Contacts of the helix formed by residues 297 - 315 (chain A) in PDB entry 3EFC
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 ASN 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU 3.5 5.6 - - - -
232A ASP* 2.8 36.7 + - - +
268A LEU* 5.6 1.8 - - + +
294A GLU* 5.7 2.2 - - - +
295A LEU 3.8 4.5 + - - +
296A TYR* 1.3 86.4 - - - +
298A GLY* 1.3 64.5 + - - +
299A THR* 3.9 0.5 - - - -
300A LYS* 2.4 51.0 + - + +
301A VAL* 3.0 17.6 + - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.3 31.1 + - - -
232A ASP* 4.1 0.2 - - - -
296A TYR* 3.4 21.8 - - - -
297A ASN* 1.3 69.5 + - - +
299A THR* 1.3 58.6 + - - +
301A VAL* 2.8 28.6 + - - +
302A THR* 3.1 8.8 + - - -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 4.8 6.6 + - - -
232A ASP* 2.7 40.5 + - - -
297A ASN* 3.9 0.4 - - - -
298A GLY* 1.3 67.7 - - - +
300A LYS* 1.3 67.2 + - - +
301A VAL 2.9 0.3 + - - -
302A THR* 3.1 13.0 + - + -
303A LYS* 2.7 31.2 + - + +
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 6.6 0.2 - - + -
294A GLU* 5.1 10.3 - - - +
297A ASN* 2.4 44.6 + - + +
299A THR* 1.3 71.8 - - - +
301A VAL* 1.3 62.2 + - + +
303A LYS* 3.4 8.8 + - - +
304A MET* 3.2 19.1 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 6.5 1.6 - - + -
296A TYR* 4.0 26.2 - - + +
297A ASN 3.0 21.3 - - - +
298A GLY* 2.8 12.8 + - - +
300A LYS* 1.3 72.0 - - + +
302A THR* 1.3 56.0 + - - +
303A LYS 3.0 1.6 - - - -
304A MET* 2.7 35.2 + - + +
305A GLU* 2.9 13.4 + - - +
324A SER* 3.4 26.2 - - - +
337A LEU* 3.7 26.9 - - + -
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY 3.1 8.8 + - - -
299A THR* 3.1 15.5 + - + -
301A VAL* 1.3 79.3 - - - +
303A LYS* 1.3 60.7 + - - +
304A MET 3.1 1.0 + - - -
305A GLU* 3.4 19.0 + - - +
306A ASP* 3.2 37.2 + - - +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 2.7 29.5 + - + +
300A LYS* 3.5 9.6 - - - +
302A THR* 1.3 72.5 - - - +
304A MET* 1.3 58.0 + - - +
306A ASP* 4.3 7.1 - - - +
307A ASP* 3.2 29.9 + - - +
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 4.5 3.6 - - + -
273A VAL* 6.0 0.7 - - - -
287A LEU* 3.9 20.8 - - + +
288A THR* 3.8 32.3 - - - +
300A LYS 3.2 9.6 + - - +
301A VAL* 2.7 26.2 + - + +
303A LYS* 1.3 76.7 - - - +
305A GLU* 1.3 71.0 + - + +
306A ASP 3.1 1.3 - - - -
307A ASP* 3.0 10.9 + - - +
308A ILE* 2.9 25.7 + - + +
337A LEU* 3.5 32.8 - - + -
339A VAL* 3.7 16.4 - - + -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 2.9 20.7 + - + +
302A THR* 3.6 19.6 + - - +
304A MET* 1.3 80.0 - - + +
306A ASP* 1.3 66.8 + - - +
308A ILE* 2.9 12.0 + - - +
309A LYS* 2.8 42.1 + - - +
322A VAL* 3.7 35.0 - - + +
323A GLN* 4.7 0.6 - - - -
324A SER* 2.4 34.2 + - - +
339A VAL* 5.7 1.1 - - + -
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 3.2 29.0 + - - +
303A LYS* 4.4 5.9 - - - +
304A MET 3.1 0.6 - - - -
305A GLU* 1.3 73.7 - - - +
307A ASP* 1.3 67.3 + - - +
309A LYS* 2.7 42.4 + - - +
310A LYS* 2.7 31.7 + - - +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.4 31.0 - - + +
303A LYS 3.2 18.7 + - - +
304A MET* 3.0 11.0 + - - +
306A ASP* 1.3 78.9 - - - +
308A ILE* 1.3 62.1 + - - +
310A LYS* 3.5 13.4 + - - +
