Contacts of the helix formed by residues 369 - 391 (chain F) in PDB entry 5UHG
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 PRO 369 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.5 39.9 - - + +
361F ASP* 6.0 0.2 - - - +
367F ARG* 4.5 6.7 - - - +
368F ILE* 1.3 93.1 - - + +
370F VAL* 1.3 64.8 + - + +
371F HIS* 3.3 36.3 - - + +
372F MET* 3.2 13.1 + - + +
373F VAL* 3.2 10.7 + - - +
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Residues in contact with VAL 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F ARG* 3.5 48.9 - - - +
360F ALA* 5.4 10.3 - - + -
361F ASP* 5.2 6.7 + - - +
369F PRO* 1.3 72.7 - - + +
371F HIS* 1.3 57.8 + - - +
373F VAL* 2.9 13.6 + - + +
374F GLU* 2.9 46.1 + - + +
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Residues in contact with HIS 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 4.4 5.0 + - - -
369F PRO* 3.3 28.6 - - + +
370F VAL* 1.3 79.0 - - + +
372F MET* 1.3 92.0 + - + +
374F GLU* 3.1 13.4 + - + +
375F VAL* 2.9 36.3 + - + +
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Residues in contact with MET 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.9 25.4 - - + +
37D ARG* 6.2 0.4 - - - -
368F ILE* 4.2 20.4 - - + -
369F PRO* 3.2 22.4 + - + +
370F VAL 3.2 0.4 - - - -
371F HIS* 1.3 105.5 + - + +
373F VAL* 1.3 60.5 - - - +
375F VAL* 3.5 17.8 + - + +
376F ILE* 3.2 34.4 + - + +
409F LYS* 5.5 9.4 - - - +
413F ILE* 5.2 6.7 - - - -
416F TYR* 4.0 26.2 - - + -
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Residues in contact with VAL 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F ALA* 3.6 34.8 - - + +
364F ARG* 3.4 24.7 - - - +
368F ILE* 3.6 30.1 - - + +
369F PRO 3.2 17.0 - - - +
370F VAL* 2.9 6.7 + - - +
372F MET* 1.3 75.8 - - - +
374F GLU* 1.3 63.3 + - - +
375F VAL 3.2 0.2 + - - -
376F ILE* 3.3 4.3 + - - +
377F ASN* 2.9 43.0 + - - +
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Residues in contact with GLU 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F VAL* 2.9 34.7 + - + +
371F HIS* 3.3 14.6 - - - +
373F VAL* 1.3 77.4 - - + +
375F VAL* 1.3 61.4 + - + +
377F ASN* 3.7 7.8 + - - +
378F LYS* 3.3 26.2 + - - +
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Residues in contact with VAL 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F HIS* 2.9 24.6 + - + +
372F MET* 3.5 18.2 - - + +
373F VAL 3.1 0.2 - - - -
374F GLU* 1.3 74.5 - - + +
376F ILE* 1.3 61.0 + - - +
378F LYS* 2.8 24.3 + - - +
379F LEU* 2.8 13.2 + - + +
403F MET* 4.6 14.5 - - + +
413F ILE* 3.6 37.9 - - + -
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Residues in contact with ILE 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 5.2 7.6 - - - +
368F ILE* 4.1 22.4 - - + -
372F MET* 3.2 20.5 + - + +
373F VAL* 3.3 5.6 + - + +
375F VAL* 1.3 74.8 - - - +
377F ASN* 1.3 63.1 + - - +
379F LEU* 3.3 9.7 + - + +
380F GLY* 3.0 23.9 + - - -
413F ILE* 3.7 20.9 - - + -
416F TYR* 4.6 7.6 - - + -
417F ALA* 3.8 41.3 - - + +
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Residues in contact with ASN 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 4.9 5.3 - - - +
373F VAL* 2.9 35.5 + - - +
374F GLU* 4.0 7.4 + - - +
376F ILE* 1.3 81.4 - - - +
378F LYS* 1.3 64.0 + - - +
380F GLY* 3.7 1.6 + - - -
381F ARG* 3.2 38.0 + - - +
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Residues in contact with LYS 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374F GLU 3.3 15.4 + - - +
375F VAL* 2.8 11.5 + - - +
377F ASN* 1.3 76.5 - - - +
379F LEU* 1.3 58.5 + - - +
381F ARG* 3.2 36.6 - - + +
382F ILE* 2.9 46.3 + - + +
403F MET* 4.6 13.2 - - + -
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Residues in contact with LEU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F VAL* 2.8 12.6 + - + +
376F ILE* 3.6 11.9 - - + +
378F LYS* 1.3 78.3 - - - +
380F GLY* 1.3 56.2 + - - +
382F ILE* 4.0 2.1 - - + +
383F GLN* 3.0 31.1 + - - +
399F LEU* 4.3 23.1 - - + -
403F MET* 3.6 28.0 - - + -
410F VAL* 4.0 31.9 - - + -
413F ILE* 3.7 29.4 - - + -
414F GLN* 4.1 18.2 - - + +
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Residues in contact with GLY 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ARG* 3.2 28.2 + - - -
376F ILE 3.0 14.7 + - - -
377F ASN* 4.0 2.2 - - - -
378F LYS 3.3 0.2 - - - -
379F LEU* 1.3 75.0 - - - +
381F ARG* 1.3 58.3 + - - +
383F GLN* 3.8 11.8 - - - +
384F ARG* 3.2 19.4 + - - +
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Residues in contact with ARG 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ARG* 5.4 1.6 - - - +
