Contacts of the helix formed by residues 309 - 324 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B LEU* 4.4 10.1 - - + +
308B PRO* 1.3 76.3 - - - +
310B GLU* 1.3 67.3 + - - +
311B GLU* 3.1 10.4 + - - +
312B GLU* 3.0 35.1 + - - +
313B GLN* 3.0 21.7 + - - +
372B ASP* 4.8 4.3 - - - -
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B THR* 1.3 75.0 - - - +
311B GLU* 1.3 54.6 + - - +
313B GLN* 3.4 2.1 - - - +
314B PHE* 2.8 35.6 + - - +
371B ARG* 4.7 2.8 + - - -
372B ASP* 3.6 43.7 - - + +
375B ARG* 2.7 51.6 + - - +
376B ALA* 3.4 8.7 - - + +
379B ARG* 3.4 31.4 + - - +
418B LYS* 5.6 0.7 - - - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.1 8.6 + - - +
310B GLU* 1.3 82.6 - - - +
312B GLU* 1.3 64.0 + - + +
314B PHE* 3.3 17.8 + - - +
315B ALA* 3.0 25.9 + - + +
379B ARG* 3.6 25.2 + - - +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ARG* 2.9 43.8 + - - +
306B ALA* 5.5 2.4 - - - +
307B LEU 4.2 2.4 - - - +
308B PRO* 3.5 19.8 - - + +
309B THR* 3.0 28.9 + - - +
311B GLU* 1.3 78.2 - - + +
313B GLN* 1.3 62.9 + - - +
315B ALA* 3.3 5.4 + - - +
316B ALA* 3.0 24.0 + - - +
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Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 4.7 2.0 - - + -
301B PHE* 3.9 16.1 - - + -
307B LEU* 4.5 2.8 - - - +
308B PRO* 2.7 36.3 + - + +
309B THR 3.0 17.3 + - - +
310B GLU 3.4 3.1 - - - +
312B GLU* 1.3 76.4 - - - +
314B PHE* 1.3 56.2 + - - +
316B ALA* 3.1 4.5 + - - -
317B TYR* 2.7 72.9 + - + +
369B ILE 5.0 1.2 + - - -
372B ASP* 3.8 22.8 - - - +
373B GLN* 3.1 28.5 - - - +
376B ALA* 3.6 8.3 - - + -
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLU 2.8 17.5 + - - +
311B GLU* 3.5 28.3 - - - +
313B GLN* 1.3 77.0 - - - +
315B ALA* 1.3 56.6 + - + +
317B TYR* 3.3 2.2 + - - +
318B LYS* 2.7 53.4 + - + +
376B ALA* 3.5 16.1 - - + +
379B ARG* 3.5 67.5 - - + +
380B ALA* 3.6 11.7 - - - -
383B PHE* 3.7 23.8 - + - -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ARG* 5.8 0.9 - - - +
311B GLU* 3.0 19.7 + - - +
312B GLU* 3.7 7.2 - - - +
314B PHE* 1.3 83.9 - - + +
316B ALA* 1.3 54.1 + - - +
318B LYS* 3.3 7.5 + - - +
319B ALA* 2.8 34.8 + - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B VAL* 4.3 2.7 - - - +
295B TYR* 4.5 0.2 - - - +
300B LEU* 3.7 39.9 - - + -
304B ARG* 4.5 4.7 - - - +
312B GLU 3.0 16.6 + - - +
313B GLN 3.4 4.3 - - - +
315B ALA* 1.3 78.5 - - - +
317B TYR* 1.3 63.7 + - + +
319B ALA* 3.4 6.0 + - - +
320B VAL* 3.2 27.3 + - - +
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B TYR* 3.0 41.1 - + + -
297B THR* 4.1 5.4 - - + -
300B LEU* 4.1 10.5 - - + -
301B PHE* 4.0 8.7 - - - -
313B GLN* 2.7 65.4 + - + +
314B PHE 3.7 0.4 - - - +
