Contacts of the helix formed by residues 323 - 339 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.3 18.8 + - - +
141F TYR 4.6 2.5 - - - -
142F ASP* 3.1 30.0 + - - +
322F PRO* 1.3 74.9 - - - +
324F ALA* 1.3 77.4 + - - +
325F ALA* 3.0 15.6 + - - +
326F ALA* 3.0 3.6 + - - +
327F ILE* 2.8 26.0 + - - +
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Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F SER* 1.3 78.3 + - - +
325F ALA* 1.3 55.2 + - - +
327F ILE* 3.6 6.0 - - - +
328F PHE* 2.9 29.8 + - - +
373F LEU* 3.9 12.5 - - + +
374F ASN* 5.5 6.3 - - + +
377F SER* 3.7 31.4 + - - +
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Residues in contact with ALA 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.4 23.6 - - + -
323F SER* 3.0 9.6 + - - +
324F ALA* 1.3 79.4 - - - +
326F ALA* 1.3 58.4 + - - +
328F PHE* 3.0 6.8 + - - +
329F LYS* 2.9 22.2 + - - -
353F LEU* 3.1 41.6 - - + +
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Residues in contact with ALA 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LEU* 5.7 9.0 - - + -
140F VAL* 4.0 18.8 - - - +
141F TYR* 6.2 0.9 - - + -
322F PRO* 3.5 26.9 - - + -
323F SER* 3.0 4.1 + - - +
325F ALA* 1.3 76.4 - - - +
327F ILE* 1.3 67.0 + - - +
329F LYS* 3.1 14.9 + - + +
330F ILE* 2.9 32.9 + - + +
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Residues in contact with ILE 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F PRO* 5.9 1.3 - - + -
322F PRO* 3.4 23.1 - - + +
323F SER 2.8 24.0 + - - +
324F ALA* 3.6 10.3 - - - +
326F ALA* 1.3 75.9 - - - +
328F PHE* 1.3 56.7 + - - +
330F ILE* 3.2 9.8 + - - +
331F TYR* 2.9 64.4 + - + +
376F ILE 4.4 1.6 - - - +
377F SER* 3.8 13.5 - - - +
380F SER* 4.0 28.7 - - - +
381F GLU* 5.1 2.2 - - - +
388F LEU* 4.3 18.6 - - + -
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Residues in contact with PHE 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F ALA 2.9 15.4 + - - +
325F ALA 3.0 8.7 + - - +
327F ILE* 1.3 77.8 - - - +
329F LYS* 1.3 55.4 + - - +
331F TYR* 3.2 10.4 + + + +
332F LEU* 2.8 66.2 + - + +
335F LEU* 6.1 2.0 - - + -
351F LEU 3.1 29.6 - - - -
352F THR* 3.6 8.1 - - - -
353F LEU* 3.4 23.3 - - + -
356F LEU* 4.1 8.5 - - + -
369F LEU* 4.4 28.3 - - + -
373F LEU* 3.4 39.0 - - + +
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Residues in contact with LYS 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ASP 3.6 6.3 + - - -
138F SER* 2.5 51.8 + - - +
139F LEU* 4.5 1.9 - - + +
140F VAL* 4.6 7.5 - - - +
325F ALA 2.9 8.8 + - - +
326F ALA* 3.1 13.9 + - + +
328F PHE* 1.3 76.0 - - - +
330F ILE* 1.3 60.2 + - + +
332F LEU* 3.0 17.4 + - + +
333F SER* 2.9 27.0 + - - -
352F THR* 6.5 0.2 - - - -
353F LEU* 3.6 32.8 - - + -
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Residues in contact with ILE 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F GLY 5.9 2.5 - - - +
322F PRO* 4.9 6.1 - - + -
326F ALA* 2.9 23.2 + - + +
327F ILE* 3.7 7.2 - - - +
329F LYS* 1.3 74.4 - - + +
331F TYR* 1.3 68.1 + - + +
333F SER* 2.3 27.9 + - - -
334F CYS* 3.0 11.3 + - - -
385F GLY* 5.5 2.5 - - - -
388F LEU* 3.9 35.0 - - + -
389F ARG* 3.4 53.2 - - + +
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Residues in contact with TYR 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F ILE* 2.9 40.0 + - + +
328F PHE* 3.3 11.7 - + + +
330F ILE* 1.3 79.1 - - + +
332F LEU* 1.3 58.0 + - + +
334F CYS* 3.2 7.0 + - - +
335F LEU* 2.8 44.0 + - + +
373F LEU* 3.9 21.1 - - + -
376F ILE* 3.2 46.0 + - + +
380F SER* 4.0 2.3 + - - -
