Contacts of the helix formed by residues 384 - 399 (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 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C PRO 4.6 2.9 - - - -
182C GLY* 3.1 28.9 - - - -
321C PRO* 5.6 0.9 - - - -
322C PRO* 4.5 2.0 - - - -
383C LEU* 1.3 77.2 - - - +
385C GLY* 1.3 52.3 + - - +
386C ARG* 3.5 3.8 + - - +
387C VAL* 2.9 32.6 + - - +
388C LEU* 2.7 33.1 + - - +
425C ARG* 4.6 8.5 - - - +
311D ASP* 3.8 3.8 + - - -
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Residues in contact with GLY 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLY 3.5 5.9 + - - -
322C PRO* 3.7 15.4 - - - +
330C ILE* 5.5 1.8 - - - -
384C SER* 1.3 72.4 - - - +
386C ARG* 1.3 61.9 + - - +
388C LEU* 3.2 17.6 - - - +
389C ARG* 2.8 29.3 + - - +
901C AGS 3.4 26.3 - - - -
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLY* 3.3 10.1 + - - -
183C THR 4.2 0.4 - - - +
384C SER* 3.0 8.0 + - - +
385C GLY* 1.3 76.1 - - - +
387C VAL* 1.3 64.3 + - - +
389C ARG* 3.4 2.5 + - - +
390C LYS* 3.0 29.8 + - + +
901C AGS 2.6 110.0 + - - +
172D ASN* 4.0 14.9 - - - +
285D ASP* 4.3 5.3 + - - -
288D LYS* 4.9 4.2 - - - +
311D ASP* 2.9 34.4 + - - +
312D ARG* 3.5 34.6 - - - +
314D ASP* 5.8 0.2 - - - +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C LEU* 5.3 9.0 - - + -
384C SER* 2.9 26.6 + - - +
386C ARG* 1.3 72.0 - - + +
388C LEU* 1.3 63.6 + - - +
390C LYS* 3.1 15.2 + - + +
391C LEU* 2.9 26.9 + - + +
421C GLN* 3.5 37.5 - - + +
425C ARG* 3.7 22.4 - - - +
311D ASP* 3.9 18.2 - - - +
313D ALA 5.6 5.6 - - - +
314D ASP* 5.8 3.1 - - - +
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C PRO* 4.3 8.7 - - + -
327C ILE* 3.5 40.4 - - + -
330C ILE* 5.2 10.5 - - + -
331C TYR* 3.7 20.8 - - + +
380C SER* 4.8 4.0 - - - -
383C LEU* 4.5 18.6 - - + +
384C SER 2.7 19.6 + - - +
385C GLY* 3.2 26.5 - - - +
386C ARG 3.0 0.2 - - - -
387C VAL* 1.3 71.4 - - + +
389C ARG* 1.3 57.1 + - + +
391C LEU* 2.5 53.9 + - + +
392C PRO* 3.1 5.5 - - - +
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASP 3.7 21.6 + - - -
138C SER* 3.7 12.4 + - - +
330C ILE* 3.7 25.2 - - + +
333C SER* 3.5 24.7 + - - -
334C CYS* 4.1 12.2 - - - +
385C GLY 2.8 17.2 + - - +
386C ARG* 4.2 2.7 - - - +
388C LEU* 1.3 72.9 - - - +
390C LYS* 1.3 62.0 + - - +
392C PRO* 3.8 7.3 - - - +
901C AGS 3.6 40.5 + - - +
167D ASN 5.1 2.5 - - - -
168D LEU* 2.1 61.5 + - - +
169D ILE* 3.7 16.9 - - - +
170D THR* 3.4 22.3 - - - +
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Residues in contact with LYS 390 (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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386C ARG* 3.0 26.0 + - + +
387C VAL* 3.1 19.7 - - + +
388C LEU 2.9 1.2 + - - -
389C ARG* 1.3 78.0 - - - +
391C LEU* 1.3 66.2 + - + +
392C PRO 3.4 0.2 - - - -
393C PHE* 3.5 4.7 + - - +
394C LEU* 3.1 35.5 + - + +
170D THR* 3.0 21.4 - - - +
171D TRP* 2.7 22.0 - - - +
172D ASN* 2.4 64.0 + - - +
314D ASP* 3.1 20.9 - - - +
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Residues in contact with LEU 391 (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* 3.2 26.0 - - - +
383C LEU* 5.3 2.0 - - + -
387C VAL* 2.9 18.1 + - + +
388C LEU* 2.5 34.9 + - + +
390C LYS* 1.3 68.7 - - + +
392C PRO* 1.3 69.2 - - + -
394C LEU* 2.8 9.3 + - + -
395C ALA* 2.8 22.1 + - - +
414C LEU* 3.6 13.0 - - + -
417C ALA* 4.4 13.9 - - + -
418C VAL* 3.6 22.2 - - + -
421C GLN* 3.7 33.0 - - + +
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Residues in contact with PRO 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TYR* 4.6 11.7 - - + -
334C CYS* 3.8 34.8 - - + -
335C LEU* 6.1 0.7 - - + -
338C LEU* 4.5 10.3 - - + -
388C LEU 3.1 23.1 - - - +
389C ARG* 3.8 8.3 - - - +