311A LEU* 3.0 22.0 + - - +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.2 8.3 - - + -
284A ILE* 3.7 38.8 - - + +
287A LEU* 4.1 12.8 - - + -
288A THR* 4.9 3.6 - - - +
304A MET* 2.9 23.4 + - + +
305A GLU* 2.9 12.4 + - - +
307A ASP* 1.3 73.2 - - - +
309A LYS* 1.3 59.1 + - - +
311A LEU* 2.6 29.2 + - - +
312A LEU* 2.8 27.0 + - + -
322A VAL* 3.9 9.9 - - + -
339A VAL* 4.5 9.0 - - + -
341A VAL* 3.7 30.7 - - + -
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU* 2.8 32.3 + - - +
306A ASP* 2.7 33.8 + - - +
308A ILE* 1.3 74.5 - - - +
310A LYS* 1.3 55.8 + - + +
312A LEU* 4.6 0.4 - - - -
313A GLY* 2.8 25.5 + - - -
320A PRO* 3.7 29.6 - - + +
322A VAL* 3.5 44.4 + - + +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 2.7 35.5 + - - +
307A ASP* 3.7 13.1 + - - +
309A LYS* 1.3 72.1 - - + +
311A LEU* 1.3 58.0 + - - +
313A GLY* 3.0 1.6 + - - -
314A ARG* 2.5 37.9 + - - +
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Residues in contact with LEU 311 (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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280A HIS* 4.2 7.6 - - + -
283A GLU* 3.9 20.2 - - + +
284A ILE* 3.5 41.5 - - + +
287A LEU* 4.9 10.1 - - + -
307A ASP 3.0 14.1 + - - +
308A ILE* 2.6 16.8 + - - +
310A LYS* 1.3 72.5 - - - +
312A LEU* 1.3 65.0 + - - +
314A ARG* 3.3 20.9 + - + +
315A TYR* 3.4 25.0 + - + +
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Residues in contact with LEU 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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277A LEU 4.1 1.6 - - - +
278A ALA* 3.6 31.2 - - + -
280A HIS* 4.9 6.7 - - + -
284A ILE* 3.9 22.9 - - + -
308A ILE* 2.8 22.4 + - + +
311A LEU* 1.3 72.6 - - + +
313A GLY* 1.3 65.8 + - - +
315A TYR* 2.8 23.4 + - - +
317A TYR* 3.5 16.6 - - + +
320A PRO* 3.5 31.0 - - + -
322A VAL* 5.1 0.2 - - + -
341A VAL* 3.4 31.6 - - + -
343A ALA* 3.8 11.7 - - + -
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Residues in contact with GLY 313 (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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309A LYS 2.8 22.4 + - - -
310A LYS* 3.0 4.2 + - - -
312A LEU* 1.3 71.2 - - - +
314A ARG* 1.3 64.1 + - - +
316A GLY* 2.7 15.4 + - - -
317A TYR 3.0 24.8 + - - -
318A ALA* 5.1 2.1 - - - -
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Residues in contact with ARG 314 (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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310A LYS* 2.5 16.2 + - - +
311A LEU* 3.3 20.0 - - + +
313A GLY* 1.3 71.1 - - - +
315A TYR* 1.3 64.0 + - + +
316A GLY* 2.7 12.0 + - - -
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Residues in contact with TYR 315 (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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280A HIS* 3.2 47.9 - + + +
283A GLU* 2.6 27.1 + - - -
311A LEU* 3.4 35.2 + - + +
312A LEU* 2.8 13.7 + - - +
314A ARG* 1.3 83.4 - - + +
316A GLY* 1.3 64.5 + - - +
317A TYR* 3.5 11.2 - - + -
346A ARG* 3.6 23.7 + - - +
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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