Contacts of the helix formed by residues 309 - 324 (chain A) in PDB entry 2N5T
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 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LEU* 4.4 9.9 - - + +
308A PRO* 1.3 76.1 - - - +
310A GLU* 1.3 67.7 + - - +
311A GLU* 3.2 9.9 + - - +
312A GLU* 3.0 35.3 + - - +
313A GLN* 3.0 21.1 + - - +
372A ASP* 4.7 4.7 - - - -
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Residues in contact with GLU 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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309A THR* 1.3 75.6 - - - +
311A GLU* 1.3 53.2 + - - +
313A GLN* 3.1 2.6 + - - +
314A PHE* 2.8 36.2 + - - +
371A ARG* 4.7 2.9 + - - -
372A ASP* 3.6 43.1 - - + +
375A ARG* 2.7 51.6 + - - +
376A ALA* 3.4 8.0 - - + +
379A ARG* 3.4 32.4 + - - +
418A LYS* 5.6 0.7 - - - -
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Residues in contact with GLU 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 THR* 3.1 8.9 + - - +
310A GLU* 1.3 81.2 - - - +
312A GLU* 1.3 64.8 + - + +
314A PHE* 3.3 17.0 + - - +
315A ALA* 3.0 26.3 + - + +
379A ARG* 3.6 25.2 + - - +
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Residues in contact with GLU 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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304A ARG* 2.9 44.4 + - - +
306A ALA* 5.5 2.3 - - - +
307A LEU 4.2 3.1 - - - +
308A PRO* 3.5 19.7 - - + +
309A THR* 3.0 27.1 + - - +
311A GLU* 1.3 78.6 - - + +
313A GLN* 1.3 62.7 + - - +
315A ALA* 3.3 6.4 + - - +
316A ALA* 3.0 24.1 + - - +
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Residues in contact with GLN 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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300A LEU* 4.7 2.5 - - + -
301A PHE* 3.9 16.1 - - + -
307A LEU* 4.5 2.8 - - - +
308A PRO* 2.7 37.5 + - + +
309A THR 3.0 15.2 + - - +
310A GLU 3.4 3.1 - - - +
312A GLU* 1.3 75.3 - - - +
314A PHE* 1.3 56.0 + - - +
316A ALA* 3.1 5.1 + - - -
317A TYR* 2.7 72.4 + - + +
369A ILE* 5.0 1.2 + - - +
372A ASP* 3.8 21.6 - - - +
373A GLN* 3.1 29.6 - - - +
376A ALA* 3.6 8.3 - - + -
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Residues in contact with PHE 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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310A GLU 2.8 17.3 + - - +
311A GLU* 3.5 23.6 - - - +
313A GLN* 1.3 78.9 - - - +
315A ALA* 1.3 56.4 + - + +
317A TYR* 3.3 2.2 + - - +
318A LYS* 2.7 55.3 + - + +
376A ALA* 3.5 15.7 - - + +
379A ARG* 3.5 72.2 - - + +
380A ALA* 3.6 11.7 - - - -
383A PHE* 3.7 23.3 - + - -
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Residues in contact with ALA 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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304A ARG* 5.8 0.9 - - - +
311A GLU* 3.0 20.1 + - + +
312A GLU* 3.7 6.3 - - - +
314A PHE* 1.3 83.3 - - + +
316A ALA* 1.3 55.0 + - - +
318A LYS* 3.3 7.7 + - - +
319A ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 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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278A VAL* 4.3 2.5 - - - +
295A TYR* 4.5 0.9 - - - +
300A LEU* 3.7 39.0 - - + -
304A ARG* 4.6 5.4 - - - +
312A GLU 3.0 16.8 + - - +
313A GLN 3.1 4.0 + - - +
315A ALA* 1.3 78.1 - - - +
317A TYR* 1.3 63.7 + - + +
319A ALA* 3.4 6.3 + - - +
320A VAL* 3.2 27.4 + - - +
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Residues in contact with TYR 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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295A TYR* 3.0 40.6 - + + -
