Contacts of the helix formed by residues 414 - 430 (chain J) 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 414 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413J ASP* 1.3 88.0 - - + +
415J SER* 1.3 73.1 + - - +
416J THR 3.4 0.9 - - - -
417J LYS* 3.3 11.6 + - - +
418J GLN* 4.3 1.7 + - - +
389N ALA 4.9 8.5 - - - +
390N ILE* 5.4 6.5 - - - +
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Residues in contact with SER 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J ASP* 4.7 1.2 + - - -
414J ALA* 1.3 80.2 - - - +
416J THR* 1.3 63.2 + - - +
417J LYS 3.0 9.7 + - - -
418J GLN* 3.3 16.0 + - - +
419J THR* 3.6 11.5 + - - -
389N ALA 5.3 5.7 + - - -
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Residues in contact with THR 416 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402J VAL* 4.4 29.2 - - + +
405J PHE* 5.1 13.1 - - + +
413J ASP* 2.9 34.0 + - - +
414J ALA 3.4 0.2 - - - -
415J SER* 1.3 79.0 - - - +
417J LYS* 1.3 60.6 + - - +
419J THR* 4.0 12.8 - - - +
420J LEU* 3.6 20.3 + - - +
389N ALA* 5.7 11.2 - - + +
390N ILE* 5.7 1.5 - - + +
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Residues in contact with LYS 417 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412J LEU* 4.2 42.3 - - + +
413J ASP* 3.2 33.8 + - - +
414J ALA 3.3 5.5 + - - +
415J SER 3.0 0.8 + - - -
416J THR* 1.3 78.9 + - - +
418J GLN* 1.3 66.6 + - - +
420J LEU* 3.5 6.2 + - - +
421J VAL* 3.3 27.5 + - + +
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Residues in contact with GLN 418 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J PHE* 6.2 1.3 - - + -
414J ALA 4.3 1.1 + - - +
415J SER* 3.3 9.6 + - - +
417J LYS* 1.3 78.1 - - - +
419J THR* 1.3 61.0 + - - +
421J VAL* 3.0 25.3 + - - +
422J ARG* 2.9 51.2 + - + +
456J ASP* 4.0 17.8 + - - +
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Residues in contact with THR 419 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J PHE* 4.7 28.2 - - + +
398J GLN* 4.7 22.4 - - + +
399J TYR* 4.1 11.8 - - + +
402J VAL* 5.6 9.2 - - + -
415J SER 3.6 12.2 + - - -
416J THR* 4.2 12.8 - - - +
417J LYS 3.3 0.6 - - - -
418J GLN* 1.3 79.8 - - - +
420J LEU* 1.3 56.1 + - - +
422J ARG* 3.7 5.8 - - - +
423J GLY* 3.1 27.4 + - - -
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Residues in contact with LEU 420 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399J TYR* 4.4 12.6 - - + -
402J VAL* 4.6 16.9 - - + +
405J PHE* 3.9 11.9 - - + +
406J ALA* 3.6 41.1 - - + +
412J LEU* 6.4 2.2 - - + -
416J THR 3.6 15.4 + - - +
417J LYS* 3.5 7.3 + - - +
418J GLN 3.3 0.4 - - - -
419J THR* 1.3 80.0 - - - +
421J VAL* 1.3 66.1 + - + +
424J GLU* 3.6 34.8 + - - +
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Residues in contact with VAL 421 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417J LYS* 3.3 22.9 - - + +
418J GLN* 3.0 25.2 + - - +
420J LEU* 1.3 84.9 - - + +
422J ARG* 1.3 59.8 + - - +
424J GLU* 4.3 1.5 + - - +
425J ARG* 3.0 44.9 + - - +
456J ASP* 3.3 30.7 - - + +
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Residues in contact with ARG 422 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J PHE* 3.9 38.6 - - + -
418J GLN* 2.9 40.4 + - + +
419J THR* 3.3 6.0 + - - +
421J VAL* 1.3 75.4 - - - +
423J GLY* 1.3 66.6 + - - +
425J ARG* 3.2 11.9 - - - +
426J LEU* 3.1 32.6 + - + +
450J GLY 4.0 11.8 + - - -
451J VAL* 3.0 24.1 + - - +
452J ASN 3.5 17.5 + - - -
453J GLY* 4.0 0.8 - - - -
456J ASP* 2.7 42.2 + - - -
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Residues in contact with GLY 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J PHE* 6.0 0.9 - - - -
