Contacts of the helix formed by residues 243 - 259 (chain A) in PDB entry 5FLZ
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 LYS 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.2 25.9 + - - +
202A GLU* 3.8 10.7 + - - -
203A ARG* 3.1 30.1 - - - +
244A GLY* 1.4 68.9 + - - +
245A GLY 3.4 0.9 - - - -
246A ALA* 3.1 14.2 + - + +
247A ILE* 2.9 34.7 + - + +
300A MET* 3.3 23.3 - - + -
330A VAL* 3.1 51.2 + - + +
332A LEU* 3.4 16.8 - - - +
333A ARG* 6.1 0.9 - - - +
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Residues in contact with GLY 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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243A LYS* 1.4 77.6 - - - +
245A GLY* 1.3 60.2 + - - +
247A ILE* 3.1 20.4 + - - +
248A LEU* 3.3 12.9 + - - +
279A TYR* 4.5 9.5 + - - -
298A GLU 5.4 8.7 - - - -
300A MET* 4.9 5.9 - - - +
332A LEU* 4.6 0.8 - - - +
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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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243A LYS 3.4 0.2 - - - -
244A GLY* 1.3 72.5 - - - +
246A ALA* 1.4 57.3 + - - +
248A LEU* 3.4 10.3 + - - +
249A LYS* 2.8 30.5 + - - +
332A LEU* 3.9 18.2 - - - +
334A ASP* 3.8 31.3 - - - +
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Residues in contact with ALA 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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243A LYS* 3.1 19.9 + - + +
245A GLY* 1.4 76.2 - - - +
247A ILE* 1.3 61.6 + - + +
249A LYS* 3.5 6.8 - - - +
250A ILE* 3.1 29.9 + - + +
332A LEU* 4.2 5.1 - - - +
333A ARG* 3.5 49.9 - - + +
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Residues in contact with ILE 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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134A VAL* 4.9 23.3 - - + -
135A LEU* 5.6 12.1 - - + +
138A PHE* 6.0 8.3 - - + -
243A LYS* 2.9 25.1 + - + +
244A GLY* 3.1 9.6 + - - +
246A ALA* 1.3 75.8 - - + +
248A LEU* 1.4 59.4 + - - +
250A ILE* 3.5 9.0 + - + +
251A PHE* 3.2 27.5 + - + +
275A ILE* 5.6 5.2 - - + -
279A TYR* 3.8 15.3 - - - +
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Residues in contact with LEU 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 GLY 3.3 8.5 + - - +
245A GLY* 3.7 12.1 - - - +
247A ILE* 1.4 76.2 - - - +
249A LYS* 1.3 57.0 + - - +
251A PHE* 3.3 7.5 + - - +
252A GLN* 3.0 51.3 + - - +
272A LEU* 3.9 21.1 - - + -
276A SER* 5.6 0.7 - - - +
279A TYR* 4.1 29.6 + - + -
334A ASP* 5.0 12.1 - - - +
384A LEU 4.6 12.1 - - - +
385A MET* 4.7 10.1 - - + -
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Residues in contact with LYS 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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245A GLY 2.8 18.9 + - - +
246A ALA* 3.5 6.3 - - - +
247A ILE 3.3 0.2 - - - -
248A LEU* 1.3 73.9 - - - +
250A ILE* 1.4 57.2 + - + +
252A GLN* 3.2 8.1 + - - +
253A GLN* 2.9 59.3 + - + +
333A ARG* 4.2 32.3 + - + +
334A ASP* 4.1 24.3 + - - +
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Residues in contact with ILE 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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191A ASN* 4.4 14.8 - - + +
194A GLU* 6.0 1.3 - - - +
195A GLU* 3.3 38.8 - - + +
246A ALA* 3.1 17.0 + - + +
247A ILE* 3.8 8.5 - - + +
249A LYS* 1.4 76.0 - - + +
251A PHE* 1.4 57.5 + - - +
253A GLN* 3.3 9.9 + - + +
254A LYS* 3.0 41.3 + - + +
333A ARG* 3.8 12.6 - - - +
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Residues in contact with PHE 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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138A PHE* 6.1 0.2 - - + -