316B ALA* 1.3 70.2 - - - +
318B LYS* 1.3 53.4 + - - +
320B VAL* 3.1 7.2 + - - +
321B ALA* 2.8 35.3 + - - +
331B VAL* 5.1 2.5 - - + -
373B GLN* 3.4 18.4 + - + -
376B ALA* 3.7 8.7 - - + -
377B ILE* 3.7 41.3 - - + -
380B ALA* 3.5 19.1 - - + -
386B LEU* 4.9 7.1 - - + +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PHE* 2.7 44.8 + - + +
315B ALA* 3.5 7.0 - - - +
317B TYR* 1.3 67.1 - - - +
319B ALA* 1.3 68.4 + - - +
321B ALA* 3.1 7.2 + - - +
322B GLU* 2.9 54.1 + - - +
380B ALA* 3.9 10.2 - - + +
383B PHE* 2.7 53.1 - - + -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B VAL* 3.6 21.1 - - + -
315B ALA 2.8 17.5 + - - +
316B ALA* 3.7 4.0 - - - +
317B TYR 3.3 0.2 - - - -
318B LYS* 1.3 77.2 - - - +
320B VAL* 1.3 50.5 + - - +
322B GLU* 3.0 8.0 + - - +
323B ALA* 2.6 37.3 + - + +
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ILE* 3.7 26.2 - - + -
277B THR* 4.7 1.3 - - - -
278B VAL* 3.6 31.9 - - + +
281B VAL* 4.6 2.2 - - + -
295B TYR* 4.5 21.3 - - + +
316B ALA 3.2 16.4 + - - +
317B TYR* 3.1 9.5 + - - +
319B ALA* 1.3 73.9 - - - +
321B ALA* 1.3 65.8 + - - +
322B GLU 2.9 0.3 + - - -
323B ALA* 2.9 5.3 + - - -
324B CYS* 2.8 38.8 + - - -
329B VAL* 4.1 15.5 - - + -
386B LEU* 5.9 0.7 - - + -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B TYR 2.8 13.1 + - - +
318B LYS* 3.4 12.3 - - - +
320B VAL* 1.3 77.3 - - - +
322B GLU* 1.3 61.9 + - - +
324B CYS* 3.6 11.5 + - - +
325B GLY 3.7 15.2 + - - +
327B GLN 4.9 2.0 - - - +
329B VAL* 4.9 2.0 - - - -
380B ALA 4.5 3.1 - - - +
383B PHE 4.3 6.4 - - - +
384B GLY* 4.2 25.3 - - - +
385B LYS 5.8 0.4 - - - -
386B LEU* 3.9 26.6 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B LYS* 2.9 58.5 + - - +
319B ALA* 3.6 6.1 - - - +
321B ALA* 1.3 75.7 - - - +
323B ALA* 1.3 61.2 + - - +
324B CYS 2.9 4.9 - - - -
325B GLY* 3.0 15.8 + - - -
383B PHE* 3.5 27.1 - - + +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B VAL* 5.0 9.0 - - + +
281B VAL* 3.1 25.5 - - + +
285B GLU* 3.0 22.2 - - - +
319B ALA* 2.6 20.9 + - + +
320B VAL* 3.5 5.2 - - - +
322B GLU* 1.3 71.8 - - - +
324B CYS* 1.3 60.0 + - - +
325B GLY 3.4 0.6 + - - -
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Residues in contact with CYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B VAL* 3.8 23.6 - - - -
285B GLU* 4.9 1.6 - - - -
292B VAL* 4.4 10.8 - - - +
320B VAL* 2.8 22.6 + - - +
321B ALA 3.9 5.2 - - - +
322B GLU 2.9 0.6 - - - -
323B ALA* 1.3 82.8 - - - +
325B GLY* 1.3 56.6 + - - +
326B SER 3.2 0.5 + - - -
327B GLN* 2.9 49.7 + - + +
329B VAL* 3.5 30.5 - - + -
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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