Contacts of the helix formed by residues 315 - 330 (chain B) in PDB entry 2I6A
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 PRO 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ASP 3.8 1.3 - - - +
314B LYS* 1.3 95.5 - - + +
316B LEU* 1.3 54.9 + - - +
317B THR* 3.0 11.0 - - - +
318B GLU* 2.7 40.9 + - + +
319B CYS 3.0 7.8 + - - -
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Residues in contact with LEU 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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219B ILE* 4.8 7.2 - - + -
261B ILE* 3.1 39.0 - - + -
273B MET* 3.6 27.1 - - + -
275B THR* 4.0 6.7 - - + -
306B PHE* 4.0 22.9 - - + -
310B LEU* 5.1 5.8 - - + -
314B LYS 3.4 3.2 + - - +
315B PRO* 1.3 70.2 - - - +
317B THR* 1.3 55.7 + - - +
319B CYS* 3.3 11.3 + - - +
320B ILE* 2.9 36.4 + - - +
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Residues in contact with THR 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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282B PHE* 4.2 27.1 - - + -
315B PRO* 2.8 9.9 + - - +
316B LEU* 1.3 75.3 - - - +
318B GLU* 1.3 61.5 + - - +
320B ILE* 3.6 6.4 + - - +
321B ARG* 3.0 30.9 + - + +
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Residues in contact with GLU 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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309B GLN* 3.9 10.9 - - - +
314B LYS* 4.0 18.2 - - + -
315B PRO* 2.7 29.6 + - + +
317B THR* 1.3 82.7 - - - +
319B CYS* 1.3 63.1 + - - +
321B ARG* 2.3 46.1 + - - +
322B ALA* 3.0 23.0 + - - +
344C PHE* 3.4 13.3 - - + -
345C HIS 4.7 2.4 - - - +
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Residues in contact with CYS 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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306B PHE* 3.5 44.0 - - + +
309B GLN* 4.0 12.6 - - - -
310B LEU* 3.9 32.5 - - - -
314B LYS 3.6 15.0 - - - -
315B PRO 3.0 17.5 + - - -
316B LEU* 3.5 10.5 - - - +
318B GLU* 1.3 73.2 - - - +
320B ILE* 1.3 66.4 + - - +
322B ALA* 3.1 3.1 + - - -
323B GLY* 2.9 19.9 + - - -
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Residues in contact with ILE 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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263B ILE* 3.9 12.8 - - + -
271B THR* 4.1 13.7 - - + -
273B MET* 2.9 32.1 - - + -
282B PHE* 3.9 31.2 - - + -
302B PHE* 3.9 8.2 - - + -
306B PHE* 4.2 11.4 - - + -
316B LEU 2.9 22.0 + - - +
317B THR* 3.8 7.2 - - - +
319B CYS* 1.3 75.0 - - - +
321B ARG* 1.3 57.7 + - - +
323B GLY* 3.4 1.0 + - - -
324B HIS* 3.0 52.5 + - + +
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Residues in contact with ARG 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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285B LEU* 5.9 0.2 - - - +
317B THR* 3.0 22.2 + - + +
318B GLU* 2.3 54.0 + - - +
319B CYS 3.1 0.2 - - - -
320B ILE* 1.3 78.4 - - - +
322B ALA* 1.4 56.5 + - - +
324B HIS* 3.3 10.3 + - + +
325B TYR* 3.0 26.5 + - - +
344C PHE* 3.3 43.1 + - - -
345C HIS* 4.3 4.8 + - - +
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Residues in contact with ALA 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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76B MET* 3.5 20.0 - - + +
305B GLY* 3.2 24.0 - - - +
309B GLN* 3.4 24.0 - - + -
318B GLU 3.0 6.5 + - - -
319B CYS 3.7 1.8 - - - +
321B ARG* 1.4 72.6 - - - +
323B GLY* 1.3 60.6 + - - +
325B TYR* 3.6 2.1 - - - +
326B ALA* 2.8 30.5 + - - +
344C PHE* 3.8 15.2 - - + -
