Contacts of the helix formed by residues 413 - 432 (chain F) in PDB entry 6C3P
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 THR 413 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F LEU* 3.6 4.9 - - - +
410F GLY 4.8 5.4 - - - +
411F GLU 4.8 3.6 - - - +
412F MET* 1.3 78.6 - - - +
414F ALA* 1.3 66.3 + - - +
415F GLY* 3.0 5.2 + - - -
416F GLN* 3.1 24.0 + - - +
417F ILE* 3.0 24.1 + - - +
497F LYS* 5.7 12.1 - - + +
1475F THR* 6.0 2.5 - - - -
1476F GLU* 4.3 25.6 - - + +
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Residues in contact with ALA 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F LEU* 3.4 10.7 - - + +
413F THR* 1.3 72.9 - - - +
415F GLY* 1.3 64.1 + - - +
417F ILE* 3.7 10.6 - - - +
418F CYS* 2.9 27.0 + - - +
1204F ALA* 6.5 1.1 - - - -
1207F VAL* 3.6 30.4 - - + +
1208F GLU* 5.2 9.2 - - - +
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Residues in contact with GLY 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F THR* 3.0 6.8 + - - -
414F ALA* 1.3 79.1 - - - +
416F GLN* 1.3 56.7 + - - +
418F CYS* 3.7 3.3 - - - +
419F ASN* 2.8 28.6 + - - +
500F ASN* 5.0 14.1 - - - -
504F ARG* 6.0 3.8 - - - -
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Residues in contact with GLN 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F GLU 2.7 30.3 + - - -
412F MET* 3.1 13.1 - - + +
413F THR* 3.1 25.3 + - - +
415F GLY* 1.3 71.5 - - - +
417F ILE* 1.3 63.4 + - + +
419F ASN* 3.7 10.0 - - + +
420F LEU* 2.9 33.3 + - + +
493F ASN* 5.3 18.2 + - + +
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Residues in contact with ILE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F ILE* 5.3 1.6 - - - +
399F ILE* 3.5 17.9 - - + +
402F LEU* 4.5 5.8 - - + -
407F LEU* 3.6 21.5 - - + -
412F MET* 3.5 37.9 - - + -
413F THR 3.0 17.8 + - - +
414F ALA* 3.7 7.2 - - - +
416F GLN* 1.3 78.4 - - + +
418F CYS* 1.3 58.5 + - - +
420F LEU* 3.0 29.4 - - + +
421F VAL* 3.9 3.6 + - - +
613F PHE* 3.5 31.4 - - + -
1207F VAL* 4.7 11.7 - - + -
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Residues in contact with CYS 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F ALA 2.9 16.5 + - - +
415F GLY* 4.0 2.7 - - - +
417F ILE* 1.3 74.6 - - - +
419F ASN* 1.3 60.7 + - - +
420F LEU 3.2 0.4 - - - -
421F VAL* 3.0 10.6 - - - +
422F ALA* 2.9 25.1 + - - +
1200F LEU* 3.7 33.2 - - - -
1203F PHE* 3.8 28.7 - - + -
1204F ALA* 4.8 6.7 - - - +
1207F VAL* 5.9 3.3 - - + +
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Residues in contact with ASN 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F GLY 2.8 19.0 + - - +
416F GLN* 3.2 11.4 + - + +
418F CYS* 1.3 74.0 - - - +
420F LEU* 1.3 60.2 + - - +
422F ALA* 4.0 6.8 - - - +
423F ILE* 2.9 48.4 + - - +
493F ASN* 4.1 10.7 + - - -
496F LEU* 3.2 33.5 - - - +
1125F SER* 5.2 8.1 + - - -
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Residues in contact with LEU 420 (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 ILE* 3.7 37.2 - - + -
416F GLN* 2.9 16.9 + - + +
417F ILE* 3.0 30.1 - - - +
419F ASN* 1.3 76.5 - - - +
421F VAL* 1.3 72.1 + - - +
424F ASP* 2.8 44.2 + - + +
609F LYS* 5.5 7.4 - - + +
610F LEU* 4.4 11.7 - - + -
613F PHE* 3.8 35.2 - - + -
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Residues in contact with VAL 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F GLN* 3.8 25.2 + - + +
395F ILE* 4.7 11.4 - - + -
417F ILE 4.2 2.0 - - - +
418F CYS* 3.0 24.0 - - - +
420F LEU* 1.3 90.7 - - + +
422F ALA* 1.3 55.4 + - - +
425F THR* 2.4 45.1 + - + -
1200F LEU* 4.8 1.3 - - + -
1203F PHE* 3.4 45.5 - - + -
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Residues in contact with ALA 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F CYS* 2.9 18.9 + - - +
419F ASN* 3.6 10.8 - - - +
420F LEU 3.1 0.4 - - - -
421F VAL* 1.3 80.4 - - - +
423F ILE* 1.3 62.0 + - + +
425F THR* 3.8 0.8 + - - -
426F ASN* 2.4 36.2 + - - -
1196F GLN* 5.3 0.9 + - - -
1200F LEU* 3.7 27.4 - - + -
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Residues in contact with ILE 423 (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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419F ASN* 2.9 31.7 + - - +
422F ALA* 1.3 87.5 - - + +
424F ASP* 1.3 66.8 + - - +
425F THR 3.1 1.1 - - - -
426F ASN* 3.2 12.2 + - + +
427F GLN* 2.9 48.7 + - + +
1125F SER 6.1 0.2 - - - +
1126F SER* 4.3 23.8 - - - +
