Contacts of the helix formed by residues 300 - 311 (chain A) in PDB entry 3QNQ
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 ALA 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ILE 4.0 10.6 + - - +
295A MET* 4.2 15.0 - - + +
296A GLY 3.9 11.9 - - - +
299A GLY* 1.3 72.3 - - - +
301A THR* 1.3 64.8 + - - +
302A LEU* 3.0 4.5 - - - -
303A ALA* 2.9 20.9 + - + +
304A LEU 3.7 2.1 + - - -
355A VAL* 3.7 11.7 - - + -
356A PRO* 4.9 0.8 - - - +
359A LEU* 4.2 13.5 - - + -
408A PHE* 6.0 0.9 - - + -
411A ALA* 3.4 27.8 - - + -
415A TYR* 3.9 2.3 - - + -
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Residues in contact with THR 301 (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 GLY 3.8 12.8 - - - +
297A GLY 4.2 0.4 - - - -
298A SER* 4.5 0.7 - - - -
299A GLY 2.7 13.1 + - - +
300A ALA* 1.3 76.2 - - - +
302A LEU* 1.3 58.0 + - - +
304A LEU* 3.1 11.0 + - - +
305A VAL* 2.8 43.0 + - + +
328A GLY* 5.6 2.7 - - - -
333A ASN* 3.1 46.6 + - + -
336A VAL* 4.3 17.6 - - + +
342A ILE* 4.8 3.6 - - - +
352A PHE* 4.8 5.7 - - - -
415A TYR* 4.6 1.5 + - - -
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Residues in contact with LEU 302 (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 MET* 4.5 5.4 - - + +
296A GLY* 3.2 24.6 - - - +
300A ALA 2.9 0.6 + - - +
301A THR* 1.3 78.1 - - - +
303A ALA* 1.3 56.9 + - - +
305A VAL* 3.2 5.4 + - + +
306A VAL* 2.8 44.3 + - + +
325A ILE* 4.7 15.9 - - + -
328A GLY* 3.9 29.4 - - - +
329A ILE* 4.4 13.9 - - + +
386A ILE* 4.4 32.1 - - + -
408A PHE* 4.5 13.2 - - + -
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Residues in contact with ALA 303 (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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300A ALA* 2.9 12.5 + - + +
302A LEU* 1.3 78.7 - - - +
304A LEU* 1.3 62.5 + - - +
306A VAL* 3.2 3.5 + - - +
307A GLY* 3.0 20.1 + - - -
408A PHE* 3.5 27.8 - - + +
411A ALA* 3.6 27.1 - - + -
412A PHE* 3.6 25.2 - - + +
415A TYR* 4.7 0.7 - - + -
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Residues in contact with LEU 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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300A ALA 3.7 1.6 + - - -
301A THR* 3.1 11.5 + - + +
303A ALA* 1.3 78.5 - - - +
305A VAL* 1.3 62.2 + - + +
307A GLY* 3.6 1.1 + - - -
308A MET* 3.4 20.1 + - + +
336A VAL* 4.9 5.4 - - + -
340A MET* 3.7 27.8 - - + -
342A ILE* 4.2 16.2 - - + -
348A LEU* 5.1 4.9 - - + -
415A TYR* 3.3 53.9 - - + -
419A LEU* 3.5 41.7 - - + +
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Residues in contact with VAL 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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301A THR* 2.8 37.5 + - + +
302A LEU* 3.5 10.5 - - + +
304A LEU* 1.3 76.1 - - + +
306A VAL* 1.3 66.6 + - - +
308A MET* 2.9 19.8 + - + +
309A LEU* 3.1 21.2 + - + +
321A GLY* 4.3 4.0 - - - +
324A SER* 4.0 14.6 - - - +
325A ILE* 3.2 39.5 - - + +
328A GLY* 5.8 0.7 - - - -
336A VAL* 3.8 22.2 - - + -
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Residues in contact with VAL 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 LEU* 2.8 35.3 + - + +
303A ALA 3.5 6.5 - - - +
305A VAL* 1.3 71.2 - - - +
307A GLY* 1.3 64.5 + - - +
309A LEU* 2.9 22.3 + - + +
310A LEU* 3.0 26.9 + - + +
325A ILE* 5.0 3.6 - - + -
408A PHE* 3.7 26.0 - - + -
412A PHE* 3.7 19.3 - - + -
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Residues in contact with GLY 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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303A ALA 3.0 10.6 + - - -
304A LEU* 3.9 1.1 - - - -
305A VAL 3.2 0.4 - - - -
306A VAL* 1.3 79.0 - - - +
308A MET* 1.3 52.9 + - - +
310A LEU* 3.2 2.9 + - - -
311A PHE* 2.6 42.1 + - - +
412A PHE* 3.9 18.8 - - - -
416A LEU* 5.2 1.1 - - - -
419A LEU* 3.4 19.5 - - - +
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Residues in contact with MET 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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304A LEU* 3.4 15.1 + - - +
305A VAL* 2.9 20.4 + - + +
307A GLY* 1.3 75.4 - - - +
309A LEU* 1.3 60.0 + - - +
310A LEU 3.3 0.5 + - - -
311A PHE 4.9 0.7 - - - -
312A ALA* 2.8 36.2 + - - +
317A LEU* 3.4 43.6 - - + +
318A LYS* 4.5 0.7 - - - -
320A LEU* 3.8 18.8 - - + -
321A GLY* 3.2 32.5 - - - +
324A SER* 4.4 4.5 - - - +
336A VAL* 4.9 2.7 - - + -
340A MET* 4.1 11.2 - - - +
419A LEU* 3.5 21.5 - - + -
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Residues in contact with LEU 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 VAL* 3.1 28.4 + - + +
306A VAL* 2.9 11.3 + - + +
308A MET* 1.3 75.5 - - - +
310A LEU* 1.3 64.1 + - + +
312A ALA* 4.9 3.4 - - - +
318A LYS 5.5 2.7 - - - +
321A GLY* 3.3 26.7 - - - +
322A ARG* 4.4 7.2 - - + +
325A ILE* 3.2 52.0 - - + -
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Residues in contact with LEU 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 VAL* 3.0 36.3 + - + +
307A GLY 3.8 1.8 - - - +
309A LEU* 1.3 84.7 - - + +
311A PHE* 1.3 84.6 + - + +
312A ALA 3.5 3.1 + - - -
412A PHE* 4.0 19.7 - - + -
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Residues in contact with PHE 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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307A GLY* 2.6 20.7 + - - +
308A MET* 4.7 1.2 - - - -
310A LEU* 1.3 99.5 - - + +
312A ALA* 1.3 57.2 + - - +
313A ARG* 3.0 10.2 + - - +
412A PHE* 4.0 19.3 - + - -
416A LEU* 3.3 48.7 - - + -
419A LEU* 5.3 6.5 - - + +
423A ASP* 3.3 9.7 - - - +
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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
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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