Contacts of the helix formed by residues 259 - 267 (chain B) in PDB entry 5FFG
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 PHE 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO 5.0 3.1 - - - -
245A ARG* 3.2 30.7 - - + -
249A THR* 3.5 26.7 - - + -
273A ALA* 3.5 44.0 - - + -
275A TYR* 3.4 33.8 - + - -
299A LEU* 4.4 5.6 - - + -
226B PHE* 3.5 22.7 - + + -
257B SER 4.0 4.3 - - - -
258B HIS* 1.3 76.7 - - - +
260B GLY* 1.3 68.2 + - - +
261B MET 3.2 0.9 + - - -
262B ASP* 2.9 27.1 + - - +
292B TYR* 3.6 5.4 - - - -
293B PRO 3.6 7.4 - - - +
294B THR* 5.0 3.8 - - - -
295B ILE 5.3 0.9 - - - +
324B TYR* 4.1 7.4 - - - -
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LEU* 4.5 0.7 - - - -
259B PHE* 1.3 75.1 - - - +
261B MET* 1.3 63.4 + - - -
262B ASP 3.2 4.9 + - - -
263B SER* 3.4 14.7 + - - -
291B GLU* 3.6 6.3 - - - +
292B TYR* 3.2 25.8 + - - +
293B PRO 3.0 14.9 + - - -
294B THR* 3.9 19.7 - - - +
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 2.7 35.0 + - - +
275A TYR* 3.1 42.1 + - + -
278A PHE* 3.7 30.7 - - + -
298A PRO* 4.2 10.5 - - + -
299A LEU* 3.9 21.1 - - + -
339A ARG* 3.3 36.8 - - - +
342A SER* 5.9 0.2 - - - +
407A TYR* 6.3 0.7 - - + -
259B PHE 3.2 1.4 + - - -
260B GLY* 1.3 71.8 - - - -
262B ASP* 1.3 64.0 + - - +
263B SER 3.1 2.5 - - - +
264B LYS* 3.1 16.1 + - + +
291B GLU* 3.9 13.0 - - - +
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Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.4 15.0 - - + +
224A TYR* 5.2 0.4 - - - -
245A ARG* 2.8 34.0 + - - +
275A TYR* 2.5 31.0 + - - -
168B PHE* 3.4 13.2 - - - -
258B HIS* 3.3 23.4 - - + -
259B PHE* 2.9 29.8 + - - +
261B MET* 1.3 78.7 - - - +
263B SER* 1.3 59.2 + - - +
264B LYS 3.1 1.8 + - - -
265B LEU* 3.3 18.5 + - - +
292B TYR* 3.9 8.7 - - + -
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LYS* 4.0 12.8 - - - -
168B PHE* 4.0 7.0 - - - -
260B GLY 3.4 2.8 + - - -
262B ASP* 1.3 74.2 - - - +
264B LYS* 1.3 59.8 + - - +
265B LEU 3.1 2.7 - - - -
266B ALA* 2.9 16.9 + - - +
268B ILE* 3.0 34.2 + - - +
291B GLU* 3.2 35.2 - - - +
292B TYR* 3.7 21.6 - - - -
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.3 25.2 - - + -
159A PHE* 3.6 36.0 - - + -
224A TYR* 3.2 24.5 - - + +
278A PHE* 4.0 11.7 - - + -
407A TYR* 2.3 38.3 + - - +
261B MET* 3.1 20.3 + - + +
262B ASP 3.1 1.4 - - - -
263B SER* 1.3 78.0 + - - +
265B LEU* 1.3 60.1 + - - +
267B GLY* 3.1 12.6 + - - +
268B ILE 3.6 12.3 + - - +
269B VAL* 4.3 9.0 - - + -
291B GLU* 5.7 0.9 - - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.4 10.7 - - - +
156A GLN* 2.8 43.1 + - - +
159A PHE* 3.6 27.8 - - + -
174A PRO* 3.6 24.7 - - + -
179A TRP* 4.0 20.6 - - + +
221A TYR* 3.7 35.7 - - + +
224A TYR* 4.6 7.0 - - + -
167B PRO* 3.7 12.3 - - + +
168B PHE* 4.5 3.8 - - + -
262B ASP 3.3 12.5 + - - +
263B SER 3.1 0.6 - - - -
264B LYS* 1.3 80.0 - - - +
266B ALA* 1.3 56.0 + - - +
267B GLY 3.3 0.7 + - - -
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TRP* 5.1 0.7 + - - -
111A LEU* 3.6 13.2 - - - +
165B VAL* 3.8 22.7 - - + +
166B SER 3.2 24.7 - - - +
168B PHE* 3.9 14.6 - - + -
263B SER* 2.9 11.3 + - - +
265B LEU* 1.3 77.4 - - - +
267B GLY* 1.3 61.8 + - - +
268B ILE* 3.5 11.7 + - + +
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 5.4 0.3 + - - -
42A LYS* 4.8 5.5 + - - -
93A TRP* 3.1 48.0 - - - -
111A LEU* 3.8 4.6 - - - +
264B LYS 3.1 13.4 + - - -
265B LEU 3.3 1.8 + - - -
266B ALA* 1.3 79.5 - - - +
268B ILE* 1.3 60.0 + - - +
269B VAL* 3.7 6.0 + - - +
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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