Contacts of the helix formed by residues 319 - 335 (chain A) in PDB entry 3DYQ
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 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ASN* 4.0 1.1 - - - +
317A ASP 3.7 2.2 + - - -
318A ILE* 1.3 77.6 - - - +
320A PRO* 1.3 75.0 - - - +
321A LEU 3.3 2.7 - - - -
322A GLU* 3.2 24.9 + - - -
323A ASN* 2.9 25.1 + - - -
361A LEU* 4.5 8.6 + - - +
364A ASP* 2.6 28.8 + - - +
367A ARG* 4.6 8.7 + - - +
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Residues in contact with PRO 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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301A ASN* 3.3 22.2 - - + +
304A GLN* 4.8 7.0 - - + -
305A ILE* 4.6 9.2 - - + -
311A LEU* 4.0 28.4 - - + +
312A ALA* 4.2 11.0 - - + +
315A TYR* 3.6 16.2 - - + -
317A ASP* 4.0 25.8 - - - +
318A ILE 3.3 5.8 - - - +
319A SER* 1.3 90.2 - - - +
321A LEU* 1.3 62.5 + - - +
323A ASN 3.4 0.2 + - - -
324A HIS* 3.0 23.2 + - - +
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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
----------------------------------------------------------
296A HIS* 3.4 24.2 - - - +
297A PRO* 3.2 35.0 - - + -
299A TYR 3.4 21.3 - - - +
300A ASN* 3.8 14.4 - - + -
301A ASN* 2.9 20.8 + - - +
304A GLN* 4.4 7.9 - - + +
311A LEU* 4.0 15.9 - - + -
320A PRO* 1.3 77.0 - - - +
322A GLU* 1.3 68.0 + - - +
324A HIS* 3.0 6.8 + - + +
325A HIS* 2.8 44.6 + - + +
900A PCG 5.9 1.6 - - - +
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 2.8 28.8 + - - -
319A SER* 3.2 16.6 + - - +
320A PRO 3.2 0.4 - - - -
321A LEU* 1.3 86.8 - - - +
323A ASN* 1.3 61.2 + - - +
325A HIS* 3.5 13.9 + - + -
326A CYS* 3.2 24.1 + - - +
360A ILE* 3.6 18.6 - - - +
361A LEU* 3.9 14.5 - - + +
363A THR* 3.8 23.2 + - - +
364A ASP* 3.5 28.1 + - + +
365A MET 4.9 0.2 + - - -
900A PCG 4.7 9.4 + - - -
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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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315A TYR* 3.6 31.6 + - + -
318A ILE* 2.7 36.8 + - - +
319A SER* 2.9 15.4 + - - +
320A PRO 3.7 2.2 - - - +
322A GLU* 1.3 75.6 - - - +
324A HIS* 1.3 57.8 + - - +
327A ALA* 2.9 27.0 + - - +
361A LEU* 3.7 22.3 - - - +
315B TYR* 4.6 3.2 - - - +
316B ASN* 3.0 32.5 + - - +
318B ILE* 4.5 6.8 - - - +
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 5.3 1.2 + - - -
294A LEU 4.1 2.5 - - - -
295A ASP* 2.8 45.6 + - + -
311A LEU* 3.7 37.5 - - + +
314A ARG* 4.3 10.8 + - - -
315A TYR* 3.8 9.1 + - - -
320A PRO 3.0 14.8 + - - +
321A LEU* 3.0 9.4 + - + +
323A ASN* 1.3 73.3 - - - +
325A HIS* 1.3 70.1 + + - +
326A CYS 3.0 1.1 + - - -
327A ALA* 3.2 3.4 + - - +
328A VAL* 2.8 42.8 + - + +
331A GLN* 6.3 0.4 - - - -
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Residues in contact with HIS 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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291A CYS 3.9 5.5 - - - +
292A HIS 2.9 29.6 - - - +
293A ASP* 3.4 19.6 + - - -
294A LEU* 2.6 44.5 + - - +
295A ASP 4.7 0.7 - - - -
296A HIS* 3.6 33.4 - + + -
321A LEU* 2.8 40.9 + - + +
322A GLU* 3.5 22.1 - - + +
324A HIS* 1.3 74.0 - + - +
326A CYS* 1.3 57.6 + - - +
328A VAL* 3.3 2.9 + - - +
329A ALA* 2.9 27.0 + - - +
360A ILE* 4.1 3.6 - - + -
902A NA 4.5 1.6 - - - -
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Residues in contact with CYS 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 GLU 3.2 16.1 + - - +
323A ASN* 3.5 2.7 - - - +
324A HIS 3.0 0.4 - - - -
325A HIS* 1.3 78.8 - - - +
327A ALA* 1.3 65.3 + - - +
329A ALA* 3.1 20.7 - - - +
330A PHE* 3.2 17.7 + - - -
357A ILE* 3.6 37.2 - - - -
360A ILE* 3.9 24.7 - - + -
361A LEU* 5.3 2.7 - - + -
316B ASN* 3.3 21.8 - - - +
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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
