Contacts of the helix formed by residues 294 - 312 (chain A) in PDB entry 3FGU
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 GLY 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A VAL* 5.6 0.7 - - - -
227A GLY 3.7 4.5 - - - -
228A THR 3.4 15.0 - - - -
229A GLY* 4.4 9.9 - - - -
230A CYS* 4.8 0.2 - - - +
290A GLU 2.7 21.1 + - - -
293A ILE* 1.3 78.7 - - - +
295A GLY* 1.3 62.6 + - - -
296A LYS 3.2 2.9 - - - -
297A TYR* 3.2 8.4 + - - +
298A MET* 3.0 22.9 + - - +
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY 2.7 21.4 + - - -
293A ILE 3.7 0.8 + - - -
294A GLY* 1.3 66.1 - - - -
296A LYS* 1.3 63.0 + - - +
297A TYR 3.0 2.4 + - - -
298A MET* 4.4 1.1 - - - -
332A THR* 2.4 36.5 + - - -
412A VAL* 3.8 17.0 - - - +
600A ANP 3.0 18.3 + - - -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 6.1 3.4 - - - +
169A LYS* 3.6 39.5 + - - +
170A GLY* 3.9 9.0 - - - +
228A THR* 3.2 30.6 + - + +
282A ALA* 6.1 0.9 - - - +
295A GLY* 1.3 76.7 - - - +
297A TYR* 1.3 86.4 + - + +
299A GLY 5.5 0.2 - - - -
300A GLU* 4.9 6.2 + - - +
600A ANP 3.1 9.6 + - - -
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 3.8 17.2 + - + -
170A GLY 4.7 0.2 + - - -
228A THR 4.2 2.9 - - - -
277A VAL* 3.9 22.9 - - + +
281A SER* 4.7 9.6 - - - -
283A ASN* 4.1 13.0 + - - -
287A GLN* 5.3 0.5 - - - +
290A GLU* 3.9 26.8 + - + -
291A LYS* 3.7 57.0 - - + +
294A GLY* 3.2 9.1 + - - +
295A GLY 3.0 0.2 - - - -
296A LYS* 1.3 119.7 - - + +
298A MET* 1.3 58.9 + - - +
299A GLY 3.5 2.0 - - - -
300A GLU* 3.4 10.0 + - - +
301A LEU* 3.0 31.3 + - - +
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU 5.4 1.3 - - - +
293A ILE 3.5 17.9 - - - +
294A GLY 3.0 13.8 + - - +
295A GLY* 3.8 1.2 + - - -
297A TYR* 1.3 75.7 - - - +
299A GLY* 1.3 64.2 + - - +
301A LEU* 3.2 14.7 + - - +
302A VAL* 3.1 21.0 + - - +
332A THR* 3.8 21.3 - - + +
335A VAL* 4.2 18.4 - - + -
374A VAL* 3.7 15.9 - - + +
375A SER* 4.1 23.1 - - - -
378A ALA* 3.4 32.3 - - + -
412A VAL* 4.0 21.1 - - + -
416A HIS* 4.9 4.9 - - - -
419A PHE* 4.4 2.0 - - + -
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR 3.5 0.4 - - - -
298A MET* 1.3 75.4 - - - +
300A GLU* 1.3 50.8 + - - +
302A VAL* 3.0 5.4 + - - +
303A ARG 2.7 30.5 + - - -
330A PHE* 3.3 27.5 - - - +
332A THR* 3.1 20.8 + - - -
335A VAL* 4.0 18.6 - - - -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.7 21.5 - - + -
280A SER* 4.7 9.5 + - - +
296A LYS 4.9 5.1 + - - +
297A TYR* 3.4 14.9 + - - +
298A MET 3.3 0.2 - - - -
299A GLY* 1.3 72.5 - - - +
301A LEU* 1.3 60.9 + - - +
303A ARG* 2.8 42.1 + - - +
304A LEU* 2.9 36.6 + - + +
327A ARG* 4.3 6.7 - - - +
328A GLY* 2.9 33.1 + - - +
330A PHE 3.8 3.7 + - - -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.8 1.6 - - + -
273A TYR* 3.7 32.5 - - + +
274A ASP* 3.4 19.5 - - - +
277A VAL* 3.8 12.3 - - + +
291A LYS 3.6 21.5 - - - +
292A LEU 4.5 7.9 - - - +
297A TYR 3.0 16.9 + - - +
298A MET* 3.2 13.0 + - - +
300A GLU* 1.3 75.1 - - - +
302A VAL* 1.3 63.4 + - - +
304A LEU* 3.3 6.4 + - - +
305A VAL* 3.1 27.5 + - - +
374A VAL* 3.9 20.0 - - + -
377A ARG* 3.4 23.3 - - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A MET 3.1 16.4 + - - +
299A GLY 3.0 8.1 + - - +
301A LEU* 1.3 73.9 - - - +
303A ARG* 1.3 65.3 + - - +
305A VAL* 3.1 5.4 + - - +
306A LEU* 2.9 34.5 + - + +
330A PHE* 3.8 27.1 - - + -
335A VAL* 3.8 17.9 - - + -
