Contacts of the helix formed by residues 315 - 327 (chain B) in PDB entry 3EXG
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 GLN 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B ARG* 5.6 1.6 + - - -
218B HIS* 5.0 10.4 - - - -
310B ASP* 2.6 46.6 + - + +
311B ASN* 5.2 1.8 - - - -
313B ILE* 3.4 25.3 + - - +
314B PRO* 1.3 77.3 - - - +
316B VAL* 1.4 67.6 + - - +
317B LYS* 4.4 11.4 - - + +
318B ASP* 2.9 31.9 + - - +
319B ILE* 3.3 12.7 + - - +
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Residues in contact with VAL 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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218B HIS* 3.8 28.6 + - + +
221B GLU* 3.8 26.7 - - + +
222B ALA* 3.7 30.1 - - + +
225B VAL* 4.9 5.2 - - + -
315B GLN* 1.4 71.3 + - - +
317B LYS* 1.3 70.4 + - - +
319B ILE* 3.3 12.2 + - - +
320B ILE* 3.0 31.9 + - + +
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Residues in contact with LYS 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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315B GLN* 3.2 9.4 - - + -
316B VAL* 1.3 83.5 - - + +
318B ASP* 1.3 60.3 + - - +
320B ILE* 3.2 9.6 + - + +
321B PHE* 2.7 36.6 + - - +
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B VAL* 4.2 9.6 - - + +
313B ILE 4.5 0.3 - - - +
315B GLN* 2.9 41.6 + - - +
317B LYS* 1.3 74.1 - - - +
319B ILE* 1.3 66.1 + - - +
320B ILE 3.2 1.1 - - - -
321B PHE* 4.1 3.3 - - - +
322B ALA* 3.1 24.8 + - - +
351C ALA* 3.4 26.6 - - + +
352C ASN* 3.4 19.7 + - - +
355C ILE* 3.5 15.0 - - - +
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Residues in contact with ILE 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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209B VAL* 4.8 2.9 - - + -
215B PRO* 5.5 0.4 - - + -
218B HIS* 3.8 38.8 - - + +
219B CYS* 4.0 9.0 - - - +
222B ALA* 3.9 17.5 - - + -
260B VAL* 5.4 1.1 - - + -
262B VAL* 3.7 44.6 - - + -
295B VAL* 4.4 13.0 - - + -
314B PRO* 4.9 4.0 - - + +
315B GLN 3.3 13.6 + - - +
316B VAL* 3.6 8.3 - - - +
318B ASP* 1.3 77.1 - - - +
320B ILE* 1.3 57.1 + - - +
322B ALA* 3.4 2.4 + - - +
323B ILE* 3.0 45.0 + - + +
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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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222B ALA* 3.7 19.7 - - + +
225B VAL* 3.7 37.7 - - + -
226B LEU* 4.1 12.6 - - + -
316B VAL* 3.0 29.6 + - + +
317B LYS* 3.5 10.5 - - + +
319B ILE* 1.3 72.8 - - - +
321B PHE* 1.3 70.2 + - - +
323B ILE* 3.0 6.8 + - - +
324B LYS* 2.9 50.9 + - + +
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Residues in contact with PHE 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 LYS 2.7 22.2 + - - +
318B ASP* 3.9 9.0 - - - +
320B ILE* 1.3 75.1 - - - +
322B ALA* 1.3 57.5 + - - +
324B LYS* 3.4 6.3 + - - +
325B LYS* 2.8 52.2 + - + +
352C ASN* 3.8 14.6 - - - +
354C TRP* 3.7 38.1 - + + -
355C ILE* 6.3 1.1 - - + -
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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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260B VAL* 4.7 4.0 - - + -
293B VAL* 4.6 9.9 - - + +
295B VAL* 3.8 21.5 - - + -
318B ASP 3.1 17.3 + - - +
319B ILE 3.6 4.7 - - - +
320B ILE 3.1 0.4 - - - -
321B PHE* 1.3 78.4 - - - +
323B ILE* 1.3 59.6 + - - +
325B LYS* 3.2 2.8 + - - +
326B THR* 2.8 31.3 + - - -
352C ASN* 4.5 3.6 - - + +
354C TRP* 4.1 22.2 - - + -
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Residues in contact with ILE 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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207B ILE* 3.6 33.2 - - + -
209B VAL* 4.0 21.3 - - + -
222B ALA* 4.9 4.0 - - + -
226B LEU* 3.6 34.1 - - + -
231B VAL* 4.6 0.9 - - + -
233B CYS* 4.1 5.8 - - - -
260B VAL* 4.7 8.7 - - + -
319B ILE* 3.0 38.7 + - + +
320B ILE* 3.0 4.8 + - - +
322B ALA* 1.3 75.3 - - - +
324B LYS* 1.3 61.3 + - + +
326B THR* 3.0 4.4 + - - -
327B LEU* 2.8 42.0 + - + +
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Residues in contact with LYS 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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225B VAL* 6.2 0.6 - - - +
226B LEU* 4.1 11.4 - - + -
229B GLU* 3.3 35.1 + - - -
320B ILE* 2.9 34.8 + - + +
321B PHE* 3.8 5.2 - - - +
323B ILE* 1.3 77.3 - - + +
325B LYS* 1.3 67.2 + - - +
327B LEU* 4.3 0.9 - - - +
328B ASN* 3.0 17.7 + - - -
329B ILE* 3.1 52.7 + - + +
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Residues in contact with LYS 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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321B PHE* 2.8 46.8 + - + +
322B ALA 3.4 5.2 - - - +
324B LYS* 1.3 79.3 - - - +
326B THR* 1.3 62.5 + - - +
328B ASN* 3.2 17.0 + - - +
329B ILE 5.0 0.2 - - - -
354C TRP* 3.2 54.7 - - + +
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.3 9.6 - - + -
258B HIS* 3.6 39.3 + - + -
259B LEU 4.6 5.6 - - - +
260B VAL* 3.6 5.0 - - - +
290B ALA* 3.9 21.4 - - + +
291B PRO 4.2 11.7 + - - +
293B VAL* 3.6 22.7 - - - +
322B ALA 2.8 17.0 + - - -
323B ILE 3.0 7.4 + - - -
325B LYS* 1.3 73.3 - - - +
327B LEU* 1.3 58.3 + - - +
328B ASN* 2.8 13.8 + - - +
354C TRP* 5.2 0.8 - - - -
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Residues in contact with LEU 327 (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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206B HIS* 3.8 21.1 - - + +
207B ILE* 4.2 13.5 - - + -
231B VAL* 3.5 37.5 - - + -
258B HIS* 3.6 40.6 - - + +
323B ILE* 2.8 30.4 + - + +
324B LYS* 3.3 1.1 + - - +
326B THR* 1.3 71.5 - - - +
328B ASN* 1.3 68.9 + - - +
329B ILE* 2.9 26.2 - - + +
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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