Contacts of the helix formed by residues 323 - 341 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C VAL* 4.9 1.7 + - - +
141C TYR* 4.2 7.9 - - - -
142C ASP* 5.3 5.0 + - - -
321C PRO 3.7 1.2 + - - -
322C PRO* 1.3 76.8 - - - +
324C ALA* 1.3 64.7 + - - +
325C ALA* 3.7 7.1 + - - +
326C ALA* 3.1 22.7 + - - +
327C ILE* 2.9 22.7 + - - +
381C GLU* 3.5 12.1 - - - -
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C SER* 1.3 72.8 - - - +
325C ALA* 1.3 66.2 + - - +
327C ILE* 2.8 20.9 + - - +
328C PHE* 2.9 11.8 + - - +
353C LEU* 5.4 0.2 - - - -
374C ASN* 5.7 1.3 - - - +
377C SER* 3.9 7.6 - - - +
378C ARG* 4.9 26.7 - - + +
381C GLU* 3.1 29.1 + - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.8 1.1 - - - -
142C ASP* 4.2 17.0 - - - +
323C SER* 3.7 5.9 + - - +
324C ALA* 1.3 77.6 - - - +
326C ALA* 1.3 56.8 + - - +
328C PHE* 3.2 4.4 + - - +
329C LYS* 2.9 37.9 + - - +
353C LEU* 3.5 32.6 - - + +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 3.4 41.0 - - + +
322C PRO* 3.9 9.6 - - + -
323C SER* 3.1 33.2 + - - +
324C ALA 3.0 1.0 - - - -
325C ALA* 1.3 73.8 - - - +
327C ILE* 1.3 67.3 + - - +
328C PHE 3.1 0.2 + - - -
329C LYS* 3.2 2.6 + - - +
330C ILE* 2.9 31.6 + - + +
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C PRO* 4.4 7.2 - - + +
323C SER 2.9 14.8 + - - +
324C ALA* 2.8 10.6 + - - +
326C ALA* 1.3 72.2 - - - +
328C PHE* 1.3 57.2 + - - +
330C ILE* 3.3 8.2 + - - +
331C TYR* 2.9 56.3 + - + +
377C SER* 3.4 22.9 - - - +
380C SER* 3.6 12.3 - - - +
381C GLU* 3.4 43.1 - - + +
383C LEU 5.6 2.2 - - - +
388C LEU* 3.5 26.7 - - + -
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ALA 2.9 9.3 + - - +
325C ALA* 3.2 13.9 - - - +
327C ILE* 1.3 78.8 - - - +
329C LYS* 1.3 68.0 + - + +
331C TYR* 3.3 3.9 + - - +
332C LEU* 3.0 41.1 + - + +
351C LEU 3.0 23.1 - - - -
352C THR* 3.3 6.5 - - - -
353C LEU* 3.2 47.1 - - + -
356C LEU* 3.3 17.9 - - + -
370C SER* 4.0 9.0 - - - -
373C LEU* 3.6 31.9 - - + -
374C ASN* 4.3 8.7 - - - +
377C SER* 3.4 15.2 + - - +
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Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.4 27.7 - - + +
142C ASP* 2.3 46.9 + - - -
325C ALA* 2.9 21.4 + - + +
326C ALA 3.2 4.5 + - - +
328C PHE* 1.3 80.5 - - + +
330C ILE* 1.3 57.5 + - - +
332C LEU* 3.2 15.5 + - + +
333C SER* 3.0 27.4 + - - -
352C THR* 5.4 10.3 - - + -
353C LEU* 6.4 0.4 - - - -
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Residues in contact with ILE 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C SER 4.2 8.1 - - - +
140C VAL* 4.1 18.6 - - + -
322C PRO* 5.1 3.6 - - + -
326C ALA* 2.9 25.8 + - + +
327C ILE* 3.8 6.5 - - - +
328C PHE 3.1 0.2 - - - -
329C LYS* 1.3 74.8 - - - +
331C TYR* 1.3 66.4 + - + +
333C SER* 2.4 26.0 + - - -
334C CYS* 2.9 14.9 + - - -
385C GLY* 5.5 1.8 - - - +
388C LEU* 5.2 11.9 - - + -
389C ARG* 3.7 43.1 - - + +
901C AGS 3.7 32.5 - - + +
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Residues in contact with TYR 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ILE* 2.9 40.0 + - + +
328C PHE* 3.6 4.0 - - - +
330C ILE* 1.3 80.3 - - + +
332C LEU* 1.3 62.0 + - - +
334C CYS* 3.1 7.2 + - - +
335C LEU* 2.9 31.6 + - + +
373C LEU* 4.0 25.8 - - + -
376C ILE* 3.5 22.2 - - + -
377C SER* 4.0 5.8 - - - -
380C SER* 3.8 8.8 + - - -
388C LEU* 3.7 29.6 - - + +
391C LEU* 3.2 25.9 - - + +
392C PRO* 4.6 13.5 - - + -
414C LEU* 3.5 22.0 - - + -
418C VAL* 3.8 5.2 - - - +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C PHE* 3.0 50.7 + - + +
329C LYS* 3.2 12.1 + - - +
331C TYR* 1.3 75.6 - - - +
333C SER* 1.3 64.4 + - - +
335C LEU* 3.1 4.6 + - - +
336C GLU* 2.9 28.6 + - + +
350C LEU* 3.6 36.6 - - + -
351C LEU 4.4 2.9 - - - +
352C THR* 3.8 27.6 - - + +