383F LEU* 4.4 1.2 - - - +
388F LEU* 4.5 19.5 - - + -
391F LEU* 3.9 17.8 - - + +
392F PRO* 4.6 12.6 - - + -
414F LEU* 4.3 16.6 - - + -
418F VAL* 4.6 0.2 - - - +
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Residues in contact with LEU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F PHE* 2.8 68.1 + - + +
329F LYS* 3.0 20.4 + - + +
331F TYR* 1.3 75.4 - - - +
333F SER* 1.3 66.1 + - - +
335F LEU* 4.9 2.5 - - + -
336F GLU* 2.8 32.8 + - + +
350F LEU* 3.1 37.4 - - + +
352F THR* 3.7 26.5 - - + -
369F LEU* 5.6 0.4 - - + -
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Residues in contact with SER 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 5.0 19.8 - - - +
329F LYS 2.9 11.5 + - - -
330F ILE* 2.3 29.5 + - - -
332F LEU* 1.3 74.8 - - - +
334F CYS* 1.3 62.7 + - - +
336F GLU* 3.3 5.7 + - - +
337F GLU* 3.0 23.8 + - - +
389F ARG* 2.7 31.0 + - - -
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Residues in contact with CYS 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU 4.3 0.2 - - - -
169A ILE* 3.6 33.9 - - + -
330F ILE* 3.0 21.6 + - - -
331F TYR* 3.4 8.3 - - - +
333F SER* 1.3 84.9 + - - +
335F LEU* 1.3 59.7 + - + +
337F GLU* 3.1 4.9 + - - +
338F LEU* 2.9 35.7 + - + +
389F ARG* 4.3 12.1 - - - -
392F PRO* 3.7 36.6 - - + -
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Residues in contact with LEU 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F PHE* 6.1 1.6 - - + -
331F TYR* 2.8 34.5 + - + +
332F LEU* 4.8 4.0 - - + -
334F CYS* 1.3 74.5 - - + +
336F GLU* 1.3 57.6 + - - +
338F LEU* 3.8 14.3 - - + +
339F MET* 2.8 34.4 + - + +
344F ILE* 5.0 2.7 - - + -
350F LEU* 3.5 35.2 - - + -
369F LEU* 5.1 5.8 - - + -
392F PRO* 6.4 0.2 - - + -
407F ILE* 3.9 25.6 - - + -
410F PHE* 3.9 29.8 - - + -
411F LEU* 4.6 10.5 - - + -
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Residues in contact with GLU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F LEU* 2.8 22.9 + - + +
333F SER* 3.7 5.8 - - - +
335F LEU* 1.3 75.6 - - - +
337F GLU* 1.3 60.1 + - - +
338F LEU 3.0 1.1 - - - -
339F MET* 3.3 11.1 + - - +
340F LYS* 2.8 28.8 + - - +
349F GLN* 5.2 2.1 - - - +
350F LEU* 3.0 33.3 + - + +
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.1 16.8 - - + +
165A ASN* 2.1 58.7 + - - +
168A LEU* 4.5 18.0 - - + +
169A ILE* 3.7 24.0 - - + -
333F SER 3.0 13.1 + - - +
334F CYS 3.3 9.2 - - - +
336F GLU* 1.3 76.2 - - - +
338F LEU* 1.3 57.4 + - + +
340F LYS* 3.1 32.0 - - - +
343F ILE* 3.1 12.3 - - - +
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Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 5.2 8.5 - - + -
164A VAL* 5.1 4.5 - - + -
169A ILE* 4.7 11.4 - - + -
334F CYS* 2.9 32.1 + - + +
335F LEU* 3.8 17.5 - - + +
337F GLU* 1.3 77.4 - - + +
339F MET* 1.3 57.4 + - + +
340F LYS 2.9 7.8 + - - -
341F CYS 3.5 0.2 + - - -
343F ILE* 2.9 59.1 + - + +
344F ILE* 3.5 41.7 - - + +
392F PRO* 5.0 3.8 - - + -
396F HIS* 5.9 1.1 - - + -
410F PHE* 4.7 7.9 - - + -
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Residues in contact with MET 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F LEU* 2.8 21.6 + - + +
336F GLU* 3.3 13.4 + - - +
338F LEU* 1.3 72.6 - - + +
340F LYS* 1.3 58.9 + - - +
341F CYS 3.3 0.9 - - - -
342F GLN 4.5 0.9 - - - +
344F ILE* 3.7 20.4 - - + +
345F TYR* 6.1 0.7 - - - -
347F ARG* 2.9 52.7 + - + +
348F GLN* 3.2 43.1 - - + +
349F GLN* 4.9 2.7 - - - -
350F LEU* 4.3 12.3 - - + -
407F ILE* 3.6 33.9 - - + -
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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