Contacts of the helix formed by residues 303 - 322 (chain A) in PDB entry 4EGA
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 SER 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 1.3 76.6 - - - +
304A PRO* 1.3 62.6 - - - +
305A TYR* 3.8 12.2 + - - +
306A ASP* 3.0 34.9 + - - +
307A PHE* 2.8 34.4 + - - +
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Residues in contact with PRO 304 (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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293A VAL* 6.1 0.2 - - + -
294A ALA* 4.9 9.6 - - + +
297A ALA* 4.1 20.0 - - + -
302A VAL 3.7 6.3 - - - +
303A SER* 1.3 82.7 - - - +
305A TYR* 1.3 60.2 + - + +
307A PHE* 4.2 0.7 - - + -
308A THR* 2.7 38.2 + - + +
457A HIS* 5.9 1.6 - - + +
459A TRP* 3.5 46.7 - - + +
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Residues in contact with TYR 305 (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 SER* 3.2 13.4 - - - +
304A PRO* 1.3 84.7 - - + +
306A ASP* 1.3 66.8 + - - +
308A THR* 3.3 3.4 + - - -
309A THR* 3.1 25.6 + - - -
459A TRP* 3.7 34.9 - + - -
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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
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302A VAL* 3.9 15.6 - - + +
303A SER* 3.0 27.3 + - - +
305A TYR* 1.3 78.4 - - - +
307A PHE* 1.3 58.2 + - - +
309A THR* 3.6 5.6 + - - -
310A ALA* 3.0 29.5 + - - +
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Residues in contact with PHE 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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251A VAL 3.2 24.2 - - - -
252A ASN* 3.8 24.5 - - - -
253A ALA* 5.4 0.4 - - - -
293A VAL* 4.3 9.4 - - + -
296A ALA* 4.2 9.4 - - + -
297A ALA* 3.6 34.3 - - + -
300A LYS* 4.2 22.9 - - + -
302A VAL* 4.3 18.3 - - + +
303A SER 2.8 19.5 + - - +
304A PRO 3.8 2.2 - - - +
306A ASP* 1.3 71.5 - - - +
308A THR* 1.3 69.5 + - + +
310A ALA* 3.0 15.3 + - + +
311A VAL* 3.0 28.7 + - + +
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Residues in contact with THR 308 (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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251A VAL* 4.2 8.9 - - + +
288A GLU* 3.4 49.8 + - + +
293A VAL* 3.9 14.1 - - + -
304A PRO* 2.7 27.1 + - + +
305A TYR* 3.3 5.9 + - - -
307A PHE* 1.3 72.7 - - + +
309A THR* 1.3 59.0 + - - +
311A VAL* 4.3 0.5 - - - +
312A ALA* 2.9 32.6 + - - +
331A ARG* 3.9 5.1 + - - -
333A THR* 4.1 2.6 - - - +
459A TRP* 3.5 22.7 - - + +
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Residues in contact with THR 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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305A TYR 3.1 17.8 + - - -
306A ASP* 3.7 6.3 - - - +
307A PHE 3.1 0.6 - - - -
308A THR* 1.3 78.8 + - - +
310A ALA* 1.3 58.3 + - - +
312A ALA* 3.6 1.3 - - - +
313A GLY* 3.0 24.9 + - - -
331A ARG* 3.3 28.3 + - - +
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Residues in contact with ALA 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 ASP 3.0 19.1 + - - +
307A PHE* 3.0 7.5 + - + +
309A THR* 1.3 77.0 - - - +
311A VAL* 1.3 63.2 + - + +
313A GLY* 3.3 3.7 + - - -
314A GLU* 3.1 27.3 + - - +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 3.4 42.2 - - + +
253A ALA* 3.8 15.5 - - - +
254A ALA* 4.8 3.6 - - - +
255A PRO* 4.9 0.2 - - + -
307A PHE* 3.0 36.6 + - + +
310A ALA* 1.3 73.5 - - + +
312A ALA* 1.3 66.9 + - - +
314A GLU* 2.9 27.2 + - + +
315A PHE* 3.0 32.8 + - + -
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Residues in contact with ALA 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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251A VAL* 4.3 1.4 - - - +
286A THR* 4.2 16.2 - - + +
288A GLU* 3.3 20.4 - - - +
308A THR 2.9 21.4 + - - +
309A THR 3.6 4.9 - - - +
311A VAL* 1.3 77.5 - - - +
313A GLY* 1.3 61.6 + - - +
315A PHE* 3.2 3.8 + - - +
316A LYS* 3.1 28.5 + - + +
329A PHE* 4.3 1.9 - - + -
331A ARG* 3.7 20.4 - - + +
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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 THR 3.0 15.1 + - - -
310A ALA 3.6 4.9 - - - -
311A VAL 3.1 0.4 - - - -
312A ALA* 1.3 76.3 - - - +
314A GLU* 1.3 55.2 + - - +
316A LYS* 3.3 9.5 + - - +