377F ASN* 3.2 42.9 + - - +
378F LYS* 3.2 55.5 + - - +
380F GLY* 1.3 77.9 - - - +
382F ILE* 1.3 66.6 + - + +
383F GLN 3.2 0.2 - - - -
384F ARG* 3.2 6.5 + - - +
385F GLU* 2.9 30.3 + - + +
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Residues in contact with ILE 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F LYS* 2.9 29.2 + - + +
379F LEU* 4.3 4.7 - - + +
381F ARG* 1.3 78.8 - - + +
383F GLN* 1.3 60.8 + - - +
385F GLU* 3.4 28.1 - - - +
386F LEU* 2.8 42.4 + - + +
399F LEU* 4.2 10.8 - - + +
402F GLU* 3.7 36.8 - - + +
403F MET* 4.8 16.2 - - + -
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Residues in contact with GLN 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ARG* 5.1 7.9 + - - +
379F LEU* 3.0 23.2 + - - +
380F GLY* 3.8 12.0 - - - +
382F ILE* 1.3 78.0 - - - +
384F ARG* 1.3 52.0 - - - +
386F LEU* 3.3 2.9 + - - +
387F LEU* 2.7 51.2 + - + +
393F GLU* 4.9 11.7 - - - +
394F PRO* 4.2 16.8 - - + +
399F LEU* 3.7 25.2 - - + +
414F GLN* 4.9 7.5 + - - -
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Residues in contact with ARG 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ARG* 6.2 1.1 - - - +
419C ASN* 4.8 6.7 - - - +
421C ARG* 4.0 18.6 - - - +
380F GLY 3.2 15.7 + - - +
381F ARG* 3.2 7.7 + - - +
383F GLN* 1.3 79.2 - - - +
385F GLU* 1.3 60.1 + - - +
387F LEU* 3.5 14.7 - - + +
388F GLN* 3.3 33.2 + - - +
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Residues in contact with GLU 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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381F ARG* 2.9 20.1 + - + +
382F ILE* 3.4 29.3 - - - +
383F GLN 3.2 0.2 - - - -
384F ARG* 1.3 79.0 - - - +
386F LEU* 1.3 63.9 + - + +
387F LEU 3.2 1.1 + - - -
388F GLN* 4.1 4.0 + - - +
389F ASP* 3.7 15.8 + - - +
402F GLU* 3.8 15.3 - - - +
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Residues in contact with LEU 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F ILE* 2.8 27.8 + - + +
383F GLN 3.5 3.4 - - - +
385F GLU* 1.3 81.6 - - + +
387F LEU* 1.3 63.4 + - - +
388F GLN 3.5 0.4 - - - -
389F ASP* 3.8 19.4 - - + +
390F LEU* 3.4 34.0 + - + +
392F ARG 4.1 3.5 - - - +
394F PRO* 4.4 16.8 - - + +
398F GLU* 4.6 7.4 - - + +
399F LEU* 3.8 32.5 - - + +
402F GLU* 3.7 27.1 - - + +
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Residues in contact with LEU 387 (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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153C PHE* 3.2 31.5 - - + -
420C ILE* 3.7 28.5 - - + -
421C ARG* 5.5 6.7 - - - +
424C VAL* 6.1 1.8 - - + -
383F GLN* 2.7 23.6 + - + +
384F ARG* 3.5 20.2 - - + +
385F GLU 3.2 0.4 - - - -
386F LEU* 1.3 79.0 - - - +
388F GLN* 1.3 66.0 + - - +
389F ASP 3.2 1.1 + - - -
391F GLY 3.5 11.4 + - - -
392F ARG 3.5 20.6 + - - +
393F GLU* 3.7 19.3 - - + -
394F PRO* 3.7 17.0 - - + -
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Residues in contact with GLN 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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151C THR 5.8 0.2 - - - +
152C VAL* 4.0 4.3 - - - +
153C PHE* 3.3 40.7 + - + +
415C GLN* 3.2 39.3 + - - +
418C ILE 4.7 10.7 + - - -
419C ASN* 5.7 0.6 + - - +
420C ILE* 4.0 21.3 - - - +
384F ARG* 3.3 26.0 + - - +
385F GLU* 4.1 4.2 + - - +
387F LEU* 1.3 84.3 - - - +
389F ASP* 1.3 59.5 + - - +
391F GLY* 4.4 2.7 + - - -
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Residues in contact with ASP 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F GLU 3.7 17.4 + - - +
386F LEU* 3.8 21.3 - - + +
387F LEU 3.2 0.8 - - - -
388F GLN* 1.3 81.5 - - - +
390F LEU* 1.3 74.6 + - + +
391F GLY 3.6 0.7 - - - -
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Residues in contact with LEU 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F LEU* 3.4 23.8 + - + +
389F ASP* 1.3 95.4 - - - +
391F GLY* 1.3 64.7 + - - +
392F ARG* 3.2 36.0 + - + +
394F PRO* 4.9 6.3 - - + -
398F GLU* 3.3 39.3 - - + +
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Residues in contact with GLY 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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116C LYS* 5.6 0.9 - - - +
132C PRO* 4.3 11.3 - - - +
134C PHE* 4.6 13.1 - - - -
153C PHE* 3.5 33.5 - - - -
156C ASP* 4.6 1.0 - - - +
387F LEU 3.5 10.5 + - - -
388F GLN 4.4 1.8 + - - -
389F ASP 3.6 2.8 - - - +
390F LEU* 1.3 77.1 - - - +
392F ARG* 1.3 60.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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