Contacts of the helix formed by residues 299 - 310 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280L TYR* 2.8 27.5 + - - -
289L ARG* 5.8 1.7 + - - -
297L PRO* 3.7 10.7 - - - +
298L GLY* 1.3 71.9 + - - +
300L VAL* 1.3 56.3 + - - +
301L PHE 2.9 6.3 - - - -
302L TYR* 2.8 31.5 + - + +
303L LEU* 3.2 9.4 + - - +
306L ARG* 5.4 2.6 + - - -
226M PRO* 4.8 6.5 - - + +
267M GLU* 3.4 34.9 + - + +
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Residues in contact with VAL 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L ALA* 4.3 16.4 - - + -
280L TYR* 4.4 7.0 - - + -
296L TYR* 4.0 26.9 - - + -
297L PRO* 3.1 24.8 + - + +
298L GLY 3.2 0.6 - - - +
299L ASP* 1.3 76.3 + - - +
301L PHE* 1.3 62.9 + - - +
303L LEU* 3.3 24.2 - - + +
304L HIS* 3.9 11.4 + - + -
339L TYR* 3.1 42.6 - - + +
340L ILE* 5.6 5.8 - - + -
343L ASN* 4.1 5.8 + - - +
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Residues in contact with PHE 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298L GLY 4.5 2.4 + - - +
299L ASP 2.9 0.4 - - - -
300L VAL* 1.3 81.4 - - + +
302L TYR* 1.3 55.0 + - - +
304L HIS* 3.2 7.2 + - - +
305L SER* 2.6 54.0 + - - -
339L TYR* 5.1 1.6 - - - +
343L ASN* 4.1 28.0 - - + +
346L SER* 4.1 6.1 - - - -
347L ILE* 4.0 19.1 - - + -
222M MET* 4.2 22.7 - - + -
229M ARG* 3.7 22.7 - - - -
260M ARG* 3.2 35.0 - - - -
263M GLN* 3.2 40.2 - - + +
267M GLU* 4.4 4.0 - - - +
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Residues in contact with TYR 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299L ASP* 2.8 22.1 + - + +
301L PHE* 1.3 80.3 - - - +
303L LEU* 1.3 63.0 + - - +
305L SER* 3.6 5.4 - - - -
306L ARG* 3.1 75.8 + - + +
222M MET 4.0 7.4 - - - -
223M ASN 3.3 26.5 + - - -
224M GLU 3.4 12.3 - - - -
225M PRO* 3.3 31.0 - - + +
226M PRO* 4.4 9.4 - - + -
229M ARG* 3.3 17.3 - - - -
267M GLU* 3.3 16.2 + - - +
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Residues in contact with LEU 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L TYR* 3.6 32.3 - - + -
250L PHE* 3.5 27.1 - - + -
276L GLN* 3.7 26.9 - - - +
277L ALA* 3.9 16.8 - - + -
280L TYR* 3.8 36.6 - - + -
299L ASP* 3.2 7.0 + - - +
300L VAL* 3.3 16.6 - - + +
301L PHE 3.1 0.6 - - - -
302L TYR* 1.3 79.7 - - - +
304L HIS* 1.3 65.6 + - + +
306L ARG* 4.6 7.9 - - - +
307L LEU* 3.5 20.1 + - - +
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Residues in contact with HIS 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273L LEU* 3.4 46.1 + - + +
276L GLN* 3.1 26.6 + - - -
277L ALA* 3.9 19.5 - - + -
300L VAL* 3.9 12.0 + - + +
301L PHE* 3.2 4.8 + - - +
303L LEU* 1.3 83.8 - - + +
305L SER* 1.3 67.4 + - - +
307L LEU* 4.0 6.3 - - + -
308L LEU* 3.3 29.6 + - + +
340L ILE* 5.0 7.3 - - + +
343L ASN* 5.8 4.2 - - + +
344L VAL* 4.2 21.7 - - + +
347L ILE* 3.6 20.3 - - + +
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Residues in contact with SER 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301L PHE* 2.6 54.2 + - - -
