Contacts of the helix formed by residues 323 - 341 (chain D) in PDB entry 6F0X
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 SER 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP* 2.6 34.3 + - - +
322D PRO* 1.3 73.4 - - - +
324D ALA* 1.3 67.4 + - - +
325D ALA* 2.9 15.6 + - - +
326D ALA 3.1 2.9 + - - -
327D ILE* 3.0 22.4 + - - +
381D GLU* 2.9 13.7 - - - -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D SER* 1.3 73.0 - - - +
325D ALA* 1.3 62.9 + - - +
327D ILE* 3.2 15.6 + - + +
328D PHE* 2.9 24.4 + - - +
353D LEU* 5.1 0.4 - - - -
374D ASN* 5.7 2.5 - - - +
377D SER* 4.2 17.0 - - - +
378D ARG* 5.1 10.5 - - + +
381D GLU* 3.0 13.4 + - - +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D SER* 2.9 11.3 + - - +
324D ALA* 1.3 77.0 - - - +
326D ALA* 1.3 64.0 + - - +
328D PHE* 3.0 6.2 + - - +
329D LYS* 3.0 30.1 + - - +
353D LEU* 3.4 27.3 - - + +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 3.7 37.6 - - + +
141D TYR 4.7 2.2 - - - +
142D ASP* 4.0 10.5 + - - +
322D PRO* 3.9 17.9 - - + -
323D SER* 3.1 8.0 + - - +
325D ALA* 1.3 79.0 - - - +
327D ILE* 1.3 62.0 + - - +
329D LYS* 3.2 5.1 + - - +
330D ILE* 2.9 32.8 + - + +
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Residues in contact with ILE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D PRO* 4.2 13.7 - - + +
323D SER 3.0 21.4 + - - +
324D ALA* 3.2 10.5 - - - +
325D ALA 3.1 0.2 - - - -
326D ALA* 1.3 77.3 - - - +
328D PHE* 1.3 61.4 + - - +
330D ILE* 3.2 9.2 + - - +
331D TYR* 2.9 43.9 + - + +
377D SER* 3.2 25.4 - - - +
380D SER* 4.0 6.7 - - - -
381D GLU* 3.4 43.5 - - + +
388D LEU* 4.5 15.5 - - + -
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA 2.9 12.7 + - - +
325D ALA 3.0 6.5 + - - +
327D ILE* 1.3 76.8 - - - +
329D LYS* 1.3 62.7 + - + +
331D TYR* 3.3 3.2 + - - +
332D LEU* 2.9 51.6 + - + +
351D LEU 3.0 24.2 - - - -
352D THR* 3.4 15.0 - - - -
353D LEU* 3.4 32.8 - - + -
356D LEU* 3.6 17.0 - - + -
370D SER* 4.2 19.3 - - - -
373D LEU* 3.7 30.1 - - + -
374D ASN* 5.0 8.3 - - + +
377D SER* 3.8 12.6 - - - +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.4 30.5 - - + +
325D ALA* 3.0 22.3 + - - +
326D ALA* 3.2 8.5 + - - +
328D PHE* 1.3 81.6 - - + +
330D ILE* 1.3 62.6 + - - +
332D LEU* 3.1 14.4 + - + +
333D SER* 3.0 21.0 + - - -
352D THR* 6.3 4.3 - - + -
353D LEU* 5.3 9.6 - - + -
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Residues in contact with ILE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D SER 4.4 3.4 - - - +
140D VAL* 4.8 7.4 - - + -
322D PRO* 5.1 6.7 - - + -
326D ALA* 2.9 25.7 + - + +
327D ILE* 3.6 7.6 - - - +
329D LYS* 1.3 75.8 - - - +
331D TYR* 1.3 65.9 + - + +
333D SER* 2.2 28.0 + - - -
334D CYS* 2.9 17.6 + - - -
385D GLY* 5.4 2.7 - - - -
388D LEU* 5.3 10.5 - - + -
389D ARG* 3.4 48.9 - - + +
901D AGS 3.4 39.9 - - + +
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Residues in contact with TYR 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ILE* 2.9 29.4 + - + +
328D PHE 3.7 1.8 - - - +
330D ILE* 1.3 81.5 - - + +
332D LEU* 1.3 58.4 + - - +
334D CYS* 3.1 15.7 + - + +
335D LEU* 2.9 35.5 + - + +
373D LEU* 3.5 36.1 - - + -
376D ILE* 3.9 12.9 - - + +
377D SER* 3.7 14.6 - - - -
380D SER* 3.6 22.4 + - - -
388D LEU* 3.3 48.4 - - + +
391D LEU* 3.3 14.3 - - + +
392D PRO* 5.3 7.0 - - + -
414D LEU* 5.4 8.5 - - + -
418D VAL* 5.1 0.7 - - - +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PHE* 2.9 45.6 + - + +
329D LYS* 3.1 13.0 + - + +
331D TYR* 1.3 77.5 - - - +
333D SER* 1.3 63.0 + - - +
335D LEU* 3.1 4.4 + - + +
336D GLU* 2.9 31.3 + - + +
350D LEU* 3.8 31.3 - - + +
351D LEU 3.2 27.8 - - - +
352D THR* 3.7 17.7 - - + -
370D SER* 5.2 0.9 - - - +
373D LEU* 4.3 7.6 - - + -
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Residues in contact with SER 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D SER* 5.6 1.8 - - - -
