Contacts of the helix formed by residues 319 - 331 (chain B) in PDB entry 6E8Z
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 PHE 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B GLU* 3.5 38.4 - - + +
237B ALA* 4.1 14.1 - - + -
238B PHE* 3.6 27.6 - + + -
241B LEU* 4.1 16.4 - - + -
310B LEU* 3.5 43.5 - - + -
315B LEU* 3.7 6.3 - - + -
316B VAL 3.5 4.8 + - - +
317B ASP 3.2 1.6 - - - -
318B LYS* 1.3 97.3 - - + +
320B PRO* 1.3 61.7 - - - +
321B LEU 3.3 2.6 + - - -
322B PHE* 3.5 22.1 + + + -
323B MET* 2.9 29.1 + - + +
403B EDO 4.2 4.9 - - - -
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Residues in contact with PRO 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLU* 3.1 12.6 - - - +
316B VAL 5.0 1.6 - - - +
317B ASP 4.1 8.5 - - - +
318B LYS 3.6 8.1 - - - +
319B PHE* 1.3 89.3 - - - +
321B LEU* 1.3 56.6 + - - +
323B MET* 4.4 4.5 - - + -
324B ALA* 2.7 32.4 + - - +
341B CYS* 3.3 28.0 - - + +
342B LEU* 4.6 1.8 - - + -
344B ASN 5.3 1.8 - - - +
345B HIS* 3.8 11.0 - - + +
346B PRO* 3.7 25.8 - - + -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 4.3 19.7 - - + +
210B GLY* 5.2 0.7 - - - -
227B VAL* 3.3 38.8 - - + +
230B LEU* 4.1 8.1 - - + -
231B GLY* 3.4 17.7 - - - +
234B GLU* 2.7 24.8 + - - +
320B PRO* 1.3 71.2 - - - +
322B PHE* 1.3 81.0 + - + +
324B ALA* 3.1 6.2 + - - +
325B VAL* 2.9 39.3 + - + +
338B PHE* 4.2 13.6 - - + -
342B LEU* 4.1 17.8 - - + +
345B HIS* 5.1 0.4 - - - +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.4 10.8 - - + -
206B VAL* 3.6 27.4 - - + -
207B VAL* 3.9 24.2 - - + -
234B GLU* 2.8 43.7 + - + +
235B MET* 3.8 29.4 - - + -
238B PHE* 4.1 14.8 - + + -
303B ALA* 4.2 4.9 - - - +
306B LEU* 3.9 22.9 - - + -
310B LEU* 5.2 1.1 - - + -
319B PHE* 3.8 17.3 - + + +
321B LEU* 1.3 77.7 - - + +
323B MET* 1.3 79.6 + - + +
325B VAL* 3.2 5.7 + - - +
326B TYR* 3.1 17.7 + - - +
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 4.1 3.1 - - - +
306B LEU* 3.9 6.7 - - + -
307B TYR* 3.5 57.4 - - + +
310B LEU* 3.8 16.6 - - + -
316B VAL* 3.4 40.8 - - + +
319B PHE* 2.9 24.4 + - + +
320B PRO* 4.2 3.8 - - + +
322B PHE* 1.3 85.4 - - + +
324B ALA* 1.3 65.8 + - - +
326B TYR* 3.3 5.8 + - + +
327B LYS* 3.0 33.3 + - + +
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Residues in contact with ALA 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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320B PRO 2.7 25.5 + - - +
321B LEU* 3.1 4.0 + - - +
323B MET* 1.3 73.8 - - - +
325B VAL* 1.3 62.2 + - - +
327B LYS* 5.2 0.7 - - - -
328B VAL* 3.1 31.4 + - + +
333B GLN* 4.4 9.4 - - - +
338B PHE* 3.8 23.8 - - + -
341B CYS* 3.8 26.2 - - + -
342B LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 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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206B VAL* 3.7 37.2 - - + +
209B VAL* 4.1 23.1 - - + -
210B GLY* 4.0 20.4 - - - +
213B PHE* 4.5 7.0 - - + -
299B GLY 4.9 2.9 - - - +
300B PRO* 5.0 1.3 - - + -
303B ALA* 3.8 9.9 - - + -
321B LEU* 2.9 20.5 + - + +
322B PHE 3.4 8.1 - - - +
323B MET 3.2 0.2 - - - -
324B ALA* 1.3 77.4 - - - +
326B TYR* 1.3 64.3 + - - +
328B VAL* 4.0 0.9 - - - +
329B CYS* 3.1 28.8 + - - -
338B PHE* 4.2 6.7 - - + -
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Residues in contact with TYR 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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303B ALA* 3.9 18.8 - - + +
304B ARG* 3.6 33.9 - - + -
307B TYR* 3.6 46.0 - + + -
322B PHE 3.1 12.2 + - - +
323B MET* 3.5 11.0 - - + +
325B VAL* 1.3 77.0 - - - +
327B LYS* 1.3 69.3 + - + +
329B CYS* 3.1 1.8 + - - -
330B TYR* 2.8 56.5 + + + +
331B GLU* 3.0 43.4 + - + +
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Residues in contact with LYS 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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307B TYR* 4.6 14.5 + - - -
316B VAL* 4.3 21.4 - - - +
323B MET* 3.0 23.5 + - + +
324B ALA* 4.2 0.7 - - - +
326B TYR* 1.3 86.2 - - + +
328B VAL* 1.3 57.3 + - - +
331B GLU* 2.9 50.5 + - + +
333B GLN* 3.1 47.7 + - + +
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Residues in contact with VAL 328 (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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213B PHE* 3.8 22.2 - - + -
277B PHE* 3.6 37.6 - - + -
324B ALA* 3.1 20.1 + - + +
325B VAL 4.0 0.4 - - - +
327B LYS* 1.3 76.4 - - - +
329B CYS* 1.3 62.3 + - - +
330B TYR 3.6 0.2 + - - -
332B GLY* 4.5 6.8 + - - -
333B GLN* 3.4 36.6 - - + +
334B PRO 4.1 1.1 - - - +
335B VAL* 3.7 25.4 - - + +
338B PHE* 5.1 7.6 - - + -
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Residues in contact with CYS 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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209B VAL* 4.5 2.0 - - - -
213B PHE* 4.1 16.4 - - - -
277B PHE* 5.9 0.4 - - - -
284B ILE* 3.9 35.5 - - + +
300B PRO* 4.0 19.1 - - + -
325B VAL* 3.1 29.4 + - - +
326B TYR* 4.7 0.2 - - - -
328B VAL* 1.3 79.4 - - - +
330B TYR* 1.3 83.3 + - + +
332B GLY 5.3 0.2 - - - -
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Residues in contact with TYR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 3.2 29.2 - - + +
301B GLU* 3.4 33.6 + - - +
304B ARG* 3.8 38.2 + - + -
326B TYR* 2.8 50.0 + + + +
329B CYS* 1.3 94.0 - - + +
331B GLU* 1.3 60.2 + - - +
332B GLY 3.6 2.4 + - - -
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Residues in contact with GLU 331 (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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307B TYR* 4.2 11.1 + - - -
326B TYR* 3.0 42.4 + - + +
327B LYS* 2.9 37.1 + - + +
330B TYR* 1.3 78.9 - - - +
332B GLY* 1.3 63.8 + - - +
333B GLN* 3.1 4.6 + - + +
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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