302L TYR* 3.6 10.8 - - - -
304L HIS* 1.3 79.4 - - - +
306L ARG* 1.3 64.0 + - - +
308L LEU* 4.4 0.7 - - - +
309L GLU* 3.1 28.6 + - - +
347L ILE* 3.8 10.8 - - - +
222M MET* 3.1 28.0 - - - -
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Residues in contact with ARG 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L GLU* 4.5 3.8 + - - -
132L GLN* 3.5 22.3 + - - +
133L VAL 5.0 3.5 - - - +
135L ALA* 4.7 1.4 - - - +
246L TYR* 3.3 26.1 + - - -
250L PHE* 3.6 20.0 - - + -
280L TYR* 5.2 7.1 + - - -
299L ASP* 5.4 1.8 + - - -
302L TYR* 3.1 55.0 + - + +
303L LEU* 4.6 5.3 - - - +
305L SER* 1.3 78.6 - - - +
307L LEU* 1.3 65.5 + - - +
309L GLU* 4.1 6.1 - - - +
310L ARG* 3.4 26.7 + - - +
68M GLU* 3.4 24.4 + - - -
222M MET 4.2 0.6 + - - -
223M ASN* 3.9 22.4 - - - +
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Residues in contact with LEU 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L PRO* 3.5 47.3 - - + +
250L PHE* 4.1 19.5 - - + +
253L ALA* 4.1 8.2 - - + +
270L TYR* 3.6 27.8 + - + +
273L LEU* 3.9 26.0 - - + -
276L GLN* 4.4 8.5 - - - +
303L LEU 3.5 17.0 + - - +
304L HIS* 3.8 6.5 + - + +
305L SER 3.2 0.8 - - - -
306L ARG* 1.3 84.5 - - - +
308L LEU* 1.3 64.0 + - + +
310L ARG* 3.6 17.0 + - - +
311L ALA* 4.5 1.4 + - - +
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Residues in contact with LEU 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG* 3.2 26.1 - - + -
270L TYR* 4.1 12.6 - - + -
273L LEU* 4.7 4.0 - - + -
304L HIS* 3.3 23.5 + - + +
307L LEU* 1.3 79.7 - - + +
309L GLU* 1.3 60.8 + - - +
310L ARG 3.0 2.2 - - - -
311L ALA* 2.9 20.5 + - - +
325L ALA* 3.9 15.3 - - + -
327L PRO* 3.6 38.1 - - + -
344L VAL* 4.5 11.9 - - + -
347L ILE* 4.0 25.8 - - + -
348L THR* 4.1 17.7 - - + -
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Residues in contact with GLU 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ALA* 3.8 18.0 - - + +
141L ARG* 3.1 28.4 + - - -
166L ARG* 3.6 18.1 + - - +
305L SER 3.1 23.8 + - - +
306L ARG 4.1 3.1 - - - +
307L LEU 3.4 0.6 - - - -
308L LEU* 1.3 77.2 - - - +
310L ARG* 1.3 59.7 + - - +
311L ALA 3.1 5.8 + - - +
347L ILE* 5.3 0.2 - - + -
190M ARG* 3.6 1.6 - - - -
191M THR* 2.8 45.1 + - - -
192M ARG 5.0 0.3 + - - -
222M MET* 3.2 33.9 - - + +
223M ASN* 3.7 17.5 - - + +
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Residues in contact with ARG 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L ALA 3.0 19.6 + - - -
132L GLN* 4.4 0.4 + - - +
133L VAL* 3.4 35.6 - - - +
134L LYS 4.8 0.2 - - - -
135L ALA* 3.9 16.6 - - + -
136L PRO* 4.1 5.3 - - - +
250L PHE* 3.7 24.2 + - - -
253L ALA* 3.6 12.1 - - + +
254L SER* 2.9 40.2 + - - +
257L GLU* 2.7 38.8 + - + +
260L ARG* 2.9 26.5 + - - -
306L ARG* 3.4 19.5 + - - +
307L LEU* 3.7 10.7 - - - +
308L LEU 3.0 1.0 - - - -
309L GLU* 1.3 76.8 - - - +
311L ALA* 1.3 59.4 + - - +
312L ALA 3.4 2.9 + - - -
323L LEU* 4.1 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