Contacts of the helix formed by residues 384 - 399 (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 384 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180F PRO* 4.9 13.7 - - - -
181F PRO* 6.1 2.5 - - - -
383F LEU* 1.3 75.3 - - - +
385F GLY* 1.3 53.0 + - - +
386F ARG* 3.7 8.6 + - - +
387F VAL* 2.7 40.0 + - - +
388F LEU* 2.3 40.3 + - - -
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Residues in contact with GLY 385 (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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170A THR* 3.9 0.2 + - - -
180F PRO* 5.1 4.8 - - - +
181F PRO 4.9 12.6 + - - -
182F GLY 5.2 5.8 - - - -
183F THR* 5.6 1.7 + - - -
330F ILE* 5.5 3.1 - - - -
384F SER* 1.3 70.8 - - - +
386F ARG* 1.3 62.8 + - - +
388F LEU* 3.3 20.1 - - - +
389F ARG* 2.9 32.0 + - - +
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Residues in contact with ARG 386 (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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170A THR* 2.8 44.1 + - + +
311A ASP* 2.5 59.4 + - - -
312A ARG* 4.7 8.1 - - - +
313A ALA* 5.3 2.2 - - - +
314A ASP* 5.6 1.8 + - - -
316A LYS* 6.6 0.4 - - - +
181F PRO* 5.5 4.9 + - - +
384F SER* 3.1 8.4 + - - +
385F GLY* 1.3 73.3 - - - +
387F VAL* 1.3 61.7 - - + +
390F LYS* 2.9 16.2 + - + +
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Residues in contact with VAL 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LYS* 5.6 8.3 - - - +
383F LEU* 3.8 22.4 - - + -
384F SER* 2.7 32.5 + - - +
386F ARG* 1.3 77.2 - - + +
388F LEU* 1.3 64.4 + - - +
390F LYS* 3.1 11.9 + - + +
391F LEU* 2.9 37.4 + - + +
394F LEU* 6.3 0.7 - - + -
421F GLN* 4.9 11.7 - - + +
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Residues in contact with LEU 388 (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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322F PRO* 4.2 22.7 - - + -
327F ILE* 4.3 25.6 - - + -
330F ILE* 3.9 31.6 - - + -
331F TYR* 4.5 8.5 - - + +
383F LEU* 3.5 35.4 - - + +
384F SER 2.3 30.1 + - - +
385F GLY* 3.3 24.7 - - - +
387F VAL* 1.3 70.9 - - - +
389F ARG* 1.3 59.6 + - - +
391F LEU* 3.0 27.2 + - + +
392F PRO* 3.3 5.7 - - - +
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Residues in contact with ARG 389 (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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167A ASN 4.9 3.1 - - - -
168A LEU* 2.6 47.6 + - - +
169A ILE* 3.4 23.9 - - - +
170A THR* 3.2 26.2 - - - +
330F ILE* 3.4 42.4 + - + +
333F SER* 2.7 30.9 + - - -
334F CYS* 4.3 6.5 - - - -
385F GLY* 2.9 19.1 + - - +
388F LEU* 1.3 72.4 - - - +
390F LYS* 1.3 60.2 + - - +
392F PRO* 3.2 14.0 - - - +
393F PHE 4.2 0.2 + - - -
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Residues in contact with LYS 390 (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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170A THR* 3.3 25.0 - - + +
313A ALA 3.2 8.3 + - - -
314A ASP* 2.9 56.4 + - - +
315A ILE* 4.4 1.0 - - - +
316A LYS 5.1 1.6 - - - +
386F ARG* 2.9 19.4 + - + +
387F VAL* 3.1 16.6 + - + +
389F ARG* 1.3 76.5 - - - +
391F LEU* 1.3 65.1 + - - +
393F PHE* 3.2 14.8 - - + +
394F LEU* 3.0 52.3 + - + +
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Residues in contact with LEU 391 (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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331F TYR* 3.9 10.5 - - + +
383F LEU* 3.6 33.7 - - + -
387F VAL* 2.9 33.0 + - + +
388F LEU* 3.0 16.4 + - - +
390F LYS* 1.3 76.3 - - - +
392F PRO* 1.3 66.6 - - + +
394F LEU* 2.8 22.1 + - + +
395F ALA 2.8 11.3 + - - -
414F LEU* 3.4 17.7 - - + +
417F ALA* 5.2 1.6 - - + -
418F VAL* 3.7 28.0 - - + +
421F GLN* 3.9 26.9 - - + -
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Residues in contact with PRO 392 (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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169A ILE* 5.5 2.7 - - + -
