Contacts of the helix formed by residues 259 - 270 (chain X) 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 PHE 259 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257X ASN* 3.0 17.7 + - - +
258X ILE* 1.3 78.8 - - - +
260X ARG* 1.3 65.9 + - - +
261X PHE 2.9 7.2 + - - -
262X THR* 3.0 16.8 + - - +
263X GLN* 3.1 49.3 + - + -
281X TYR* 3.4 20.4 - + - -
289X MET* 6.5 0.4 - - - -
310X VAL* 4.4 7.2 - - + -
311X TYR* 3.5 44.9 - + + +
313X PRO* 3.6 19.7 - - + -
321X ALA* 3.3 35.9 - - + -
322X PRO* 4.7 2.5 - - + -
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Residues in contact with ARG 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301T PHE* 3.2 31.2 - - - -
346T SER* 3.5 27.1 + - - -
187X VAL* 3.3 31.4 - - + +
188X GLY* 3.4 18.9 + - - +
189X GLU* 3.5 22.6 + - - -
222X MET* 4.2 5.9 - - - +
229X ARG* 4.0 8.9 - - + +
257X ASN* 3.5 16.0 - - + +
258X ILE 3.3 0.4 - - - -
259X PHE* 1.3 80.0 - - - +
261X PHE* 1.3 56.6 + - - +
262X THR 3.3 0.2 - - - -
263X GLN* 2.8 34.4 + - - +
264X ALA* 2.8 33.6 + - - +
311X TYR* 4.2 25.5 - - - -
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Residues in contact with PHE 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X VAL* 4.3 2.5 - - + +
229X ARG 3.9 11.2 + - - +
230X ALA* 3.5 33.7 - - + +
231X ARG* 5.0 8.1 - - - -
233X ALA* 4.7 11.7 - - + -
234X LEU* 5.2 5.6 - - + -
258X ILE* 3.4 20.3 + - + +
259X PHE 2.9 0.6 + - - -
260X ARG* 1.3 79.5 - - - +
262X THR* 1.3 73.0 + - - +
264X ALA* 4.0 2.1 - - - +
265X GLY* 3.2 16.8 + - - -
282X GLN* 6.1 1.1 - - - -
288X ASP* 3.2 46.7 - - + -
289X MET* 4.3 6.7 - - + -
292X LEU* 3.7 33.7 - - + -
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Residues in contact with THR 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X ILE 4.8 1.9 + - - -
259X PHE* 3.0 11.1 + - - -
261X PHE* 1.3 86.0 - - + +
263X GLN* 1.3 60.8 + - - +
265X GLY 2.9 1.0 + - - -
266X SER* 2.8 26.3 + - - -
281X TYR* 4.4 9.2 - - + -
282X GLN* 3.2 32.1 + - - +
285X LEU* 3.7 32.3 - - + +
289X MET* 3.8 22.5 - - + +
321X ALA* 4.7 11.5 - - + +
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Residues in contact with GLN 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298T GLY 4.5 10.7 + - - +
301T PHE* 3.1 44.2 - - - +
339T TYR* 4.8 8.9 + - - +
343T ASN* 4.9 3.6 + - - -
229X ARG* 5.6 1.5 + - - -
259X PHE* 3.1 36.6 + - + +
260X ARG* 2.8 41.7 + - + +
261X PHE 3.4 0.2 - - - -
262X THR* 1.3 77.4 - - - +
264X ALA* 1.3 59.7 + - - +
266X SER* 2.8 24.1 + - - +
267X GLU* 3.2 18.3 - - - +
281X TYR* 4.9 4.7 - - + -
311X TYR* 5.6 1.8 - - - -
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Residues in contact with ALA 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X PRO* 3.2 38.8 - - + +
229X ARG* 3.6 28.9 - - + +
230X ALA* 4.2 4.3 - - - +
260X ARG 2.8 22.4 + - - +
261X PHE 4.0 1.3 - - - +
263X GLN* 1.3 73.3 - - - +
265X GLY* 1.3 56.2 + - - +
267X GLU* 4.1 11.2 - - - -
268X VAL* 3.3 19.6 + - - +
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Residues in contact with GLY 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X ALA* 5.1 4.5 - - - -
261X PHE 3.2 12.2 + - - -
262X THR 2.9 9.6 + - - -
264X ALA* 1.3 79.3 - - - +
266X SER* 1.3 58.9 + - - +
267X GLU 3.3 0.2 - - - -
268X VAL* 3.3 9.1 - - - +
269X SER* 2.9 28.2 + - - -
272X LEU* 5.7 0.2 - - - +
274X ARG* 5.4 0.9 + - - -
282X GLN* 3.7 13.7 - - - -
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Residues in contact with SER 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298T GLY* 4.0 23.5 + - - -
262X THR 2.8 8.7 + - - -
263X GLN* 2.8 22.8 + - - +
265X GLY* 1.3 74.7 - - - +
267X GLU* 1.3 64.2 + - - +
268X VAL 3.1 3.2 + - - -
269X SER* 3.3 11.8 + - - -
270X ALA* 3.7 13.0 + - - +
280X GLY 5.0 4.5 - - - +
281X TYR* 4.0 23.9 - - - -
282X GLN* 3.1 18.8 + - - +
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Residues in contact with GLU 267 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298T GLY 3.9 5.3 - - - +
299T ASP* 3.4 47.8 - - + +
301T PHE* 5.0 1.0 - - - +
302T TYR* 3.2 21.5 + - - +
226X PRO* 3.1 26.5 - - + +
229X ARG* 3.0 34.3 + - - -
263X GLN* 3.2 24.6 - - - +
264X ALA* 4.1 3.1 - - - +
265X GLY 3.3 0.4 - - - -
266X SER* 1.3 81.3 + - - +
268X VAL* 1.3 59.7 + - - +
270X ALA* 4.7 3.6 + - - +
271X LEU* 4.1 17.8 + - - +
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Residues in contact with VAL 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X ALA* 4.7 4.9 - - + -
20X ILE* 3.7 27.0 - - + +
62X ILE* 4.1 25.1 - - + -
226X PRO* 4.3 18.8 - - + +
227X GLY* 5.0 1.8 - - - +
230X ALA* 5.7 3.4 - - + -
264X ALA 3.3 17.9 - - - +
265X GLY* 3.3 17.9 - - - +
267X GLU* 1.3 78.4 - - - +
269X SER* 1.3 66.2 + - - +
270X ALA 3.3 2.5 - - - -
271X LEU* 3.1 6.5 + - + +
272X LEU* 3.0 31.7 + - + +
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Residues in contact with SER 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265X GLY 2.9 18.9 + - - -
266X SER* 3.3 8.4 + - - -
268X VAL* 1.3 77.8 - - - +
270X ALA* 1.3 61.5 + - - +
272X LEU* 3.1 27.2 + - - +
274X ARG* 3.3 31.6 + - - +
276X PRO* 6.1 0.7 - - - +
282X GLN* 3.1 34.9 - - - +
283X PRO* 3.8 2.4 - - - +
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Residues in contact with ALA 270 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289T ARG* 5.7 4.9 - - - -
290T PRO* 3.8 36.8 - - + +
266X SER 3.7 10.3 + - - +
267X GLU 5.0 3.8 - - - +
268X VAL 3.3 0.4 - - - -
269X SER* 1.3 79.9 - - - +
271X LEU* 1.3 65.4 + - + +
272X LEU 3.2 0.9 + - - -
273X GLY* 3.4 12.0 + - - -
274X ARG 4.3 9.0 + - - +
276X PRO* 6.1 0.9 - - + -
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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