Contacts of the helix formed by residues 299 - 310 (chain U) 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 ASP 299 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280U TYR* 2.7 37.2 + - - -
289U ARG* 4.6 6.2 + - - -
297U PRO* 3.8 6.8 - - - +
298U GLY* 1.3 72.1 + - - +
300U VAL* 1.3 58.6 + - - +
301U PHE 3.2 2.2 - - - -
302U TYR* 3.5 31.5 - - + +
303U LEU* 3.0 24.3 + - - +
306U ARG* 5.2 4.7 + - - -
18V GLY* 5.8 3.0 - - - -
226V PRO* 5.1 2.9 - - + -
267V GLU* 4.0 4.0 - - - +
271V LEU* 4.3 26.9 - - + +
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Residues in contact with VAL 300 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277U ALA* 4.4 12.3 - - + +
280U TYR* 5.0 2.2 - - + -
296U TYR* 3.9 23.3 - - + -
297U PRO* 3.4 26.7 + - + +
298U GLY 3.2 1.2 - - - -
299U ASP* 1.3 77.4 - - - +
301U PHE* 1.3 62.5 + - - +
303U LEU* 3.4 25.5 - - + +
304U HIS* 3.8 12.2 + - - +
339U TYR* 3.1 43.5 - - + +
340U ILE* 4.0 10.2 - - + +
343U ASN* 3.8 7.3 + - - +
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Residues in contact with PHE 301 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298U GLY 4.4 0.4 + - - +
299U ASP 3.2 0.4 - - - -
300U VAL* 1.3 80.2 - - + +
302U TYR* 1.3 58.7 + - - +
303U LEU 3.1 1.7 + - - -
304U HIS* 3.5 5.4 + - + +
305U SER* 2.7 45.6 + - - -
339U TYR* 5.1 2.5 - - - +
343U ASN* 3.4 49.8 - - + +
346U SER* 3.8 6.3 - - - -
347U ILE* 3.7 17.2 - - + +
222V MET* 4.8 6.7 - - + -
229V ARG* 3.2 36.6 - - - -
260V ARG* 4.0 12.6 - - - -
263V GLN* 3.4 35.2 - - - +
267V GLU* 3.5 16.3 + - + +
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Residues in contact with TYR 302 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299U ASP* 3.3 32.5 + - + +
301U PHE* 1.3 78.8 - - - +
303U LEU* 1.3 66.4 + - - +
305U SER* 3.4 13.5 + - - -
306U ARG* 3.3 47.8 + - + +
66V GLY* 4.7 5.7 - - - -
68V GLU* 3.5 16.5 + - - -
223V ASN 4.0 11.9 + - - -
224V GLU 3.7 9.2 - - - -
225V PRO* 3.4 48.1 - - + +
226V PRO* 4.1 11.9 - - + -
229V ARG* 5.0 2.2 - - - +
267V GLU* 3.4 11.3 + - - +
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Residues in contact with LEU 303 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246U TYR* 3.5 31.0 - - + -
250U PHE* 3.6 29.2 - - + -
276U GLN* 4.5 19.5 - - + +
277U ALA* 4.8 2.7 - - - -
280U TYR* 3.7 44.0 - - + -
299U ASP* 3.0 12.4 + - - +
300U VAL* 3.4 18.6 - - + +
302U TYR* 1.3 81.1 - - - +
304U HIS* 1.3 72.2 + - + +
305U SER 3.4 0.2 + - - -
306U ARG* 3.5 24.2 - - - +
307U LEU* 3.7 4.2 - - - +
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Residues in contact with HIS 304 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273U LEU* 3.5 51.1 + - + +
276U GLN* 2.8 32.3 + - - -
277U ALA* 4.3 16.8 - - + -
300U VAL* 3.8 12.5 + - + +
301U PHE* 3.5 6.9 + - + +
302U TYR 3.4 0.2 - - - -
303U LEU* 1.3 85.1 - - + +
305U SER* 1.3 58.7 + - - +
307U LEU* 4.1 10.3 - - + -
308U LEU* 3.3 39.5 + - + +
340U ILE* 5.3 4.9 - - + +
343U ASN* 6.3 1.8 - - + -
344U VAL* 4.2 21.1 - - + +
347U ILE* 4.4 6.8 - - + +