331F TYR* 4.6 8.3 - - + -
334F CYS* 3.7 32.5 - - + -
335F LEU* 6.0 0.2 - - + -
338F LEU* 5.0 4.9 - - + -
388F LEU 3.3 11.0 - - - +
389F ARG* 3.2 15.0 - - - +
391F LEU* 1.3 89.8 - - + +
393F PHE* 1.3 61.7 + - - +
395F ALA 3.3 0.2 + - - -
396F HIS* 2.9 22.7 + - - +
410F PHE* 3.1 34.3 - - + -
414F LEU* 4.0 16.2 - - + -
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Residues in contact with PHE 393 (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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152A TYR* 3.0 47.8 - + - -
156A THR* 3.8 15.5 - - - -
159A PHE* 3.3 40.8 - + - -
169A ILE* 4.4 10.8 - - + +
170A THR 4.0 10.5 - - - +
171A TRP* 3.5 31.9 - + + -
172A ASN 4.7 4.5 - - - -
389F ARG 4.2 0.8 + - - -
390F LYS* 3.2 22.0 + - + +
392F PRO* 1.3 80.6 - - - +
394F LEU* 1.3 68.9 + - + +
396F HIS* 3.3 6.2 + - - +
397F ALA* 2.9 26.9 + - + +
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Residues in contact with LEU 394 (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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152A TYR* 3.5 33.0 - - + -
314A ASP 4.7 0.2 - - - +
387F VAL* 6.3 0.9 - - + -
390F LYS* 3.4 47.6 - - + +
391F LEU* 2.8 18.6 + - + +
393F PHE* 1.3 75.2 - - + +
395F ALA* 1.3 64.8 + - - +
397F ALA* 2.9 7.2 + - + +
398F LEU* 2.9 30.9 + - + +
417F ALA* 5.0 6.1 - - + -
421F GLN* 4.2 24.5 - - + +
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Residues in contact with ALA 395 (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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391F LEU 2.8 5.9 + - - -
392F PRO 3.5 7.9 - - - +
394F LEU* 1.3 75.2 - - - +
396F HIS* 1.3 63.9 + - - +
398F LEU* 2.9 15.7 + - - +
399F TYR* 3.3 13.7 + - - -
400F VAL 4.1 1.4 + - - -
410F PHE* 3.6 11.2 - - + -
413F ALA* 4.0 4.8 - - + +
414F LEU* 3.4 49.1 - - + +
417F ALA* 4.2 10.2 - - - +
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Residues in contact with HIS 396 (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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155A THR* 3.2 31.7 + - + +
158A LEU* 5.6 1.6 - - + -
159A PHE* 4.0 16.4 - + + -
338F LEU* 5.9 1.3 - - + -
343F ILE* 4.3 16.8 + - + +
344F ILE* 3.9 25.4 - - + -
392F PRO 2.9 17.0 + - - +
393F PHE* 3.6 6.1 - - - +
395F ALA* 1.3 75.8 - - - +
397F ALA* 1.3 63.1 + - - +
400F VAL* 3.2 50.8 - - + +
401F GLN 3.6 4.5 + - - -
402F ALA 3.5 20.1 + - - -
403F PRO 4.4 3.6 + - - -
404F THR* 4.8 0.6 - - - -
410F PHE* 3.5 7.2 - - + -
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Residues in contact with ALA 397 (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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148A HIS 5.4 0.9 - - - +
151A ASP* 3.3 24.0 - - - +
152A TYR* 3.9 38.6 - - + +
155A THR* 4.7 12.1 - - - +
159A PHE* 6.5 0.2 - - + -
393F PHE* 2.9 16.2 + - + +
394F LEU* 2.9 16.2 + - + +
396F HIS* 1.3 78.0 - - - +
398F LEU* 1.3 63.7 + - + +
401F GLN* 3.9 4.2 + - - +
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Residues in contact with LEU 398 (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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148A HIS* 4.4 36.1 - - + +
151A ASP* 4.8 1.1 - - - -
394F LEU* 2.9 15.5 + - + +
395F ALA 2.9 4.9 + - - +
397F ALA* 1.3 82.8 - - + +
399F TYR* 1.3 94.6 - - + +
401F GLN* 3.2 24.6 + - - +
417F ALA* 4.2 24.7 - - + -
420F LYS* 5.0 21.1 - - + +
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Residues in contact with TYR 399 (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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395F ALA 3.3 3.4 + - - -
398F LEU* 1.3 107.5 - - + +
400F VAL* 1.3 68.8 + - - +
401F GLN* 4.5 3.1 - - - +
413F ALA* 3.5 47.8 - - + -
416F LEU* 3.7 34.9 + - + +
417F ALA 4.7 0.2 - - - -
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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