Contacts of the helix formed by residues 310 - 329 (chain A) in PDB entry 5A6C
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 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A HIS* 5.5 1.0 + - - -
305A ALA* 2.8 26.7 + - - +
306A GLN* 4.9 0.2 - - - +
308A LEU* 4.6 8.7 - - + +
309A ASN* 1.3 70.7 - - - +
311A ARG* 1.3 53.3 + - - +
312A ILE* 3.6 10.2 + - - +
313A GLY* 3.2 27.0 + - - -
314A GLU* 2.8 35.6 + - - +
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Residues in contact with ARG 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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309A ASN 3.6 6.4 + - - +
310A ASP* 1.3 69.8 + - - +
312A ILE* 1.3 66.0 + - - +
314A GLU* 2.7 50.4 + - - +
315A GLY 2.9 18.4 + - - -
340A LYS* 5.7 1.6 - - - +
343A GLU* 5.9 3.0 + - - +
344A ILE* 3.3 38.3 - - + +
347A GLU* 2.7 42.9 + - - +
348A VAL* 4.8 5.8 - - + -
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Residues in contact with ILE 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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310A ASP* 3.4 9.1 + - - +
311A ARG* 1.3 75.9 - - + +
313A GLY* 1.3 59.6 + - - +
315A GLY* 2.9 18.6 + - - -
316A ARG* 2.9 48.6 + - + +
348A VAL* 4.3 29.8 - - + +
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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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301A HIS* 3.3 25.7 - - - -
305A ALA* 4.2 3.1 - - - -
310A ASP* 3.2 28.3 + - - -
312A ILE* 1.3 82.1 - - - +
314A GLU* 1.3 56.7 + - - +
316A ARG* 3.5 8.2 + - - +
317A ALA* 3.0 22.3 + - - +
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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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302A LEU* 3.8 16.9 - - + +
305A ALA* 4.1 8.2 - - + +
306A GLN* 3.3 31.6 - - + +
310A ASP 2.8 13.0 + - - +
311A ARG* 2.7 50.1 + - - +
313A GLY* 1.3 78.9 - - - +
315A GLY* 1.3 57.1 + - - +
317A ALA* 3.2 7.4 + - - +
318A CYS* 2.9 35.6 + - - -
340A LYS* 4.1 15.6 - - - -
344A ILE* 3.5 12.6 - - + +
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Residues in contact with GLY 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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311A ARG 2.9 12.1 + - - -
312A ILE* 2.9 4.4 + - - -
314A GLU* 1.3 73.4 - - - +
316A ARG* 1.3 63.3 + - - +
318A CYS* 3.3 3.4 + - - +
319A TRP* 3.0 18.7 + - - +
341A HIS* 3.2 24.5 + - - -
344A ILE* 4.0 20.6 - - - +
345A SER 5.9 0.4 - - - -
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Residues in contact with ARG 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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155A PRO* 6.3 0.6 - - - +
279A TYR* 3.7 23.0 + - + +
301A HIS* 5.4 0.7 - - + -
312A ILE* 2.9 42.7 + - + +
313A GLY* 3.9 8.4 - - - +
315A GLY* 1.3 75.6 - - - +
317A ALA* 1.3 57.0 + - - +
319A TRP* 3.3 8.4 + - + +
320A SER* 3.0 32.9 + - - -
341A HIS* 5.6 0.4 - - - -
371A LYS* 3.3 55.1 - - - +
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Residues in contact with ALA 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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279A TYR* 4.3 4.9 - - - -
298A HIS* 4.7 3.7 - - - +
301A HIS* 3.6 22.4 - - + +
302A LEU* 4.0 26.2 - - + -
313A GLY 3.0 15.5 + - - +
314A GLU* 3.2 10.8 - - - +
315A GLY 3.1 0.2 - - - -
316A ARG* 1.3 78.1 - - - +
318A CYS* 1.3 57.2 + - - +
320A SER* 3.4 2.2 + - - -
321A LEU* 2.9 37.2 + - - +
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Residues in contact with CYS 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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302A LEU* 4.7 6.7 - - - -
314A GLU* 2.9 27.7 + - - -
315A GLY 3.3 7.2 + - - +
317A ALA* 1.3 78.1 - - - +
319A TRP* 1.3 56.3 + - - +
321A LEU* 4.6 0.2 - - - -
322A GLY* 2.9 26.5 + - - -
337A PHE* 3.5 40.3 - - + +
340A LYS* 3.8 31.0 - - - -
341A HIS* 3.8 8.5 - - - +
344A ILE* 4.0 14.8 - - - -
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Residues in contact with TRP 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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279A TYR* 4.3 8.1 - - - -
283A ASN* 5.5 0.9 - - - -
315A GLY 3.0 16.7 + - - +
316A ARG* 3.6 8.7 - - + +
318A CYS* 1.3 78.1 - - - +
320A SER* 1.3 90.6 + - - +
322A GLY* 3.4 0.9 + - - -
323A ASN* 3.1 55.4 + - + +
338A ALA* 6.2 0.4 - - - +
341A HIS* 3.9 34.9 - + + +
358A LYS* 3.0 34.8 + - + +