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Residues in contact with GLY 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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302B PHE* 3.1 49.9 - - - -
305B GLY* 3.7 2.1 - - - -
306B PHE 3.8 2.2 - - - -
319B CYS 2.9 14.6 + - - -
320B ILE 3.8 0.7 - - - -
322B ALA* 1.3 73.8 - - - +
324B HIS* 1.3 64.9 + - - +
326B ALA* 3.4 0.7 + - - +
327B ALA* 3.0 21.5 + - - +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 2.8 30.7 + - - -
282B PHE* 3.6 15.6 + - + +
283B ALA 3.7 13.2 + - - -
284B VAL* 4.0 28.5 - - + +
285B LEU* 4.5 19.1 - - + +
287B GLN* 4.3 4.4 + - - +
302B PHE* 4.0 14.1 - + - -
320B ILE* 3.0 37.9 + - + +
321B ARG* 3.6 9.9 - - + +
323B GLY* 1.3 75.6 - - - +
325B TYR* 1.3 66.2 + - - +
327B ALA* 3.3 6.3 + - - +
328B SER* 3.2 19.8 + - - -
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Residues in contact with TYR 325 (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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75B TRP* 3.5 19.8 - + - -
76B MET* 3.5 34.1 - - + -
285B LEU* 4.3 14.1 - - + +
321B ARG 3.0 16.5 + - - +
322B ALA* 3.6 6.1 - - - +
323B GLY 3.2 0.2 - - - -
324B HIS* 1.3 77.4 - - - +
326B ALA* 1.3 63.6 + - - +
328B SER* 2.6 27.3 + - - -
329B ILE* 3.1 42.9 + - + +
57C LYS* 6.2 0.4 - - - -
339C PRO* 5.4 2.3 - - - +
343C ASP* 3.5 37.1 + - + +
344C PHE* 4.3 19.1 - + + -
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Residues in contact with ALA 326 (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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72B VAL* 3.9 17.5 - - + -
75B TRP* 5.3 0.9 - - - -
76B MET* 5.0 4.0 - - - -
301B ALA* 3.0 34.9 - - - +
305B GLY* 3.9 5.2 - - - -
322B ALA 2.8 20.7 + - - +
323B GLY 3.6 1.6 - - - +
325B TYR* 1.3 80.4 - - - +
327B ALA* 1.3 63.8 + - - +
328B SER 3.2 0.2 + - - -
329B ILE* 4.9 1.8 - - - -
330B ILE* 3.1 26.9 + - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 4.0 12.4 - - - +
298B ALA* 3.8 36.7 - - + +
301B ALA* 4.0 10.0 - - - +
302B PHE* 4.3 6.1 - - + +
323B GLY 3.0 19.6 + - - +
324B HIS* 3.7 7.4 - - - +
325B TYR 3.2 0.2 - - - -
326B ALA* 1.3 76.4 - - - +
328B SER* 1.3 58.6 + - - +
329B ILE 3.6 0.3 + - - -
330B ILE 4.0 9.5 - - - +
331B ILE* 4.1 6.2 - - - +
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.8 15.2 - - - +
287B GLN* 3.4 42.4 + - - +
324B HIS 3.2 6.9 + - - -
325B TYR* 2.6 26.6 + - - -
327B ALA* 1.3 74.8 - - - +
329B ILE* 1.3 67.7 + - - +
331B ILE* 2.9 19.7 - - - +
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Residues in contact with ILE 329 (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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75B TRP* 3.8 24.0 - - + -
325B TYR* 3.1 49.6 - - + +
326B ALA 3.2 3.0 + - - +
328B SER* 1.3 85.4 - - - +
330B ILE* 1.3 63.0 + - + +
331B ILE* 2.7 33.1 + - - +
57C LYS* 4.0 27.4 - - - +
338C PHE* 5.6 1.4 - - - -
339C PRO* 4.3 18.6 - - + -
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Residues in contact with ILE 330 (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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72B VAL* 4.5 24.0 - - + -
75B TRP* 4.1 39.7 - - + -
297B GLY 5.0 5.9 - - - +
298B ALA* 5.4 0.9 - - - -
301B ALA* 4.3 14.9 - - + +
326B ALA* 3.1 13.7 + - - +
327B ALA 4.0 8.0 - - - +
329B ILE* 1.3 71.8 - - + +
331B ILE* 1.3 59.9 + - - +
332B ARG 4.2 1.1 + - - +
338C PHE* 3.2 63.5 - - + -
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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