
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Residues in contact with TYR 262 (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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107F LYS* 3.6 21.2 - - + +
108F TRP* 3.2 47.0 + + + -
110F LYS 5.0 1.3 - - - -
144F THR* 4.3 7.0 - - - -
145F PRO* 3.2 33.7 - - + +
146F LEU* 3.8 36.6 - - + -
223F LEU* 2.5 33.1 + - + -
258F ILE* 3.0 36.8 + - + +
259F GLN* 4.8 0.2 - - - -
261F LEU* 1.3 87.2 - - + +
263F GLY* 1.3 66.3 + - - +
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Residues in contact with GLY 263 (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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143F VAL 4.9 2.3 - - - +
144F THR* 5.2 0.2 - - - -
145F PRO* 4.4 7.7 - - - +
259F GLN* 2.9 36.7 + - - +
260F SER 4.8 0.2 - - - -
261F LEU 3.6 2.0 - - - -
262F TYR* 1.3 82.6 - - - +
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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