370C SER* 5.3 0.4 - - - +
373C LEU* 3.7 24.7 - - + -
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Residues in contact with SER 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 5.6 4.3 - - - -
329C LYS 3.0 11.2 + - - -
330C ILE* 2.4 32.6 + - - -
332C LEU* 1.3 74.1 - - - +
334C CYS* 1.3 61.9 + - - +
336C GLU* 3.1 9.2 + - - +
337C GLU* 3.0 24.3 + - - +
389C ARG* 3.5 22.8 + - - -
168D LEU* 5.2 9.9 - - - +
169D ILE* 5.3 0.2 - - - -
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Residues in contact with CYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ILE* 2.9 27.7 + - - -
331C TYR* 3.1 11.6 + - - +
333C SER* 1.3 83.0 + - - +
335C LEU* 1.3 64.7 + - + +
336C GLU 3.1 0.3 + - - -
337C GLU* 3.3 2.6 + - - +
338C LEU* 2.9 29.8 + - + +
389C ARG* 4.1 19.1 - - - -
392C PRO* 3.8 34.5 - - + -
169D ILE* 3.9 26.0 - - + +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C TYR* 2.9 24.1 + - + +
332C LEU 3.4 5.6 - - - +
334C CYS* 1.3 76.5 - - + +
336C GLU* 1.3 59.5 + - - +
338C LEU* 3.3 10.9 + - + +
339C MET* 2.9 42.5 + - + +
344C ILE* 4.6 7.0 - - + -
350C LEU* 3.6 35.0 - - + -
373C LEU* 4.4 19.7 - - + -
392C PRO* 6.1 1.1 - - + -
407C ILE* 5.4 6.1 - - + -
410C PHE* 3.8 30.5 - - + -
411C LEU* 5.0 10.1 - - + -
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Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C LEU* 2.9 21.1 + - + +
333C SER* 3.5 9.0 - - - +
334C CYS 3.1 0.2 - - - -
335C LEU* 1.3 74.1 - - - +
337C GLU* 1.3 67.0 + - - +
339C MET* 3.3 14.0 + - - +
340C LYS* 2.9 24.5 + - - +
348C GLN 4.8 6.1 - - - +
349C GLN* 5.8 0.7 + - - -
350C LEU* 2.8 35.1 + - + +
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C SER 3.0 9.1 + - - +
334C CYS 3.7 0.2 - - - +
336C GLU* 1.3 75.6 - - - +
338C LEU* 1.3 63.2 + - - +
340C LYS* 3.2 17.6 + - - +
341C CYS* 2.9 26.7 + - - +
164D VAL* 3.1 24.3 - - + +
165D ASN* 2.2 44.7 + - - +
168D LEU* 3.0 28.9 - - + +
169D ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C CYS 2.9 25.7 + - - +
335C LEU* 3.4 14.4 - - + +
336C GLU 3.1 0.2 - - - -
337C GLU* 1.3 77.9 - - + +
339C MET* 1.3 51.4 + - - +
341C CYS* 2.8 9.6 + - - -
342C GLN 2.7 31.0 + - - -
343C ILE* 3.3 35.7 + - + -
344C ILE* 4.1 21.5 - - + +
392C PRO* 4.5 12.6 - - + -
393C PHE* 6.1 7.9 - - + +
396C HIS* 6.3 1.8 - - + -
410C PHE* 4.0 27.1 - - + -
164D VAL* 5.7 4.0 - - + -
169D ILE* 5.2 11.9 - - + -
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Residues in contact with MET 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C LEU* 2.9 34.0 + - + +
336C GLU* 4.0 15.3 - - - +
338C LEU* 1.3 73.0 - - - +
340C LYS* 1.3 60.8 + - - +
342C GLN* 3.3 9.0 + - - -
344C ILE* 4.1 27.6 - - + +
345C TYR 5.7 0.2 - - - +
346C PRO 4.3 5.2 - - - +
347C ARG* 3.5 43.8 + - + +
348C GLN* 3.0 56.8 - - + +
350C LEU* 5.4 7.9 - - + -
407C ILE* 4.7 16.2 - - + -
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Residues in contact with LYS 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C GLU 2.9 17.6 + - - +
337C GLU* 3.5 17.3 - - - +
338C LEU 3.0 0.2 - - - -
339C MET* 1.3 79.0 - - - +
341C CYS* 1.3 63.9 + - - +
342C GLN* 3.3 8.9 + - - +
347C ARG* 4.7 6.8 + - - +
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Residues in contact with CYS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C GLU* 2.9 21.8 + - - +
338C LEU 2.8 5.2 + - - +
340C LYS* 1.3 82.3 - - - +
342C GLN* 1.3 60.6 + - - +
343C ILE* 2.8 26.6 + - + +
162D LYS* 4.0 20.7 - - + +
163D ASN 3.8 8.3 - - - -
164D VAL* 3.5 45.3 - - + -
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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
------------------------------------------------------------
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