Contacts of the helix formed by residues 241 - 253 (chain A) in PDB entry 5F0P
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 ILE 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A SER* 5.5 4.0 - - - +
180A MET* 3.6 41.3 - - + -
181A ASP* 5.1 6.7 - - - +
184A LEU* 3.9 20.0 - - + +
237A ARG* 2.7 25.9 + - + +
240A GLN* 1.3 82.9 - - + +
242A VAL* 1.3 60.8 + - - +
243A LEU 3.7 0.7 - - - -
244A THR* 3.8 1.5 - - - -
245A GLY* 2.8 28.2 + - - -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 3.9 30.3 - - + -
184A LEU* 3.7 7.3 - - + +
227A LEU* 4.0 23.8 - - + -
233A VAL* 4.0 22.0 - - + -
237A ARG 3.1 9.0 + - - +
238A TYR* 4.0 10.3 - - + -
241A ILE* 1.3 74.0 - - + +
243A LEU* 1.3 59.9 + - - +
245A GLY* 3.2 2.6 + - - -
246A ILE* 2.9 51.0 + - + +
270A PHE* 4.0 17.5 - - + -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 2.9 48.6 + - + +
239A LYS 4.6 3.6 - - - +
242A VAL* 1.3 71.5 - - - +
244A THR* 1.3 57.1 + - - +
246A ILE* 4.3 6.7 - - + +
247A LEU* 2.8 71.2 + - + +
266A ILE* 4.0 22.4 - - + -
278A THR* 3.6 39.9 - - + +
281A PRO* 4.7 6.5 - - + -
282A PHE* 5.0 7.4 - - + +
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LYS 2.9 20.7 + - - -
240A GLN* 3.0 22.3 + - - +
241A ILE 3.6 3.1 + - - -
242A VAL 3.3 0.6 - - - -
243A LEU* 1.3 78.1 - - - +
245A GLY* 1.3 61.0 + - - +
247A LEU* 4.2 4.5 - - - +
248A GLU* 3.2 26.1 + - + +
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Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.1 17.0 - - - -
187A PHE* 5.3 0.4 - - - -
241A ILE 2.8 16.5 + - - -
242A VAL 3.5 4.0 - - - -
244A THR* 1.3 76.4 - - - +
246A ILE* 1.3 63.3 + - - +
248A GLU* 3.4 15.7 + - - +
249A GLN* 3.5 18.2 + - - +
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.0 11.0 - - + -
187A PHE* 4.0 17.5 - - + -
224A LEU* 3.6 30.3 - - + -
227A LEU* 4.2 2.5 - - + -
238A TYR* 5.5 0.2 - - + -
242A VAL* 2.9 40.5 + - + +
243A LEU* 3.3 8.0 + - + +
245A GLY* 1.3 73.7 - - - +
247A LEU* 1.3 58.8 + - - +
249A GLN* 3.2 6.2 + - - +
250A VAL* 3.0 39.4 + - + +
266A ILE* 3.7 30.3 - - + -
270A PHE* 4.1 17.9 - - + -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 2.8 56.6 + - + +
244A THR* 4.4 4.3 - - - +
246A ILE* 1.3 70.0 - - - +
248A GLU* 1.3 63.8 + - - +
249A GLN 3.3 0.2 - - - -
250A VAL* 4.2 6.5 - - + -
251A VAL* 3.2 31.9 + - + +
263A MET* 3.9 21.5 - - + -
266A ILE* 4.3 6.1 - - + -
281A PRO* 4.0 26.7 - - + +
282A PHE* 4.7 3.1 - - + +
285A ALA* 3.8 23.1 - - + -
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A THR* 3.2 23.1 + - + +
245A GLY* 3.6 8.8 - - - +
246A ILE 3.2 0.8 - - - -
247A LEU* 1.3 77.0 - - - +
249A GLN* 1.3 70.5 + - - +
251A VAL* 4.5 2.0 - - - -
252A ASN* 2.7 44.4 + - - +
18C LEU* 3.8 16.6 - - + +
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Residues in contact with GLN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU 5.5 0.4 - - - +
187A PHE* 4.0 21.3 - - + -
188A ALA* 3.4 31.8 - - + +
191A ASN* 4.4 4.5 - - - +
245A GLY 3.5 13.9 + - - +
246A ILE 3.2 6.3 + - - +
248A GLU* 1.3 84.0 + - - +
250A VAL* 1.3 59.1 + - - +
252A ASN 3.8 0.3 - - - -
253A CYS* 3.0 34.4 + - - +
18C LEU* 3.8 24.8 - - - +
22C TYR* 2.6 42.0 + - - +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 4.9 1.1 - - + -
246A ILE* 3.0 33.2 + - + +
247A LEU* 4.0 8.7 - - + +
248A GLU 3.4 0.4 - - - -
249A GLN* 1.3 74.8 - - - +
251A VAL* 1.3 65.7 + - + +
253A CYS* 3.3 13.0 - - - -
259A GLN* 3.1 33.8 + - + +
262A LEU* 3.8 34.1 - - + -
263A MET* 3.9 30.5 - - + -
266A ILE* 5.1 4.5 - - + -
289A LEU* 4.1 13.0 - - + -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.2 20.3 + - + +
248A GLU* 3.9 1.6 - - - +
250A VAL* 1.3 78.6 - - + +
252A ASN* 1.3 77.5 + - - +
254A ARG* 3.2 35.8 + - - +
259A GLN* 3.6 10.8 + - - +
285A ALA* 4.4 24.7 - - + +
288A GLU* 4.4 26.7 - - + +
289A LEU* 4.7 4.9 - - + -
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLU* 2.7 34.8 + - - +
249A GLN 4.2 0.9 - - - +
250A VAL 3.3 0.4 - - - -
251A VAL* 1.3 85.1 - - - +
253A CYS* 1.3 62.7 + - - +
254A ARG* 3.2 29.1 + - - +
18C LEU* 3.3 37.1 - - + +
19C ASN* 5.3 6.6 - - - +
22C TYR* 3.8 14.2 - - + +
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Residues in contact with CYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN* 3.9 7.4 - - - +
195A VAL* 4.1 8.2 - - + +
249A GLN 3.0 16.1 + - - +
250A VAL* 3.3 21.8 - - - -
251A VAL 3.5 0.8 - - - -
252A ASN* 1.3 76.2 - - - +
254A ARG* 1.3 68.4 + - - +
255A ASP* 3.0 26.0 + - - +
258A ALA* 4.0 16.2 - - - -
259A GLN* 3.9 9.2 - - - -
262A LEU* 5.4 0.2 - - - -
22C TYR* 3.4 43.4 - - + +
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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