360A GLN 3.6 17.5 - - - -
362A LEU* 4.3 13.5 - - + -
369A THR* 3.3 36.8 - - - -
370A ALA* 4.6 8.1 - - + -
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 2.9 30.7 + - - -
283A ASN* 4.1 3.7 + - - -
298A HIS* 3.6 32.2 - - - -
316A ARG 3.0 10.6 + - - -
317A ALA 3.8 3.8 - - - -
319A TRP* 1.3 91.6 - - - +
321A LEU* 1.3 57.8 + - - +
323A ASN* 3.3 4.4 + - - +
324A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 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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295A ILE* 3.8 29.8 - - + +
298A HIS* 3.5 26.5 - - + +
299A LEU* 4.0 13.2 - - + -
302A LEU* 3.6 25.4 - - + -
317A ALA 2.9 26.7 + - - +
318A CYS* 3.7 3.6 - - - +
320A SER* 1.3 75.5 - - - +
322A GLY* 1.3 65.7 + - - +
324A ALA* 3.2 4.6 + - - +
325A TYR* 2.9 34.4 + - + +
337A PHE* 3.5 37.5 - - + -
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Residues in contact with GLY 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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318A CYS 2.9 15.2 + - - -
319A TRP* 3.8 1.6 - - - -
321A LEU* 1.3 76.2 - - - +
323A ASN* 1.3 56.4 + - - +
325A TYR* 3.8 1.6 - - - +
326A THR* 2.7 38.9 + - - -
334A ALA* 4.1 14.9 - - - -
337A PHE* 3.7 15.6 - - - +
338A ALA* 4.6 4.9 - - - -
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Residues in contact with ASN 323 (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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319A TRP* 3.1 53.5 + - + +
320A SER* 3.8 5.6 - - - +
321A LEU 3.2 0.4 - - - -
322A GLY* 1.3 77.9 - - - +
324A ALA* 1.3 57.7 + - - +
326A THR* 3.3 8.9 + - - -
327A ALA* 2.9 26.7 + - - +
358A LYS 4.8 2.4 + - - +
359A THR 5.1 0.4 + - - -
360A GLN 4.6 0.4 + - - -
361A VAL* 3.5 34.8 - - + +
362A LEU 4.9 0.8 - - - +
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Residues in contact with ALA 324 (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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286A THR* 5.3 6.1 - - + +
291A TYR* 4.2 12.7 - - + +
294A ALA* 4.9 10.1 - - + -
295A ILE* 3.7 27.5 - - + +
298A HIS* 5.0 5.2 - - + -
320A SER 2.9 16.9 + - - +
321A LEU* 3.6 6.1 - - - +
323A ASN* 1.3 75.4 - - - +
325A TYR* 1.3 59.6 + - - +
327A ALA* 3.2 10.2 + - - +
328A LEU* 3.0 25.6 + - - +
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Residues in contact with TYR 325 (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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295A ILE* 3.4 44.1 - - + +
299A LEU* 4.2 9.6 - - + +
321A LEU* 2.9 22.2 + - + +
322A GLY 3.8 1.3 - - - +
324A ALA* 1.3 69.7 - - - +
326A THR* 1.3 61.9 + - - +
328A LEU* 3.1 8.5 + - + +
329A GLY 2.9 24.6 + - - -
330A ASN* 3.0 24.6 + - + +
333A GLN* 3.4 37.6 + - + -
334A ALA* 3.7 17.3 - - - +
337A PHE* 3.2 39.1 - + - -
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Residues in contact with THR 326 (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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322A GLY 2.7 20.3 + - - -
323A ASN* 3.3 13.4 + - - -
325A TYR* 1.3 76.9 - - - +
327A ALA* 1.3 64.8 + - - +
328A LEU 3.2 0.3 + - - -
329A GLY* 3.2 13.3 + - - +
330A ASN 5.0 1.6 - - - +
334A ALA* 3.5 19.2 - - + +
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Residues in contact with ALA 327 (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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291A TYR* 3.4 43.1 - - + -
323A ASN 2.9 15.1 + - - +
324A ALA 3.2 10.7 + - - +
326A THR* 1.3 77.7 - - - +
328A LEU* 1.3 65.9 + - - +
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Residues in contact with LEU 328 (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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291A TYR* 3.7 27.1 - - + -
292A GLU* 3.9 35.9 - - + +
295A ILE* 3.6 28.0 - - + -
324A ALA 3.0 7.6 + - - +
325A TYR* 3.6 13.9 - - + +
326A THR 3.1 0.6 - - - -
327A ALA* 1.3 81.3 - - - +
329A GLY* 1.3 57.3 + - - +
330A ASN* 4.6 3.8 - - + +
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Residues in contact with GLY 329 (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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325A TYR 2.9 3.2 + - - -
326A THR* 3.2 11.2 + - - -
328A LEU* 1.3 80.0 - - - +
330A ASN* 1.3 60.6 + - - +
331A HIS* 3.0 10.6 + - - +
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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