1129F ASN* 4.5 22.4 - - - +
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Residues in contact with ASP 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F ILE* 4.4 1.9 - - - +
395F ILE* 5.0 0.2 - - - +
419F ASN 4.0 0.4 + - - -
420F LEU* 2.8 31.8 + - + +
423F ILE* 1.3 74.3 - - - +
425F THR* 1.3 63.8 + - - +
427F GLN* 3.2 5.5 + - - +
428F LEU* 2.9 37.1 + - - +
606F SER* 2.0 47.9 + - - +
609F LYS* 6.5 0.2 - - + -
610F LEU* 3.1 40.0 - - + +
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Residues in contact with THR 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F ARG* 4.4 11.4 - - - +
391F ILE* 3.6 32.5 - - + +
392F GLN* 4.3 14.9 + - + -
395F ILE* 4.9 3.4 - - + -
421F VAL* 2.4 55.3 + - + +
422F ALA 3.8 3.8 + - - -
424F ASP* 1.3 80.7 - - - +
426F ASN* 1.3 67.2 + - - +
428F LEU* 3.3 2.4 + - - +
429F MET* 2.8 30.4 + - - +
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Residues in contact with ASN 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F ARG* 5.2 5.5 + - - -
422F ALA 2.4 28.4 + - - -
423F ILE* 3.2 16.9 + - + +
425F THR* 1.3 85.8 + - - +
427F GLN* 1.3 58.7 + - + +
429F MET* 3.3 25.7 - - + +
430F TRP* 2.9 47.1 + - + -
1196F GLN* 4.3 20.5 + - - +
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Residues in contact with GLN 427 (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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423F ILE* 2.9 41.5 + - + +
424F ASP* 3.6 4.6 - - - +
426F ASN* 1.3 76.5 - - + +
428F LEU* 1.3 61.0 + - - +
430F TRP* 3.3 16.2 + - + +
431F PHE* 2.8 28.1 + - - +
489F LEU* 5.7 7.4 - - - +
599F SER* 4.3 2.9 + - - +
602F LYS* 3.4 48.2 - - + +
603F ALA* 4.8 3.1 - - - +
606F SER* 3.7 23.5 + - - +
1133F GLN* 4.7 6.1 - - - +
1134F HIS* 5.9 0.8 - - + -
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Residues in contact with LEU 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F LEU* 6.4 0.7 - - + -
387F LEU* 4.9 10.5 - - + -
391F ILE* 4.2 17.0 - - + -
424F ASP* 2.9 40.7 + - - +
425F THR* 3.8 3.8 - - - +
427F GLN* 1.3 72.6 - - - +
429F MET* 1.3 61.0 + - - +
431F PHE* 3.2 2.3 + - + +
432F PHE* 2.9 53.1 + - + -
603F ALA* 3.9 24.5 - - + +
606F SER* 4.6 1.1 - - - +
607F VAL* 3.6 23.8 - - + -
610F LEU* 3.5 18.8 - - + -
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Residues in contact with MET 429 (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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384F GLY* 4.7 22.2 - - - +
385F ILE* 4.5 6.1 - - + -
388F ARG* 3.4 38.8 - - + +
425F THR 2.8 17.7 + - - +
426F ASN* 3.3 22.4 - - - +
427F GLN 3.3 0.2 - - - -
428F LEU* 1.3 76.8 - - - +
430F TRP* 1.3 83.6 + - + +
432F PHE* 3.3 2.3 + - - +
433F PHE* 2.9 58.2 + - + -
1237F SER* 5.2 1.8 - - - -
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Residues in contact with TRP 430 (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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426F ASN* 2.9 32.4 + - + +
427F GLN* 3.3 15.2 + - + +
429F MET* 1.3 90.5 - - + +
431F PHE* 1.3 66.1 + - - +
433F PHE* 3.0 31.8 + + + +
434F LEU* 3.0 27.5 + - + +
599F SER* 3.9 8.3 - - - +
602F LYS* 5.6 1.1 - - - -
1134F HIS* 3.3 41.5 - + - -
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Residues in contact with PHE 431 (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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427F GLN 2.8 17.4 + - - +
428F LEU* 3.2 6.9 + - + +
430F TRP* 1.3 77.9 - - - +
432F PHE* 1.3 92.1 + + - +
434F LEU* 3.2 7.3 - - + -
435F CYS* 2.8 31.5 + - + -
438F LEU* 5.6 6.3 - - + -
439F TRP* 5.6 9.6 - + - -
596F VAL 5.5 0.2 - - - -
599F SER* 3.4 19.7 + - - +
600F THR* 3.6 35.2 - - + -
603F ALA* 3.4 29.4 - - + -
604F LEU* 5.5 5.4 - - + -
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Residues in contact with PHE 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TRP* 6.6 0.2 - + - -
291F LEU* 4.1 20.2 - - + -
295F PHE* 4.9 4.3 - + - -
299F LEU* 4.0 24.9 - - + -
380F ALA* 3.4 25.6 - - - +
383F THR* 3.8 10.9 + - - +
384F GLY* 4.4 10.5 - - - -
387F LEU* 3.4 32.1 - - + -
428F LEU* 2.9 41.4 + - + +
429F MET* 3.5 3.8 - - - +
431F PHE* 1.3 101.6 - + - +
433F PHE* 1.3 62.5 + - - +
435F CYS* 3.5 26.6 - - + +
439F TRP* 6.3 0.4 - + - -
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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