----------------------------------------------------------
315A TYR* 3.6 16.6 - - - +
323A ASN 2.9 18.5 + - - +
324A HIS* 3.6 5.8 - - - +
326A CYS* 1.3 76.4 - - - +
328A VAL* 1.3 62.7 + - + +
330A PHE* 3.1 2.9 + - - +
331A GLN* 3.0 37.7 + - - +
313B VAL* 3.5 26.9 - - - +
314B ARG* 3.8 6.3 - - - +
316B ASN* 3.3 2.1 + - - +
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Residues in contact with VAL 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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245A ASN* 4.5 12.6 - - + +
294A LEU* 4.1 17.3 - - + +
295A ASP* 4.2 10.3 - - + +
324A HIS* 2.8 54.5 + - + +
325A HIS 3.7 4.3 - - - +
327A ALA* 1.3 73.1 - - + +
329A ALA* 1.3 64.0 + - - +
331A GLN* 3.2 20.8 + - + +
332A ILE* 3.0 40.9 + - + +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TRP* 5.5 0.3 + - - -
291A CYS* 3.9 21.7 - - + -
294A LEU* 3.6 18.8 - - + +
325A HIS 2.9 14.8 + - - +
326A CYS* 3.1 14.6 - - - +
328A VAL* 1.3 78.1 - - - +
330A PHE* 1.3 69.5 + - + +
332A ILE* 3.3 5.4 + - - +
333A LEU* 3.0 30.8 + - + +
356A MET* 4.8 4.9 - - + -
360A ILE* 4.8 1.3 - - + -
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A CYS* 3.2 27.0 + - - +
327A ALA* 3.1 5.9 + - - +
329A ALA* 1.3 79.5 - - + +
331A GLN* 1.3 60.7 + - - +
333A LEU* 3.4 19.9 + - + +
334A ALA* 3.0 29.6 + - - +
341A PHE* 4.8 2.5 - + - -
349A PHE* 4.1 22.0 - + - -
353A ARG* 3.1 66.0 - - + +
356A MET* 3.9 32.3 - - + -
357A ILE* 4.2 15.0 - - + -
313B VAL* 4.3 16.1 - - + +
316B ASN* 4.9 0.9 - - - -
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Residues in contact with GLN 331 (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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324A HIS* 6.3 0.6 - - - -
327A ALA* 3.0 29.7 + - - +
328A VAL* 3.5 26.0 - - + +
330A PHE* 1.3 77.3 - - - +
332A ILE* 1.3 63.6 + - + +
334A ALA* 3.2 17.5 + - - +
335A GLU* 3.5 14.0 + - - +
313B VAL* 3.9 15.1 - - + +
314B ARG* 5.4 5.3 - - - +
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Residues in contact with ILE 332 (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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238A TRP* 3.8 27.8 - - + +
241A CYS* 3.4 34.1 - - + +
242A VAL* 4.3 5.8 - - + -
245A ASN* 3.6 33.4 - - + +
294A LEU* 4.0 17.9 - - + -
328A VAL* 3.0 28.3 + - + +
329A ALA* 3.6 6.5 - - - +
331A GLN* 1.3 76.0 - - + +
333A LEU* 1.3 64.3 + - - +
335A GLU* 3.0 25.5 + - - +
338A CYS* 3.6 9.7 - - + +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TRP* 3.8 21.8 - - + +
287A THR* 5.1 2.2 - - + -
291A CYS* 5.7 1.3 - - - -
329A ALA* 3.0 22.9 + - + +
330A PHE* 3.4 28.4 + - + +
332A ILE* 1.3 76.0 - - - +
334A ALA* 1.3 56.2 + - - +
335A GLU 3.3 1.1 - - - -
338A CYS 4.1 8.3 - - - +
339A ASN* 3.1 33.9 + - - +
340A ILE* 3.7 34.8 - - + +
341A PHE* 3.7 32.3 - - + -
349A PHE* 5.5 4.0 - - + -
356A MET* 4.5 12.1 - - + -
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Residues in contact with ALA 334 (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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330A PHE 3.0 17.4 + - - +
331A GLN* 3.5 9.4 - - - +
332A ILE 3.0 0.8 + - - -
333A LEU* 1.3 75.5 - - - +
335A GLU* 1.3 66.6 + - - +
336A PRO* 3.3 8.5 - - - +
339A ASN* 5.3 1.1 - - - +
313B VAL* 6.2 3.4 - - + -
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Residues in contact with GLU 335 (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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241A CYS* 5.9 2.9 - - - -
331A GLN 3.8 10.8 - - - +
332A ILE* 3.0 18.2 + - - +
333A LEU 3.7 1.4 - - - +
334A ALA* 1.3 79.6 - - - +
336A PRO* 1.3 72.2 - - - +
337A GLU* 3.2 22.1 - - - +
338A CYS* 2.9 25.5 + - - -
339A ASN 3.3 7.8 + - - -
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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