390C LYS 3.7 3.4 - - - -
391C LEU* 1.3 79.0 - - + +
393C PHE* 1.3 58.6 + - - +
395C ALA* 3.3 2.3 + - + +
396C HIS* 2.9 28.5 + - - +
410C PHE* 4.1 23.7 - - + -
414C LEU* 4.4 11.4 - - + -
169D ILE* 5.1 5.4 - - + -
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Residues in contact with PHE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 6.1 6.9 - - + +
343C ILE* 6.0 2.2 - - + -
390C LYS 3.5 4.4 + - - +
391C LEU 3.2 0.4 - - - -
392C PRO* 1.3 79.4 - - - +
394C LEU* 1.3 85.8 + - + +
396C HIS* 3.1 11.7 + - + +
397C ALA* 2.9 19.6 + - + +
152D TYR* 4.9 3.8 - + - -
155D THR* 3.6 34.6 - - + +
156D THR* 4.0 12.1 - - - -
159D PHE* 3.2 42.4 - - + -
160D SER* 5.0 0.4 - - - -
169D ILE* 3.7 27.2 - - + +
170D THR 5.1 1.3 - - - +
171D TRP* 3.9 34.1 - + + -
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Residues in contact with LEU 394 (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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390C LYS* 3.1 38.5 + - + +
391C LEU* 2.8 9.0 + - + +
393C PHE* 1.3 91.5 - - + +
395C ALA* 1.3 56.9 + - - +
397C ALA* 3.3 6.7 - - + +
398C LEU* 2.9 37.2 + - + +
152D TYR* 3.4 35.7 - - + -
171D TRP* 4.2 6.7 - - + -
314D ASP* 3.5 37.9 - - + +
315D ILE* 5.0 3.4 - - + -
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Residues in contact with ALA 395 (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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391C LEU 2.8 16.8 + - - +
392C PRO* 3.6 5.2 - - + +
394C LEU* 1.3 74.1 - - - +
396C HIS* 1.3 58.2 + - - +
397C ALA 2.9 4.3 - - - -
398C LEU* 2.7 27.4 + - - +
399C TYR* 3.0 15.4 + - + +
400C VAL* 3.4 5.5 + - - -
410C PHE* 5.5 3.4 - - + -
413C ALA* 4.7 6.9 - - + +
414C LEU* 4.5 17.5 - - + +
417C ALA* 3.9 23.8 - - + +
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Residues in contact with HIS 396 (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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338C LEU* 6.3 1.8 - - + -
343C ILE* 3.3 28.6 + - + +
344C ILE* 5.7 0.7 - - + -
392C PRO 2.9 14.8 + - - +
393C PHE* 3.3 14.3 - + + +
395C ALA* 1.3 74.6 - - - +
397C ALA* 1.3 59.4 + - - +
400C VAL* 3.1 29.8 - - + +
401C GLN* 3.8 2.1 + - - -
402C ALA 3.9 14.7 + - - +
403C PRO 4.5 1.6 + - - -
405C VAL* 4.0 23.1 - - + +
410C PHE* 4.4 11.8 - + + -
155D THR* 4.1 6.5 + - - +
159D PHE* 3.3 54.2 - + - +
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Residues in contact with ALA 397 (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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393C PHE 2.9 8.2 + - - +
394C LEU* 3.3 14.4 - - + +
395C ALA 2.9 1.0 - - - -
396C HIS* 1.3 79.8 + - - +
398C LEU* 1.3 69.5 + - + +
401C GLN* 3.9 8.8 + - - +
151D ASP* 4.0 16.7 - - - +
152D TYR* 4.5 19.5 - - + +
155D THR* 3.2 37.4 + - + +
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 2.9 27.6 + - + +
395C ALA* 2.7 13.1 + - - +
397C ALA* 1.3 77.0 - - + +
399C TYR* 1.3 84.2 + - + +
401C GLN* 3.1 22.9 + - - +
417C ALA* 5.1 8.5 - - + -
420C LYS* 4.1 32.3 - - + +
421C GLN* 5.9 4.5 - - - +
148D HIS* 4.3 31.2 - - + +
151D ASP* 5.0 3.2 - - - +
315D ILE* 6.3 7.6 - - + -
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Residues in contact with TYR 399 (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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395C ALA* 3.0 8.4 + - - +
398C LEU* 1.3 102.2 - - + +
400C VAL* 1.3 68.6 + - - +
401C GLN* 3.4 15.5 - - - +
413C ALA* 4.4 31.6 - - + -
416C LEU* 4.6 27.9 + - + -
417C ALA* 4.7 11.4 - - + -
420C LYS* 4.2 20.4 + - + +
148D HIS* 5.9 5.1 - + - -
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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