188A LEU* 5.7 0.2 - - + -
247A ILE* 3.2 19.7 + - + +
248A LEU* 3.4 10.1 - - - +
249A LYS 3.3 0.2 - - - -
250A ILE* 1.4 77.5 - - - +
252A GLN* 1.3 61.6 + - - +
254A LYS* 3.3 27.4 + - - +
255A ILE* 3.0 28.7 + - + +
268A LEU* 3.1 50.0 - - + -
271A LEU* 4.0 24.7 - - + -
272A LEU* 3.5 49.1 - - + -
275A ILE* 4.8 13.5 - - + -
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Residues in contact with GLN 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 LEU* 3.0 39.6 + - - +
249A LYS* 3.2 13.2 + - + +
251A PHE* 1.3 79.0 - - - +
253A GLN* 1.4 63.1 + - - +
255A ILE* 3.0 40.6 - - + +
256A LEU* 3.1 13.4 + - - +
272A LEU* 3.5 23.8 - - - +
385A MET* 3.6 25.0 - - - +
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Residues in contact with GLN 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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249A LYS* 2.9 50.5 + - + +
250A ILE* 3.6 9.6 - - + +
252A GLN* 1.4 77.2 - - - +
254A LYS* 1.4 59.1 + - - +
256A LEU* 3.2 23.7 + - - +
257A GLU* 2.8 44.5 + - + +
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Residues in contact with LYS 254 (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 GLU* 5.8 4.9 - - + +
188A LEU* 3.4 30.1 - - - +
191A ASN* 3.5 41.4 + - + +
192A ILE* 5.4 4.4 - - - +
250A ILE* 3.0 27.0 + - + +
251A PHE* 3.4 32.1 - - - +
252A GLN 3.2 0.2 - - - -
253A GLN* 1.4 74.7 - - - +
255A ILE* 1.3 63.7 + - - +
257A GLU* 3.4 8.4 + - - +
258A ASN* 2.9 33.4 + - - +
268A LEU* 3.9 21.1 - - + -
271A LEU* 5.8 0.4 - - - +
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Residues in contact with ILE 255 (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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251A PHE* 3.0 23.7 + - + +
252A GLN* 3.0 49.4 - - + +
254A LYS* 1.3 74.9 - - - +
256A LEU* 1.4 63.5 + - + +
258A ASN* 3.2 6.8 + - - +
259A LEU* 3.1 25.7 + - - +
265A VAL* 4.2 17.5 - - + +
268A LEU* 4.1 28.0 - - + -
269A LYS* 5.1 5.6 - - + +
272A LEU* 4.6 9.0 - - + -
385A MET* 6.1 2.2 - - + -
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Residues in contact with LEU 256 (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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252A GLN 3.1 13.4 + - - +
253A GLN* 3.2 30.5 + - - +
255A ILE* 1.4 79.7 - - + +
257A GLU* 1.3 63.0 + - - +
259A LEU* 3.6 22.7 + - + +
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Residues in contact with GLU 257 (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 GLU* 5.7 3.6 - - - +
253A GLN* 2.8 43.4 + - + +
254A LYS* 3.4 8.9 + - - +
256A LEU* 1.3 81.8 - - - +
258A ASN* 1.4 63.9 + - - +
259A LEU 3.4 4.0 + - - +
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Residues in contact with ASN 258 (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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183A ASN* 5.2 1.8 + - - +
187A GLU* 4.0 31.9 + - - +
254A LYS* 2.9 24.2 + - - +
255A ILE* 3.2 6.7 + - - +
257A GLU* 1.4 66.9 - - - +
259A LEU* 1.4 63.3 - - - +
260A GLY 3.4 2.1 + - - -
261A ASP* 3.4 15.6 + - - +
264A SER* 3.3 33.3 + - - +
265A VAL* 3.7 16.4 - - + +
268A LEU* 4.2 17.7 - - + +
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Residues in contact with LEU 259 (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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255A ILE 3.1 10.6 + - - +
256A LEU* 3.7 23.6 - - + +
257A GLU 3.3 5.8 - - - +
258A ASN* 1.4 60.6 - - - +
260A GLY* 1.3 64.2 + - - +
265A VAL* 4.4 11.7 - - + -
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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