396J LEU* 4.9 2.9 - - - +
399J TYR* 3.5 31.2 - - - -
419J THR 3.1 9.0 + - - -
422J ARG* 1.3 78.9 - - - +
424J GLU* 1.3 62.6 + - - +
426J LEU* 3.0 23.1 + - - +
427J THR* 3.1 18.8 + - - -
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Residues in contact with GLU 424 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399J TYR* 3.4 25.1 - - + +
420J LEU* 3.6 29.1 + - + +
421J VAL* 4.7 3.7 - - - +
422J ARG 3.3 1.2 + - - -
423J GLY* 1.3 75.9 - - - +
425J ARG* 1.3 63.8 + - + +
427J THR* 4.1 4.3 + - - -
428J GLN* 3.8 15.8 + - - +
460J LEU* 3.8 28.6 - - + +
399M GLN* 4.9 12.5 + - - +
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Residues in contact with ARG 425 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421J VAL* 3.0 51.1 + - - +
422J ARG* 3.2 10.1 - - - +
424J GLU* 1.3 77.7 + - - +
426J LEU* 1.3 60.7 + - + +
427J THR 3.4 0.4 - - - -
428J GLN* 3.4 10.2 + - - +
429J LEU* 3.1 26.0 + - - +
455J LEU* 3.1 28.2 + - - -
456J ASP* 3.8 11.9 + - - +
457J GLY* 5.2 0.8 - - - -
458J ILE 2.9 30.8 + - - +
459J GLU* 4.9 0.2 - - - +
460J LEU* 3.2 31.4 - - + +
463J ILE* 3.7 22.2 - - + +
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Residues in contact with LEU 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392J LEU* 4.1 27.8 - - + -
395J PHE* 4.8 14.1 - - + -
396J LEU* 4.2 15.0 - - + -
422J ARG* 3.1 32.5 + - + +
423J GLY* 3.0 12.7 + - - +
425J ARG* 1.3 76.9 - - + +
427J THR* 1.3 60.9 + - - +
429J LEU* 2.9 28.1 + - + +
430J LEU* 3.0 21.0 + - + +
447J ILE* 5.7 0.4 - - - +
450J GLY* 3.8 37.2 - - - +
451J VAL* 4.6 1.8 - - + +
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Residues in contact with THR 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363J ILE* 4.0 31.7 - - + +
396J LEU* 4.3 9.3 - - + +
399J TYR* 4.0 17.4 - - + -
423J GLY 3.1 15.1 + - - -
424J GLU 4.3 5.4 - - - -
425J ARG 3.4 0.2 - - - -
426J LEU* 1.3 76.7 - - - +
428J GLN* 1.3 62.0 + - - +
430J LEU* 3.4 15.6 + - + +
431J LYS* 3.4 24.6 + - - +
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Residues in contact with GLN 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424J GLU 3.8 9.3 + - - +
425J ARG* 3.4 17.1 + - - +
426J LEU 3.1 0.2 - - - -
427J THR* 1.3 78.0 - - - +
429J LEU* 1.3 63.1 + - - +
431J LYS* 3.2 54.1 + - - +
460J LEU* 4.5 20.0 + - + +
463J ILE* 4.4 25.6 - - + +
464J GLY* 5.3 10.5 - - - +
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Residues in contact with LEU 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J LYS* 2.8 40.4 + - + +
425J ARG 3.1 12.8 + - - +
426J LEU* 2.9 21.2 + - + +
428J GLN* 1.3 77.6 - - - +
430J LEU* 1.3 59.2 + - + +
431J LYS 3.2 0.7 - - - -
446J LEU* 3.1 54.5 - - + +
447J ILE* 5.2 1.6 - - - -
450J GLY* 4.5 16.2 - - - -
455J LEU* 4.6 14.6 - - + -
463J ILE* 4.8 14.1 - - + -
466J PHE* 6.3 0.7 - - + -
467J GLU* 5.6 2.9 - - + -
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Residues in contact with LEU 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J LYS* 4.1 17.0 - - + +
154J ALA* 4.0 37.7 + - + +
157J ALA* 5.5 0.7 - - + -
158J LEU* 4.2 12.1 - - + -
364J ARG 4.8 0.2 - - - -
365J PRO* 4.1 13.0 - - - +
369J VAL* 5.3 4.3 - - + -
392J LEU* 5.0 13.5 - - + -
396J LEU* 3.9 29.4 - - + -
426J LEU* 3.0 16.4 + - + +
427J THR* 3.4 18.8 + - + +
428J GLN 3.3 0.2 - - - -
429J LEU* 1.3 77.2 - - + +
431J LYS* 1.3 65.6 + - - +
432J GLN* 3.6 4.9 + - - +
447J ILE* 6.4 1.8 - - + -
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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