Contacts of the helix formed by residues 258 - 270 (chain F) in PDB entry 3FKS
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 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187F VAL* 4.9 2.7 - - - -
233F ALA* 5.8 2.2 - - + -
255F ILE* 3.9 26.2 + - + +
257F ASN* 1.3 75.6 + - - +
259F PHE* 1.3 67.5 + - - +
261F PHE* 3.2 22.5 + - + +
262F THR* 4.2 3.0 + - - +
289F MET* 5.4 7.9 - - + -
292F LEU* 4.2 20.4 - - + -
293F GLN* 3.8 24.0 - - - +
308F GLN* 3.3 27.6 - - + +
309F ALA 3.1 17.1 + - - +
310F VAL* 3.6 22.2 - - + -
325F THR* 5.2 3.8 - - + +
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Residues in contact with PHE 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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257F ASN* 2.9 15.4 + - - +
258F ILE* 1.3 84.7 - - - +
260F ARG* 1.3 71.7 + - - +
261F PHE 3.0 2.0 + - - -
262F THR* 3.3 5.5 + - - -
263F GLN* 3.0 56.8 + - + -
281F TYR* 3.9 7.2 - + - -
310F VAL* 4.4 4.9 - - + -
311F TYR* 3.4 48.0 - + + +
313F PRO* 3.3 34.5 - - + -
321F ALA* 3.5 30.7 - - + -
322F PRO* 4.8 0.9 - - + -
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Residues in contact with ARG 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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301B PHE* 3.2 38.0 - - - -
346B SER* 3.7 23.2 + - - -
163F LYS* 5.7 0.8 - - - +
187F VAL* 3.0 35.7 - - + +
188F GLY* 3.0 22.0 + - - +
189F GLU* 3.5 19.4 + - - -
222F MET* 4.7 0.4 - - - +
229F ARG* 4.5 7.1 - - - +
257F ASN* 3.1 15.1 + - + +
259F PHE* 1.3 90.0 - - - +
261F PHE* 1.3 56.9 + - - +
262F THR 3.5 0.2 - - - -
263F GLN* 3.1 31.3 - - - +
264F ALA* 2.8 33.2 + - - +
311F TYR* 4.0 20.6 - - - +
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Residues in contact with PHE 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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187F VAL* 4.0 9.0 - - + +
229F ARG 4.4 7.9 - - - -
230F ALA* 3.2 31.1 - - + +
231F ARG* 4.9 12.1 - - - -
233F ALA* 4.7 6.7 - - + -
234F LEU* 5.2 6.3 - - + -
258F ILE* 3.2 19.6 + - + +
259F PHE 3.0 0.8 - - - -
260F ARG* 1.3 76.4 - - - +
262F THR* 1.3 75.5 + - - +
264F ALA* 4.0 2.1 - - - +
265F GLY* 3.0 22.9 + - - -
288F ASP* 3.6 48.0 - - + -
289F MET* 4.1 4.7 - - + -
292F LEU* 3.6 33.2 - - + -
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Residues in contact with THR 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F ILE* 4.2 2.8 + - - +
259F PHE* 3.3 7.2 + - - -
261F PHE* 1.3 91.9 - - + +
263F GLN* 1.3 64.5 + - - +
266F SER* 3.1 9.2 + - - -
281F TYR* 4.4 8.4 - - + -
282F GLN* 3.1 41.4 + - - +
285F LEU* 3.7 33.6 + - + +
288F ASP* 6.2 0.7 - - + -
289F MET* 3.4 26.4 - - + +
321F ALA* 4.9 8.1 - - + -
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Residues in contact with GLN 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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298B GLY 5.1 6.6 + - - +
301B PHE* 3.2 39.1 - - - +
339B TYR* 5.4 3.2 + - - -
343B ASN* 5.2 1.4 - - - +
229F ARG* 3.7 14.5 + - - -
259F PHE* 3.0 43.9 + - + +
260F ARG* 3.1 36.3 + - - +
262F THR* 1.3 77.5 - - - +
264F ALA* 1.3 60.1 + - - +
266F SER* 2.6 26.1 + - - +
267F GLU* 3.5 13.4 + - - +
281F TYR* 5.2 4.9 - - - -
311F TYR* 5.6 1.2 - - - -
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Residues in contact with ALA 264 (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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226F PRO* 3.8 30.8 - - + +
