Contacts of the helix formed by residues 439 - 452 (chain S) in PDB entry 3FKS
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 ALA 439 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149S GLN* 5.5 1.1 - - - -
187S ASN* 5.7 0.7 - - - +
190S ARG* 3.0 38.6 - - - +
191S TRP* 6.0 1.6 - - + -
438S LEU* 1.3 74.0 - - - +
440S THR* 1.3 58.8 + - - +
441S GLU* 3.0 34.8 - - + +
442S GLU* 2.8 30.2 + - - +
443S GLN* 3.1 12.5 + - - +
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Residues in contact with THR 440 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149S GLN* 2.7 37.5 + - - +
156S ASP* 4.8 1.9 + - - -
191S TRP* 6.0 0.4 - - - -
382S VAL* 3.6 38.2 - - + +
385S LEU* 4.0 21.9 - - + +
438S LEU 3.8 1.6 + - - -
439S ALA* 1.3 72.2 - - - +
441S GLU* 1.3 58.5 + - - +
443S GLN* 3.7 15.0 + - - +
444S VAL* 3.1 28.2 + - + +
485S ILE* 4.5 3.8 - - + +
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Residues in contact with GLU 441 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190S ARG* 5.6 1.7 + - - -
439S ALA* 3.5 21.8 - - + +
440S THR* 1.3 80.2 + - - +
442S GLU* 1.3 65.9 + - + +
444S VAL* 3.7 8.5 - - - +
445S PRO* 3.4 8.7 - - - +
482S LEU* 3.3 46.0 - - + +
485S ILE* 4.2 6.5 - - + +
486S ARG* 3.1 53.9 + - + +
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Residues in contact with GLU 442 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190S ARG* 4.4 8.7 + - - -
438S LEU* 3.4 27.0 - - + +
439S ALA* 2.8 28.6 + - + +
441S GLU* 1.3 84.7 - - + +
443S GLN* 1.3 59.5 + - - +
445S PRO* 3.1 14.6 - - - +
446S LEU* 3.4 20.5 - - - +
471S LEU* 3.5 34.1 - - + +
475S LYS* 4.5 26.3 + - + +
482S LEU* 5.1 3.4 - - + -
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Residues in contact with GLN 443 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151S GLY 3.5 11.1 + - - -
153S LYS* 3.9 27.3 - - + +
156S ASP* 3.4 27.6 + - - +
157S ALA* 5.1 0.2 - - - +
385S LEU* 3.6 29.6 - - + +
438S LEU* 3.0 27.9 + - + -
439S ALA 3.1 14.3 + - - +
440S THR* 3.5 12.4 + - - +
442S GLU* 1.3 76.7 - - - +
444S VAL* 1.3 65.8 + - - +
446S LEU* 3.1 8.8 + - - +
447S ILE* 2.9 37.1 + - + +
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Residues in contact with VAL 444 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384S ALA* 3.4 41.7 - - + +
385S LEU* 3.9 8.7 - - + +
388S VAL* 3.7 22.6 - - + +
440S THR* 3.1 19.7 + - + +
441S GLU 3.7 2.7 - - - +
443S GLN* 1.3 74.7 - - - +
445S PRO* 1.3 73.4 - - + +
448S TYR* 3.1 25.3 + - - +
485S ILE* 3.5 32.8 - - + -
491S LEU* 4.5 4.3 - - + -
499S LEU* 4.3 3.7 - - + +
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Residues in contact with PRO 445 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441S GLU 3.4 11.0 - - - +
442S GLU* 3.1 20.0 - - - +
444S VAL* 1.3 101.8 - - + +
446S LEU* 1.3 63.8 + - - +
448S TYR* 3.6 5.9 - - + +
449S ALA* 3.2 19.4 + - - +
470S PHE* 3.6 28.8 - - + -
471S LEU* 4.6 1.1 - - + -
474S LEU* 3.6 21.3 - - + -
482S LEU* 3.9 8.7 - - + -
485S ILE* 5.0 0.4 - - + -
499S LEU* 4.5 20.2 - - + -
503S THR* 5.0 1.1 + - - +
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Residues in contact with LEU 446 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 3.7 26.7 - - + -