297A THR* 4.1 5.1 - - + -
300A LEU* 4.1 11.0 - - + -
301A PHE* 4.0 7.8 - - - -
313A GLN* 2.7 65.2 + - + +
314A PHE 3.7 0.2 - - - +
316A ALA* 1.3 70.8 - - - +
318A LYS* 1.3 53.3 + - - +
320A VAL* 3.1 7.8 + - - +
321A ALA* 2.8 34.8 + - - +
331A VAL* 5.1 2.9 - - + -
373A GLN* 3.4 19.0 + - - -
376A ALA* 3.7 8.3 - - + -
377A ILE* 3.7 40.2 - - + -
380A ALA* 3.5 18.1 - - + +
386A LEU* 4.9 8.7 - - + +
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Residues in contact with LYS 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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314A PHE* 2.7 46.4 + - + +
315A ALA* 3.5 8.1 - - - +
317A TYR* 1.3 67.7 - - - +
319A ALA* 1.3 70.0 + - - +
321A ALA* 3.1 7.8 + - - +
322A GLU* 2.9 53.0 + - - +
380A ALA* 3.9 9.4 - - + +
383A PHE* 2.7 52.0 - - + -
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Residues in contact with ALA 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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278A VAL* 3.6 21.5 - - + -
315A ALA 2.8 17.5 + - - +
316A ALA* 3.7 4.7 - - - +
317A TYR 3.3 0.2 - - - -
318A LYS* 1.3 77.3 - - - +
320A VAL* 1.3 51.4 + - - +
322A GLU* 3.0 8.7 + - - +
323A ALA* 2.6 36.0 + - - +
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Residues in contact with VAL 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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275A ILE* 3.7 26.0 - - + -
277A THR 4.7 0.4 - - - -
278A VAL* 3.6 32.8 - - + +
281A VAL* 4.6 2.5 - - + -
295A TYR* 4.5 22.0 - - + +
316A ALA 3.2 16.4 + - - +
317A TYR* 3.1 9.4 + - - +
319A ALA* 1.3 73.0 - - - +
321A ALA* 1.3 64.9 + - - +
322A GLU 2.9 0.7 + - - -
323A ALA* 2.9 4.9 + - - -
324A CYS* 2.8 38.4 + - - -
329A VAL* 4.1 16.6 - - + -
386A LEU* 5.9 0.7 - - + -
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Residues in contact with ALA 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 TYR 2.8 13.9 + - - +
318A LYS* 3.4 12.6 - - - +
320A VAL* 1.3 76.5 - - - +
322A GLU* 1.3 61.4 + - - +
324A CYS* 3.6 10.9 + - - +
325A GLY 3.7 16.1 + - - +
327A GLN 4.9 2.0 - - - +
329A VAL* 5.0 2.0 - - - -
380A ALA 4.5 3.6 - - - +
383A PHE 4.3 5.9 - - - +
384A GLY* 4.2 24.8 - - - +
385A LYS 5.8 0.2 - - - -
386A LEU* 3.9 27.1 - - + +
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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
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318A LYS* 2.9 58.3 + - - +
319A ALA* 3.6 5.6 - - - +
321A ALA* 1.3 76.4 - - - +
323A ALA* 1.3 61.6 + - - +
324A CYS 2.9 4.7 - - - -
325A GLY* 3.0 15.7 + - - +
383A PHE* 3.5 26.8 - - + +
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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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278A VAL* 5.0 8.5 - - + +
281A VAL* 3.1 26.0 - - + +
285A GLU* 3.0 22.3 - - - +
319A ALA* 2.6 21.7 + - + +
320A VAL* 2.9 5.1 + - - +
322A GLU* 1.3 72.1 - - - +
324A CYS* 1.3 59.5 + - - +
325A GLY 3.4 0.4 + - - -
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Residues in contact with CYS 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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281A VAL* 3.8 23.8 - - - -
285A GLU* 4.6 3.1 - - - -
292A VAL* 4.2 10.3 - - - -
320A VAL* 2.8 21.5 + - - +
321A ALA 3.9 5.6 - - - +
322A GLU 2.9 0.4 - - - -
323A ALA* 1.3 82.8 - - - +
325A GLY* 1.3 58.2 + - - +
326A SER 3.2 0.5 + - - -
327A GLN* 2.9 48.8 + - + +
329A VAL* 3.5 30.7 - - + -
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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