Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 4FGB
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 2.5 35.6 + - - -
245A ILE* 1.3 76.9 - - - +
247A ASP* 1.3 64.3 + - - +
248A SER* 3.8 5.5 + - - -
249A ALA* 3.2 19.6 + - - +
250A LYS* 3.2 12.3 + - - +
275A TRP* 3.9 0.2 - - - -
280A THR 3.6 14.1 + - - -
282A LEU* 3.6 23.9 - - - +
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Residues in contact with ASP 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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245A ILE 3.7 1.3 + - - +
246A SER* 1.3 71.3 - - - +
248A SER* 1.3 55.3 + - - +
250A LYS* 3.2 24.9 + - - +
251A ASP* 2.7 37.4 + - - +
254A ARG* 4.5 4.1 + - - +
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Residues in contact with SER 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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246A SER* 3.1 10.2 - - - -
247A ASP* 1.3 78.7 - - - +
249A ALA* 1.3 57.3 + - - +
251A ASP* 3.2 5.8 + - - +
252A PHE 2.9 24.6 + - - -
273A HIS* 3.2 14.7 - - - -
274A PRO* 4.5 2.2 - - - +
275A TRP* 3.2 15.6 + - - +
280A THR* 2.8 38.8 + - - -
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Residues in contact with ALA 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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115A GLU* 3.5 4.0 - - - +
212A LEU* 3.5 22.8 - - + +
245A ILE* 3.6 5.4 - - + -
246A SER* 3.2 16.7 + - - +
248A SER* 1.3 79.2 + - - +
250A LYS* 1.3 59.9 + - - +
252A PHE* 3.3 4.7 - - - +
253A ILE* 3.1 28.9 + - - +
275A TRP* 3.2 34.5 - - - +
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Residues in contact with LYS 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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237A PHE* 3.6 43.5 + - + +
242A TRP* 3.3 51.5 + - + +
243A ASP* 5.0 3.6 + - - +
245A ILE 3.6 12.7 + - - -
246A SER 3.2 7.1 + - - +
247A ASP* 3.2 23.5 + - - +
249A ALA* 1.3 73.5 - - - +
251A ASP* 1.3 57.2 + - - +
253A ILE* 3.0 3.3 + - - +
254A ARG* 2.7 58.7 + - - +
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Residues in contact with ASP 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 ASP 2.7 21.3 + - - +
248A SER* 3.4 8.7 - - - +
250A LYS* 1.3 72.1 - - - +
252A PHE* 1.3 61.4 + - - +
254A ARG* 3.5 13.1 + - - +
255A HIS* 2.4 56.7 + - - -
265A PHE* 5.4 0.5 - - - -
273A HIS* 2.8 26.2 + - - +
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Residues in contact with PHE 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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122A ILE* 3.4 32.8 - - + -
126A LEU* 3.7 3.6 - - + -
208A ALA* 3.9 7.9 - - + -
248A SER 2.9 13.3 + - - +
249A ALA 3.3 11.7 - - - +
251A ASP* 1.3 76.3 - - - +
253A ILE* 1.3 69.7 + - + +
255A HIS* 3.4 4.8 + - - +
256A LEU* 3.2 46.7 + - + +
265A PHE* 5.3 1.6 - + - -
270A ALA* 3.4 22.9 - - + -
273A HIS* 3.5 35.6 + + + -
275A TRP* 3.6 23.6 - + + -
276A ILE* 3.3 21.1 - - + -
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Residues in contact with ILE 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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205A GLY 3.8 3.4 - - - +
208A ALA* 3.8 20.9 - - + -
209A TYR* 3.8 12.6 - - + +
212A LEU* 3.8 12.1 - - + -
235A TYR* 4.3 1.1 - - + -
237A PHE* 3.8 18.2 - - + -
242A TRP* 3.5 36.8 - - + -
249A ALA 3.1 14.8 + - - +
250A LYS 3.0 6.6 + - - +
252A PHE* 1.3 78.3 - - + +
254A ARG* 1.3 55.6 + - - +
256A LEU* 2.9 5.5 + - - +
257A MET* 2.4 64.7 + - + +
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Residues in contact with ARG 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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235A TYR* 3.0 19.7 + - + +
237A PHE* 3.5 32.2 - - + -
247A ASP* 4.5 4.6 + - - +
250A LYS* 2.7 29.3 + - - +
251A ASP* 3.5 36.1 + - - +
252A PHE 3.4 0.2 - - - -
253A ILE* 1.3 72.2 - - - +
255A HIS* 1.3 67.9 + - + +
257A MET 3.4 17.8 - - - +
258A GLU* 3.5 9.5 + - - +
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Residues in contact with HIS 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 ASP* 2.4 59.2 + - - +
252A PHE 3.9 2.9 - - - +
253A ILE 3.1 1.0 - - - -
254A ARG* 1.3 83.5 - - + +
256A LEU* 1.3 56.6 + - - +
258A GLU* 4.5 3.6 - - - -
263A LYS 5.6 2.5 - - - -
264A ARG* 3.5 5.9 - - - -
265A PHE* 2.7 79.2 + + + -
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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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126A LEU* 4.8 1.8 - - + -
201A CYS* 3.6 18.6 - - + +
202A TRP* 3.6 8.0 - - - -
204A ILE* 3.8 11.0 - - + -
205A GLY* 3.4 31.9 - - - +
252A PHE* 3.2 48.6 + - + +
253A ILE 2.9 4.1 + - - +
255A HIS* 1.3 77.6 - - - +
257A MET* 1.3 58.5 + - - +
258A GLU 3.0 11.0 + - - -
264A ARG* 3.1 24.3 + - - +
265A PHE* 3.8 26.9 - - + +
270A ALA* 3.8 21.1 - - + -
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Residues in contact with MET 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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202A TRP* 3.5 16.9 - - + +
205A GLY* 3.5 20.4 - - - +
206A VAL* 3.7 26.2 - - + +
209A TYR* 4.0 4.0 - - - -
217A PRO* 3.6 17.7 - - + -
218A PHE* 3.3 42.6 - - + -
233A ALA* 4.2 1.7 - - - +
235A TYR* 3.1 42.8 + - + +
253A ILE* 2.4 46.2 + - + +
254A ARG 3.4 5.9 - - - +
256A LEU* 1.3 64.8 - - - +
258A GLU* 1.3 56.1 + - - +
259A LYS 4.1 0.7 + - - -
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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