429S LEU* 3.8 25.7 - - + +
438S LEU* 4.0 10.8 - - + -
442S GLU 3.4 18.2 - - - +
443S GLN* 3.1 8.8 + - - +
445S PRO* 1.3 77.9 - - - +
447S ILE* 1.3 67.9 + - + +
449S ALA* 2.9 22.1 + - - +
450S GLY 3.7 2.4 + - - -
466S PHE* 5.4 5.2 - - + -
467S GLU* 3.9 47.1 - - + +
470S PHE* 4.6 10.3 - - + -
471S LEU* 4.0 11.7 - - + -
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Residues in contact with ILE 447 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 4.5 18.4 - - + -
157S ALA* 4.7 13.9 - - + -
385S LEU* 4.7 9.2 - - + -
388S VAL* 3.2 42.2 - - + +
389S ALA* 3.9 7.0 - - + +
392S LEU* 4.7 9.6 - - + -
426S LEU* 5.1 1.4 - - - +
429S LEU* 4.8 11.7 - - + -
430S LEU* 5.2 4.9 - - + -
443S GLN* 2.9 38.0 + - + +
446S LEU* 1.3 79.9 - - + +
448S TYR* 1.3 63.6 + - - +
450S GLY* 3.0 12.3 + - - -
451S VAL* 3.1 21.3 + - + +
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Residues in contact with TYR 448 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388S VAL* 3.7 24.9 - - + -
444S VAL 3.1 19.1 + - - +
445S PRO 3.6 4.7 - - - +
446S LEU 3.1 0.2 - - - -
447S ILE* 1.3 79.5 - - - +
449S ALA* 1.3 63.7 + - - +
450S GLY 3.0 1.6 + - - -
452S ASN* 3.1 61.3 + - - +
454S HIS* 3.8 14.5 + + - -
496S LEU* 3.8 28.1 - - + +
499S LEU* 3.6 19.7 - - + -
500S LYS* 3.1 55.7 - - + +
503S THR* 4.1 10.8 - - - -
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Residues in contact with ALA 449 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445S PRO 3.2 7.9 + - - +
446S LEU* 2.9 14.1 + - - +
448S TYR* 1.3 79.1 - - - +
450S GLY* 1.3 56.9 + - - +
454S HIS* 2.8 36.7 + - + -
455S LEU* 3.0 34.2 + - + -
466S PHE* 4.8 8.5 - - + -
470S PHE* 5.3 1.6 - - + -
503S THR* 4.2 19.3 - - + -
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Residues in contact with GLY 450 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422S ARG* 3.6 17.5 - - - -
426S LEU* 3.6 24.2 - - - -
429S LEU* 4.5 7.5 - - - +
446S LEU 3.7 2.4 + - - -
447S ILE 3.0 8.5 + - - -
449S ALA* 1.3 77.9 - - - +
451S VAL* 1.3 64.4 + - - +
452S ASN 3.2 2.8 + - - -
453S GLY* 3.2 10.6 + - - -
455S LEU* 4.9 5.6 - - - -
456S ASP* 4.2 1.5 - - - +
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Residues in contact with VAL 451 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388S VAL 3.3 28.5 - - - +
389S ALA* 4.4 0.2 - - - -
390S GLY 4.8 1.1 - - - +
391S SER* 3.7 28.3 - - - +
392S LEU* 4.2 31.2 - - + -
422S ARG* 3.3 23.2 + - - +
426S LEU* 3.9 7.3 - - + +
447S ILE* 3.1 19.5 + - + +
450S GLY* 1.3 72.6 - - - +
452S ASN* 1.3 65.6 + - - +
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Residues in contact with ASN 452 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388S VAL* 4.4 4.9 + - - +
422S ARG* 3.1 13.8 + - - -
448S TYR* 3.1 55.6 + - - +
450S GLY 3.2 0.6 - - - -
451S VAL* 1.3 90.9 - - - +
453S GLY* 1.3 60.7 + - - +
454S HIS* 3.9 17.6 - - + +
496S LEU* 5.5 0.5 - - - +
500S LYS* 5.3 3.4 - - - -
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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
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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