Contacts of the helix formed by residues 299 - 310 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280S TYR* 2.8 27.6 + - - -
289S ARG* 5.9 0.5 + - - -
297S PRO* 3.8 12.0 - - - +
298S GLY* 1.3 69.8 - - - +
300S VAL* 1.3 59.7 + - - +
301S PHE 3.2 2.5 - - - -
302S TYR* 3.1 24.4 + - + +
303S LEU* 3.0 23.6 + - - +
306S ARG* 5.1 3.6 + - - -
226W PRO* 4.4 8.1 - - + -
267W GLU* 3.3 15.7 - - + +
271W LEU* 3.9 26.2 - - + +
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Residues in contact with VAL 300 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277S ALA* 4.5 4.3 - - + +
280S TYR* 4.4 8.3 - - + -
296S TYR* 3.9 16.8 - - + -
297S PRO* 3.0 19.5 + - + +
298S GLY 3.2 0.8 - - - -
299S ASP* 1.3 75.7 - - - +
301S PHE* 1.3 65.3 + - - +
303S LEU* 3.3 30.9 - - + +
304S HIS* 3.7 10.7 + - + +
339S TYR* 3.3 41.5 - - + +
340S ILE* 3.6 24.2 - - + +
343S ASN* 4.3 6.9 + - - +
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Residues in contact with PHE 301 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298S GLY 4.5 0.6 + - - +
299S ASP* 3.2 0.4 - - - +
300S VAL* 1.3 81.1 - - + +
302S TYR* 1.3 60.7 + - - +
303S LEU 3.1 0.4 - - - -
304S HIS* 3.7 2.5 + - - -
305S SER* 3.1 31.0 + - - -
339S TYR* 5.6 1.3 - - - +
343S ASN* 3.6 31.2 - - + +
346S SER* 3.8 21.1 - - - -
347S ILE* 3.8 15.0 - - + +
188W GLY* 6.4 0.4 - - - -
222W MET* 3.4 32.8 - - + -
229W ARG* 3.8 17.7 - - - -
260W ARG* 4.2 14.6 - - + -
263W GLN* 3.6 34.1 - - - +
267W GLU* 3.5 24.0 - - - +
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Residues in contact with TYR 302 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299S ASP* 3.1 33.2 + - + +
301S PHE* 1.3 80.2 - - - +
303S LEU* 1.3 64.9 + - - +
305S SER* 3.7 4.7 - - - -
306S ARG* 3.2 59.6 + - + +
66W GLY* 4.7 9.7 + - - -
222W MET 4.5 3.6 - - - -
223W ASN 2.9 27.7 + - - -
224W GLU 3.3 9.9 - - - -
225W PRO* 3.4 26.4 - - + +
226W PRO* 3.8 16.4 - - + -
229W ARG* 3.6 17.5 - - - +
267W GLU* 3.9 8.5 + - - +
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Residues in contact with LEU 303 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246S TYR* 3.7 20.9 - - + -
250S PHE* 3.4 53.9 - - + -
276S GLN* 3.7 15.9 + - - +
277S ALA* 4.2 7.2 - - - -
280S TYR* 3.5 35.7 - - + -
299S ASP 3.0 10.6 + - - +
300S VAL* 3.3 14.8 - - + +
302S TYR* 1.3 77.1 - - - +
304S HIS* 1.3 83.1 + - + +
305S SER 3.0 7.3 + - - -
306S ARG* 4.4 9.4 - - - +
307S LEU* 3.7 6.6 + - - +
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Residues in contact with HIS 304 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273S LEU* 3.2 57.6 + - + +
276S GLN* 3.5 11.4 + - - +
277S ALA* 3.8 12.8 - - + +
300S VAL* 3.7 12.7 + - + +
301S PHE* 3.7 2.5 + - - +
303S LEU* 1.3 100.4 - - + +
305S SER* 1.3 59.8 + - - +
307S LEU* 4.2 9.0 - - - -
308S LEU* 3.2 37.0 + - + +
340S ILE* 4.6 9.1 - - + +
343S ASN* 6.3 1.8 - - + -
344S VAL* 3.5 20.0 - - + +
347S ILE* 3.8 17.1 - - + +
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Residues in contact with SER 305 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301S PHE* 3.1 25.7 + - - -