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Residues in contact with SER 305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301U PHE* 2.7 41.0 + - - -
302U TYR* 3.7 11.2 - - - -
303U LEU 3.2 1.2 - - - -
304U HIS* 1.3 77.2 - - - +
306U ARG* 1.3 65.9 + - - +
308U LEU* 4.6 0.4 - - - +
309U GLU* 3.2 32.0 + - - +
347U ILE* 3.6 17.5 - - - +
222V MET* 3.2 23.8 + - - +
223V ASN* 4.3 2.2 - - - -
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Residues in contact with ARG 306 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U GLU* 4.5 4.8 + - - -
132U GLN* 3.4 20.7 + - - +
133U VAL 4.5 4.3 - - - +
135U ALA* 4.8 1.9 - - - +
246U TYR* 3.2 25.1 + - - -
250U PHE* 3.8 11.9 - - + -
280U TYR* 5.3 2.0 + - - -
299U ASP* 5.2 4.0 + - - -
302U TYR* 3.3 48.5 + - + +
303U LEU* 3.5 26.0 + - - +
305U SER* 1.3 79.6 - - - +
307U LEU* 1.3 61.0 + - - +
309U GLU* 4.3 1.4 - - - +
310U ARG* 3.1 30.0 + - - +
68V GLU* 3.2 33.9 + - - +
223V ASN* 4.2 22.8 - - + +
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Residues in contact with LEU 307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249U PRO* 3.3 50.9 - - + +
250U PHE* 3.7 23.6 - - + -
253U ALA* 3.7 11.0 - - + -
270U TYR* 3.5 30.6 + - + +
273U LEU* 4.7 5.2 - - + -
276U GLN* 4.0 17.7 - - - +
303U LEU 3.7 9.1 + - - +
304U HIS* 4.4 7.4 - - + +
305U SER 3.2 0.2 - - - -
306U ARG* 1.3 79.9 - - - +
308U LEU* 1.3 71.8 + - + +
310U ARG* 3.2 26.5 - - - +
311U ALA* 4.3 1.2 + - - +
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Residues in contact with LEU 308 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166U ARG* 3.2 22.6 - - + -
270U TYR* 4.1 25.4 - - + -
273U LEU* 4.7 6.1 - - + -
304U HIS* 3.3 28.6 + - + +
305U SER 4.6 0.2 - - - +
307U LEU* 1.3 81.5 - - + +
309U GLU* 1.3 66.1 + - - +
311U ALA* 3.1 15.8 + - - +
325U ALA* 4.5 7.0 - - + -
327U PRO* 3.6 35.7 - - + -
344U VAL* 4.2 18.8 - - + -
347U ILE* 3.6 28.0 - - + -
348U THR* 4.7 1.8 - - + -
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Residues in contact with GLU 309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U ALA* 3.8 7.2 - - + +
136U PRO* 3.8 0.2 - - - +
141U ARG* 3.3 31.9 + - - -
166U ARG* 3.3 25.0 + - - +
305U SER 3.2 20.9 + - - +
306U ARG 4.3 1.1 - - - +
307U LEU 3.3 0.2 - - - -
308U LEU* 1.3 79.1 - - - +
310U ARG* 1.3 63.3 + - - +
311U ALA 2.9 11.1 + - - +
347U ILE* 5.9 0.7 - - + -
190V ARG* 4.1 0.5 - - - -
191V THR* 2.8 47.3 + - - +
222V MET* 3.7 22.2 - - + +
223V ASN* 3.5 25.7 - - + +
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Residues in contact with ARG 310 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131U ALA 2.9 20.9 + - - -
132U GLN* 4.1 1.2 + - - +
133U VAL* 3.3 38.2 + - - +
135U ALA* 3.9 8.9 - - - +
136U PRO* 3.8 8.9 - - - +
250U PHE* 3.6 29.5 + - - -
253U ALA* 3.7 13.5 - - + +
254U SER* 3.1 26.1 + - - +
257U GLU* 3.0 43.6 + - + +
260U ARG* 2.6 30.5 + - - -
306U ARG 3.1 20.9 - - - +
307U LEU* 3.2 16.6 - - - +
308U LEU 3.1 0.4 - - - -
309U GLU* 1.3 78.1 - - - +
311U ALA* 1.3 57.0 + - - +
312U ALA 3.4 0.5 + - - -
323U LEU* 4.1 5.2 - - + +
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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