370A ALA* 4.3 9.6 - - + +
371A CYS* 3.9 21.1 - - - -
374A VAL* 3.7 28.3 - - + -
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLY 2.7 16.7 + - - +
300A GLU* 2.8 46.9 + - - +
302A VAL* 1.3 71.6 - - - +
304A LEU* 1.3 73.8 + - - +
306A LEU* 3.4 9.6 + - - +
307A LEU* 3.0 40.6 + - + +
324A LEU* 2.9 39.6 + - + +
325A ARG* 3.3 23.4 + - - +
326A THR 3.2 20.5 + - - -
327A ARG* 3.9 13.1 - - - +
329A ALA* 4.1 1.3 - - - +
330A PHE* 3.7 29.6 - - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TYR* 3.8 32.3 - - + +
276A LEU* 4.0 27.6 - - + -
277A VAL* 3.7 26.7 - - + +
300A GLU* 2.9 25.8 + - + +
301A LEU 3.6 5.2 - - - +
303A ARG* 1.3 103.9 - - - +
305A VAL* 1.3 63.2 + - - +
307A LEU* 3.5 11.7 + - + +
308A ARG* 3.3 16.8 + - - +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.5 0.2 - - + -
20A LEU* 3.6 28.7 - - + -
23A PHE* 3.6 31.2 - - + -
273A TYR* 3.8 21.5 - - + +
301A LEU 3.1 16.1 + - - +
302A VAL* 3.1 6.9 + - - +
304A LEU* 1.3 71.7 - - - +
306A LEU* 1.3 67.2 + - - +
308A ARG* 3.1 5.9 + - - +
309A LEU* 3.0 36.6 + - + +
370A ALA* 4.2 9.4 - - + -
374A VAL* 4.2 9.2 - - + -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 2.9 19.9 + - + +
303A ARG* 3.6 7.4 - - - +
305A VAL* 1.3 76.0 - - - +
307A LEU* 1.3 57.3 + - - +
309A LEU* 3.4 7.9 + - + +
310A VAL* 2.8 34.5 + - - +
315A LEU* 3.8 23.0 - - + +
316A PHE* 4.8 6.3 - - + -
324A LEU* 4.3 18.8 - - + -
330A PHE* 3.9 33.4 - - + -
352A LEU* 4.9 1.6 - - + -
367A VAL* 3.9 27.4 - - + +
370A ALA* 3.7 27.4 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ARG* 3.0 48.1 + - + +
304A LEU* 3.7 13.9 - - + +
305A VAL 3.2 0.4 - - - -
306A LEU* 1.3 74.2 - - - +
308A ARG* 1.3 61.6 + - - +
310A VAL* 3.2 7.3 + - + +
311A ASP* 2.9 29.2 + - - +
320A ALA* 3.7 29.8 - - + -
324A LEU* 3.6 32.1 - - + +
325A ARG* 4.2 9.9 - - + -
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.7 37.5 - - - +
22A GLU* 4.6 8.7 + - - -
272A GLU* 3.3 25.2 + - - +
273A TYR* 3.4 27.2 + - + -
304A LEU 3.3 10.0 + - - +
305A VAL 3.1 9.3 + - - +
307A LEU* 1.3 78.2 - - - +
309A LEU* 1.3 58.4 + - - +
311A ASP* 3.2 10.1 + - + +
312A GLU* 2.8 62.3 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.4 17.9 - - + -
19A ILE* 4.0 40.2 - - + -
20A LEU* 5.0 1.8 - - + -
305A VAL* 3.0 36.6 + - + +
306A LEU* 3.6 18.6 - - + +
308A ARG* 1.3 76.0 - - - +
310A VAL* 1.3 61.1 + - - +
312A GLU* 3.4 2.9 + - - +
313A ASN 3.3 4.0 + - - -
314A LEU* 2.8 35.5 + - + +
315A LEU* 4.0 13.9 - - + -
366A ILE* 3.8 28.0 - - + -
370A ALA* 4.7 3.6 - - + -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU 2.8 27.3 + - - +
307A LEU* 3.2 11.2 + - + +
309A LEU* 1.3 76.2 - - - +
311A ASP* 1.3 65.6 + - + +
313A ASN* 3.2 10.2 + - - +
315A LEU* 3.6 18.8 - - + +
316A PHE* 3.8 27.8 - - + -
318A GLY* 3.3 28.9 - - - +
319A GLU 4.5 1.6 - - - +
320A ALA* 3.8 27.8 - - + +
324A LEU* 4.2 8.3 - - + -
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 2.9 14.3 + - - +
308A ARG* 3.4 14.2 - - + +
310A VAL* 1.3 82.0 - - + +
312A GLU* 1.3 60.7 - - - +
313A ASN* 3.2 7.3 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.0 10.8 - - + -
308A ARG* 2.8 63.1 + - + +
309A LEU 3.4 1.3 + - - +
310A VAL 3.3 0.2 - - - -
311A ASP* 1.3 80.9 - - + +
313A ASN* 1.3 68.9 + - - +
314A LEU* 3.4 27.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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