317A LYS* 3.0 30.5 + - - +
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Residues in contact with GLU 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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254A ALA* 3.8 23.9 - - - +
255A PRO* 3.6 15.2 - - + +
310A ALA* 3.1 20.3 + - - +
311A VAL* 2.9 24.1 + - - +
313A GLY* 1.3 75.4 - - - +
315A PHE* 1.3 57.8 + - - +
317A LYS* 3.6 6.7 + - - +
318A CAS 2.9 29.1 + - - +
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 3.8 18.4 - + + -
250A TYR 4.1 9.6 - - - -
251A VAL* 4.2 11.2 - - + -
253A ALA 3.7 7.6 - - - -
255A PRO* 3.7 34.8 - - + -
259A HIS* 3.7 37.7 - + - -
286A THR* 4.0 6.7 - - + -
311A VAL* 3.0 45.1 + - + -
312A ALA 3.5 7.2 - - - +
314A GLU* 1.3 74.1 - - - +
316A LYS* 1.3 55.1 + - - +
318A CAS 3.1 3.0 + - - +
319A PHE* 2.7 55.2 + + + -
329A PHE* 3.8 16.2 - - + -
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Residues in contact with LYS 316 (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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312A ALA 3.1 16.1 + - - +
313A GLY* 3.3 12.1 + - - +
315A PHE* 1.3 72.3 - - - +
317A LYS* 1.3 55.8 + - - +
319A PHE* 3.3 1.7 + - - +
320A GLU* 2.8 51.1 + - - +
329A PHE* 3.6 53.6 + - + -
331A ARG* 4.5 19.7 - - - +
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Residues in contact with LYS 317 (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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313A GLY 3.0 17.2 + - - +
314A GLU* 3.8 7.2 - - - +
316A LYS* 1.3 76.6 - - - +
318A CAS 1.3 65.4 + - + +
320A GLU* 3.3 12.3 + - + +
321A GLN* 2.9 27.8 + - + +
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Residues in contact with CAS 318 (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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255A PRO* 3.6 44.4 - - + +
256A HIS* 4.3 2.0 - - - -
260A VAL* 3.8 22.7 - - - -
314A GLU 2.9 18.8 + - - +
315A PHE 3.1 5.1 + - - +
317A LYS* 1.3 80.3 + - + +
319A PHE* 1.3 64.2 + - + +
321A GLN* 3.3 5.6 + - + +
322A MET* 3.1 28.5 + - - +
564A ASP* 3.9 10.1 - - - +
565A PRO* 3.1 40.8 - - + -
566A VAL* 3.2 37.9 - - + -
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Residues in contact with PHE 319 (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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249A TYR* 3.7 17.5 - + - -
255A PRO* 5.2 0.2 - - + -
259A HIS* 4.2 11.0 - - + -
260A VAL* 4.3 11.7 - - + -
263A THR* 3.4 28.9 - - + -
284A THR* 3.8 20.0 - - + -
285A GLY 5.3 0.4 - - - -
315A PHE* 2.7 35.5 + + - +
316A LYS* 4.0 3.8 - - - +
318A CAS 1.3 88.9 + - - -
320A GLU* 1.3 66.5 + - - +
322A MET 3.6 5.4 + - - +
323A ASP 3.6 6.4 + - - -
324A TYR* 3.6 40.6 + + + +
326A ILE* 6.1 1.1 - - + -
329A PHE* 3.7 28.9 - + + -
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Residues in contact with GLU 320 (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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316A LYS* 2.8 36.3 + - - +
317A LYS* 3.7 11.5 - - - +
319A PHE* 1.3 73.3 - - - +
321A GLN* 1.3 57.9 + - - +
323A ASP* 3.1 20.3 + - - +
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Residues in contact with GLN 321 (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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317A LYS* 2.9 20.7 + - + +
318A CAS 3.3 7.4 + - + +
320A GLU* 1.3 76.2 - - - +
322A MET* 1.3 60.0 + - - +
323A ASP* 3.3 2.0 + - - +
566A VAL* 3.7 26.5 - - + -
570A GLU* 5.1 2.8 + - - -
574A TYR* 2.9 49.6 + - - +
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Residues in contact with MET 322 (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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260A VAL* 4.0 32.5 - - + -
318A CAS 3.1 20.0 + - - +
319A PHE 4.0 3.6 - - - +
320A GLU 3.2 0.6 - - - -
321A GLN* 1.3 76.4 - - - +
323A ASP* 1.3 63.0 + - - +
324A TYR* 3.5 22.9 + - + +
565A PRO* 3.4 21.3 - - + +
566A VAL* 3.4 48.5 - - + +
574A TYR* 4.2 19.7 - - + -
577A LEU* 5.0 7.2 - - - -
578A LYS* 2.9 36.0 + - - -
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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
------------------------------------------------------------
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