329D LYS 3.0 10.8 + - - -
330D ILE 2.2 29.3 + - - -
332D LEU* 1.3 74.9 - - - +
334D CYS* 1.3 64.9 + - - +
336D GLU* 3.2 8.7 + - - +
337D GLU* 3.0 22.0 + - - +
389D ARG* 3.0 30.4 + - - -
168E LEU* 4.7 16.6 - - - +
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Residues in contact with CYS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ILE* 2.9 29.1 + - - -
331D TYR* 3.1 18.4 + - + +
333D SER* 1.3 86.0 + - - +
335D LEU* 1.3 60.8 + - + +
337D GLU 3.1 2.3 + - - -
338D LEU* 2.9 25.1 + - + +
389D ARG* 4.2 20.0 - - - -
392D PRO* 4.4 20.0 - - + -
168E LEU 5.0 0.2 - - - -
169E ILE* 3.2 37.2 - - + +
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Residues in contact with LEU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D TYR* 2.9 21.9 + - + +
332D LEU* 3.1 5.6 + - - +
334D CYS* 1.3 79.2 - - + +
336D GLU* 1.3 58.7 + - - +
338D LEU* 3.7 10.1 - - + +
339D MET* 2.9 39.2 + - + +
350D LEU* 4.1 26.2 - - + -
373D LEU* 3.7 32.8 - - + -
392D PRO* 6.3 1.1 - - + -
407D ILE* 3.8 31.0 - - + -
408D GLU* 5.8 1.6 - - - +
410D PHE* 4.6 13.0 - - + -
411D LEU* 4.8 8.7 - - + -
414D LEU* 6.1 1.1 - - + -
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Residues in contact with GLU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D LEU* 2.9 22.4 + - + +
333D SER* 3.6 8.1 - - - +
335D LEU* 1.3 73.9 - - - +
337D GLU* 1.3 60.9 + - - +
339D MET* 3.4 10.1 + - - +
340D LYS* 2.9 32.4 + - - +
347D ARG* 4.0 14.7 + - - -
350D LEU* 3.2 26.3 - - + +
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D SER 3.0 12.8 + - - +
334D CYS 3.3 8.1 - - - +
336D GLU* 1.3 76.1 - - - +
338D LEU* 1.3 63.7 + - + +
340D LYS* 3.2 7.2 + - - +
341D CYS* 2.9 55.2 + - - +
343D ILE* 6.0 0.2 - - + -
164E VAL* 3.0 27.0 - - + +
165E ASN* 3.4 16.4 + - - +
168E LEU* 3.1 37.0 - - + +
169E ILE* 3.6 21.5 - - + -
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Residues in contact with LEU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D CYS* 2.9 12.0 + - + +
335D LEU* 3.3 12.5 + - + +
337D GLU* 1.3 79.1 - - + +
339D MET* 1.3 60.8 + - + +
343D ILE* 3.3 26.2 + - + -
344D ILE* 3.2 43.3 + - + +
392D PRO* 4.4 8.7 - - + -
396D HIS* 6.4 1.8 - - + -
407D ILE* 6.1 0.2 - - + -
410D PHE* 4.0 33.9 - - + -
159E PHE* 3.9 29.2 - - + -
164E VAL* 5.7 0.4 - - + -
169E ILE* 3.6 25.1 - - + -
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Residues in contact with MET 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D LEU* 2.9 21.9 + - + +
336D GLU* 3.8 15.0 - - - +
338D LEU* 1.3 77.7 - - + +
340D LYS* 1.3 60.0 + - - +
342D GLN* 2.8 25.6 + - - +
344D ILE* 4.1 12.0 - - + +
345D TYR 5.5 1.0 - - - +
346D PRO 5.6 0.4 - - - +
347D ARG* 3.0 58.5 + - + +
348D GLN* 3.3 43.1 - - + +
350D LEU* 4.1 24.5 - - + -
407D ILE* 5.5 9.0 - - + -
408D GLU* 5.9 0.4 - - - +
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Residues in contact with LYS 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D GLU 2.9 19.6 + - - +
337D GLU* 3.2 10.1 + - - +
339D MET* 1.3 77.4 - - - +
341D CYS* 1.3 67.6 + - - +
342D GLN* 3.0 13.9 + - - +
347D ARG* 3.2 14.9 + - - +
168E LEU* 5.9 4.3 - - + -
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Residues in contact with CYS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D GLU* 2.9 40.5 + - - +
338D LEU 4.4 0.2 - - - -
340D LYS* 1.3 83.4 - - - +
342D GLN* 1.3 69.1 + - - +
343D ILE* 3.0 27.5 + - + +
162E LYS* 3.4 22.1 - - - +
163E ASN 3.2 23.6 - - - -
164E VAL* 4.0 0.2 - - - -
165E ASN 4.5 0.7 - - - -
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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
------------------------------------------------------------
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