302S TYR* 3.7 12.1 - - - -
303S LEU 3.0 0.8 - - - -
304S HIS* 1.3 76.2 - - - +
306S ARG* 1.3 68.5 + - - +
307S LEU 3.2 1.1 - - - -
308S LEU 3.3 0.7 + - - -
309S GLU* 3.0 29.4 + - - +
347S ILE* 4.1 11.7 - - - -
222W MET* 2.9 44.4 + - - +
223W ASN* 4.8 0.4 - - - -
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Residues in contact with ARG 306 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S GLU* 5.1 5.3 + - - -
132S GLN* 3.7 29.1 + - - +
133S VAL 6.1 0.4 - - - +
135S ALA* 4.8 0.5 - - - +
246S TYR* 3.6 21.6 + - - -
250S PHE* 4.0 19.9 - - + -
280S TYR* 5.0 7.3 + - - -
299S ASP* 5.1 2.2 + - - -
302S TYR* 3.2 63.2 + - + +
303S LEU* 4.4 12.5 - - - +
305S SER* 1.3 80.6 - - - +
307S LEU* 1.3 63.2 + - - +
309S GLU* 4.1 2.1 - - - +
310S ARG* 3.1 29.1 + - - +
66W GLY* 6.1 1.4 - - - -
68W GLU* 4.7 10.7 + - - -
223W ASN* 3.9 13.9 - - + +
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Residues in contact with LEU 307 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249S PRO* 3.2 39.5 - - + +
250S PHE* 3.8 21.7 - - + +
253S ALA* 3.9 8.4 - - + +
270S TYR* 3.5 41.4 + - + +
273S LEU* 3.5 31.9 - - + -
276S GLN* 4.5 5.6 - - - +
303S LEU 3.7 9.9 + - - +
304S HIS* 4.4 4.9 - - - +
305S SER 3.2 0.8 - - - -
306S ARG* 1.3 83.1 - - - +
308S LEU* 1.3 65.3 + - + +
309S GLU 3.5 0.2 + - - -
310S ARG* 3.5 18.0 + - - +
311S ALA* 4.2 2.9 + - - +
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Residues in contact with LEU 308 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166S ARG* 2.8 35.0 + - + -
270S TYR* 3.9 24.7 - - + -
273S LEU* 4.0 21.5 - - + -
304S HIS* 3.2 24.3 + - + +
305S SER 3.3 2.0 + - - -
307S LEU* 1.3 77.1 - - + +
309S GLU* 1.3 62.8 + - - +
310S ARG 3.3 0.4 - - - -
311S ALA* 3.7 9.6 + - - +
325S ALA* 4.5 5.6 - - + -
327S PRO* 3.9 25.1 - - + -
344S VAL* 4.3 17.5 - - + -
347S ILE* 4.1 22.2 - - + -
348S THR* 4.4 8.5 - - + -
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Residues in contact with GLU 309 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135S ALA* 3.5 15.9 - - + -
141S ARG* 2.8 28.4 + - - -
166S ARG* 3.1 30.0 + - - +
305S SER* 3.0 22.3 + - - +
306S ARG 4.1 1.1 - - - +
308S LEU* 1.3 74.0 - - - +
310S ARG* 1.3 63.3 + - - +
311S ALA 3.1 8.0 + - - +
347S ILE* 4.2 4.1 - - + +
190W ARG* 4.7 0.3 - - - -
191W THR* 2.7 40.6 + - - -
222W MET* 3.8 29.0 - - + +
223W ASN* 3.7 24.5 - - + +
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Residues in contact with ARG 310 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131S ALA 2.9 25.5 + - - -
132S GLN* 4.4 0.2 - - - +
133S VAL* 3.1 42.0 + - - +
134S LYS 4.4 1.1 - - - +
135S ALA* 3.5 18.4 - - + +
136S PRO* 3.3 7.5 - - + +
250S PHE* 3.4 18.3 + - - -
253S ALA* 3.6 12.3 - - + +
254S SER* 3.1 33.9 + - - +
257S GLU* 2.8 30.7 + - - +
260S ARG* 2.7 29.8 + - - +
306S ARG* 3.1 22.7 - - - +
307S LEU* 3.7 11.9 - - - +
308S LEU 3.3 0.6 - - - -
309S GLU* 1.3 77.1 - - - +
311S ALA* 1.3 57.5 + - - +
312S ALA 3.6 0.7 + - - -
323S LEU* 4.5 4.4 - - + +
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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