229F ARG* 3.9 23.1 - - + +
230F ALA* 4.1 7.6 - - - +
260F ARG 2.8 21.7 + - - +
261F PHE 4.0 2.7 - - - +
263F GLN* 1.3 77.3 + - - +
265F GLY* 1.3 62.3 + - - +
267F GLU* 3.2 25.5 + - - +
268F VAL* 3.7 6.8 + - - +
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Residues in contact with GLY 265 (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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230F ALA* 5.1 5.8 - - - +
261F PHE* 3.0 16.4 + - - -
262F THR 3.3 5.1 + - - -
263F GLN 3.2 0.4 - - - -
264F ALA* 1.3 77.8 - - - +
266F SER* 1.3 56.1 + - - +
268F VAL* 3.3 11.1 - - - +
269F SER* 3.3 24.4 + - - -
274F ARG* 5.1 2.4 + - - -
282F GLN* 3.7 14.7 + - - +
288F ASP* 5.9 1.3 - - - -
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Residues in contact with SER 266 (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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298B GLY* 4.7 13.4 + - - -
262F THR 3.1 6.5 + - - -
263F GLN* 2.6 25.2 + - - +
265F GLY* 1.3 75.4 - - - +
267F GLU* 1.3 65.6 + - - +
268F VAL 3.2 3.0 + - - -
269F SER* 3.3 16.1 + - - -
270F ALA* 3.9 6.1 + - - +
280F GLY 4.6 7.0 - - - +
281F TYR* 4.5 15.2 - - - -
282F GLN* 3.2 26.7 - - - -
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Residues in contact with GLU 267 (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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298B GLY* 3.9 8.3 - - - +
299B ASP* 3.4 47.1 - - + +
301B PHE* 5.0 1.0 - - - +
302B TYR* 3.3 20.6 + - - +
226F PRO* 3.6 20.3 - - + +
229F ARG* 2.8 35.3 + - - -
263F GLN* 3.6 19.5 - - - +
264F ALA* 3.2 8.4 + - - +
266F SER* 1.3 79.7 + - - +
268F VAL* 1.3 58.1 + - - +
270F ALA* 4.4 8.0 + - - +
271F LEU* 4.3 11.4 - - - +
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Residues in contact with VAL 268 (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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19F ALA* 4.2 6.1 - - + -
20F ILE* 3.5 26.4 - - + +
62F ILE* 4.4 19.5 - - + -
226F PRO* 3.8 32.5 - - + -
227F GLY 5.0 0.4 - - - +
264F ALA 3.7 3.3 + - - +
265F GLY* 3.3 18.8 - - - +
267F GLU* 1.3 76.3 - - - +
269F SER* 1.3 61.0 + - - +
270F ALA 3.1 2.9 - - - -
271F LEU* 2.8 29.7 + - + +
272F LEU* 3.2 24.2 + - + +
274F ARG* 6.0 0.4 - - - +
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Residues in contact with SER 269 (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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265F GLY 3.3 15.4 + - - -
266F SER* 3.3 9.5 + - - -
268F VAL* 1.3 83.5 - - - +
270F ALA* 1.3 60.8 + - - +
272F LEU* 3.3 12.2 + - - -
274F ARG* 3.2 45.8 + - - +
276F PRO* 6.1 0.5 - - - +
282F GLN* 3.2 33.7 - - - +
283F PRO* 3.7 0.7 - - - +
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Residues in contact with ALA 270 (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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289B ARG* 5.1 7.4 - - - -
290B PRO* 3.5 40.5 - - + +
266F SER 3.9 5.5 + - - +
267F GLU 4.7 7.9 - - - +
268F VAL 3.1 1.0 - - - -
269F SER* 1.3 78.7 - - - +
271F LEU* 1.3 65.9 + - + +
272F LEU 3.2 1.1 + - - -
273F GLY* 3.4 12.6 + - - -
274F ARG 4.2 7.7 + - - +
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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