Contacts of the helix formed by residues 319 - 333 (chain A) in PDB entry 3Q36
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 THR 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A GLY 4.7 4.5 - - - +
318A LEU* 1.3 76.1 - - - +
320A LEU* 1.3 63.6 + - - +
321A GLU* 3.2 13.9 + - - +
322A GLN* 2.6 44.6 + - - +
323A ALA* 3.2 16.1 + - - +
353A PHE* 3.2 11.8 - - - -
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Residues in contact with LEU 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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319A THR* 1.3 73.6 - - - +
321A GLU* 1.3 66.8 + - + +
324A LEU* 3.2 27.0 + - + +
349A ILE* 3.6 12.6 - - + -
350A ARG* 3.3 62.8 - - + +
353A PHE* 3.3 47.3 - - + -
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Residues in contact with GLU 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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319A THR* 3.2 11.5 + - - +
320A LEU* 1.3 82.0 - - + +
322A GLN* 1.3 64.3 + - + +
324A LEU* 3.5 6.5 + - - +
325A GLN* 3.2 24.7 + - - +
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Residues in contact with GLN 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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271A ILE* 2.8 31.8 + - - +
273A LEU* 3.5 35.7 - - + +
317A GLY 4.2 1.6 - - - +
318A LEU* 3.4 16.3 - - + +
319A THR* 2.6 47.1 + - - +
321A GLU* 1.3 73.4 - - + +
323A ALA* 1.3 55.3 + - - +
325A GLN* 3.2 4.8 + - - +
326A PHE* 2.7 38.4 + - - +
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Residues in contact with ALA 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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313A LEU* 6.3 2.0 - - + -
318A LEU* 4.5 9.1 - - + +
319A THR 3.2 15.8 + - - +
320A LEU 3.8 4.3 - - - +
321A GLU 3.3 0.2 - - - -
322A GLN* 1.3 79.7 - - - +
324A LEU* 1.3 57.7 + - - +
326A PHE* 3.1 5.9 + - - +
327A TRP* 2.8 46.1 + - + +
349A ILE* 4.1 9.2 - - + -
353A PHE* 3.6 24.9 - - + -
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Residues in contact with LEU 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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320A LEU* 3.2 19.7 + - + +
321A GLU* 4.0 5.4 - - - +
323A ALA* 1.3 78.4 - - - +
325A GLN* 1.3 58.6 + - - +
327A TRP* 5.0 1.8 - - - -
328A LYS* 2.8 38.8 + - + +
341A PHE* 4.4 5.5 - - + -
346A SER* 4.0 24.5 - - - -
349A ILE* 3.5 32.1 - - + -
350A ARG* 3.9 34.8 - - + +
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Residues in contact with GLN 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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273A LEU* 4.0 20.9 - - + +
321A GLU 3.2 17.6 + - - +
322A GLN* 3.6 6.4 - - - +
324A LEU* 1.3 80.4 - - - +
326A PHE* 1.3 57.5 + - - +
328A LYS* 4.7 4.9 - - - -
329A GLN* 2.9 33.8 + - + +
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Residues in contact with PHE 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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273A LEU* 4.3 16.4 - - + -
276A ILE* 3.7 28.3 - - + -
292A HIS* 4.1 8.7 - + - -
295A LEU* 3.6 32.8 - - + -
296A ARG* 3.8 27.4 - - - -
309A TYR* 4.0 14.4 - + - -
313A LEU* 3.5 23.3 - - + -
318A LEU* 4.9 1.1 - - + -
322A GLN 2.7 21.5 + - - +
323A ALA* 3.4 5.8 - - - +
325A GLN* 1.3 73.6 - - - +
327A TRP* 1.3 84.7 + + - +
329A GLN* 3.9 9.7 - - - +
330A GLU* 3.2 24.8 + - - +
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Residues in contact with TRP 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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295A LEU* 3.9 23.1 - - + -
301A LEU* 3.7 18.6 - - + -
305A GLY 4.3 0.2 - - - -
306A ARG* 3.7 35.4 - - + -
309A TYR* 4.1 16.6 - + - -
310A GLY* 3.7 30.1 + - - -
313A LEU* 4.0 9.0 - - + +
323A ALA* 2.8 39.8 + - + +
324A LEU 4.5 0.2 - - - +
326A PHE* 1.3 88.6 - + - +
328A LYS* 1.3 58.7 + - - +
330A GLU* 4.8 1.6 - - - -
331A PHE* 3.0 59.6 + + - +
341A PHE* 3.9 15.7 - - + -
349A ILE* 4.3 24.5 - - + +
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Residues in contact with LYS 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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324A LEU* 2.8 22.7 + - + +
325A GLN* 4.6 3.1 - - - +
327A TRP* 1.3 73.8 - - - +
329A GLN* 1.3 66.6 - - - +
331A PHE* 3.3 1.4 + - - +
332A ILE* 3.0 51.7 + - + +
338A PRO* 3.6 15.9 + - - +
341A PHE* 3.2 28.8 - - + -
342A ASP* 2.9 37.8 + - - -
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Residues in contact with GLN 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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273A LEU* 6.0 1.4 - - - +
296A ARG* 4.1 10.1 + - - +
325A GLN* 2.9 26.4 + - + +
326A PHE* 3.9 12.9 - - - +
328A LYS* 1.3 82.3 - - - +
330A GLU* 1.3 72.4 + - - +
332A ILE* 3.5 8.3 + - - +
333A LYS* 2.9 62.2 + - - +
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Residues in contact with GLU 330 (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 LEU* 3.6 42.4 - - + +
296A ARG* 2.6 52.6 + - - +
299A HIS* 3.1 43.1 + - - +
326A PHE 3.2 16.4 + - - +
327A TRP* 4.2 2.9 - - - +
329A GLN* 1.3 91.0 + - - +
331A PHE* 1.3 63.5 + - - +
333A LYS* 3.2 24.4 + - - +
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Residues in contact with PHE 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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295A LEU* 3.8 10.1 - - + -
299A HIS 3.7 13.1 - - - +
300A HIS* 3.4 42.0 - + - -
301A LEU 3.8 6.5 - - - -
306A ARG* 3.9 17.5 - - - -
327A TRP* 3.0 45.4 + + - +
328A LYS 3.8 3.1 - - - +
330A GLU* 1.3 78.6 - - - +
332A ILE* 1.3 61.3 + - - +
334A GLY* 3.5 8.1 + - - -
336A MET* 3.0 37.1 + - + +
341A PHE* 4.0 17.0 - + + -
345A TYR* 3.6 42.4 - + - -
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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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328A LYS* 3.0 44.3 + - + +
329A GLN* 3.9 7.0 - - - +
330A GLU 3.2 0.4 - - - -
331A PHE* 1.3 75.1 - - + +
333A LYS* 1.3 53.8 + - - +
334A GLY 2.7 5.6 - - - -
335A LYS* 2.7 29.6 + - - +
336A MET* 3.7 21.3 - - + +
337A ASP 5.4 0.2 - - - +
338A PRO* 3.7 32.3 - - + -
341A PHE* 5.5 2.9 - - + -
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Residues in contact with LYS 333 (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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296A ARG* 4.4 6.5 - - - +
299A HIS* 3.2 44.4 + - + +
329A GLN* 2.9 40.8 + - + +
330A GLU* 3.2 19.5 + - - +
332A ILE* 1.3 77.3 - - - +
334A GLY* 1.3 55.3 + - - +
335A LYS* 3.2 12.4 + - - +
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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