Contacts of the helix formed by residues 427 - 444 (chain J) in PDB entry 6GYS
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 427 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415J PHE* 3.4 30.3 + - - +
418J TYR* 3.9 5.4 - - - +
419J LEU* 3.7 11.9 - - - -
424J THR* 3.3 31.0 + - - +
425J ALA 3.2 4.8 + - - -
426J ASP* 1.3 79.6 + - - +
428J LEU* 1.3 57.9 + - - +
429J LEU 3.2 0.9 - - - -
430J LYS* 2.9 8.3 + - - +
431J VAL* 2.4 37.8 + - - +
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Residues in contact with LEU 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419J LEU* 3.6 28.8 - - + +
426J ASP 4.8 0.2 - - - +
427J SER* 1.3 73.6 - - - +
429J LEU* 1.3 59.1 + - - +
431J VAL* 4.1 10.1 - - + -
432J ILE* 2.9 52.4 + - + +
469J PHE* 4.8 2.2 - - + -
470J ILE* 4.8 4.9 - - + -
473J TYR* 3.6 40.2 - - + +
479J SER* 5.6 3.4 - - - +
482J VAL* 3.8 24.5 - - + -
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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
----------------------------------------------------------
426J ASP* 3.8 42.1 - - + +
427J SER 3.8 0.4 - - - +
428J LEU* 1.3 76.9 - - - +
430J LYS* 1.3 68.6 + - + +
432J ILE* 3.8 3.3 - - - +
433J HIS* 2.8 38.2 + - + +
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Residues in contact with LYS 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374J ARG* 4.8 6.5 - - - +
412J TRP* 4.0 1.0 - - - -
415J PHE* 3.5 57.1 - - + -
426J ASP* 3.2 18.8 + - - +
427J SER* 2.9 12.1 + - - +
429J LEU* 1.3 83.2 - - + +
431J VAL* 1.3 61.8 + - - +
433J HIS* 3.8 10.8 - - + +
434J TYR* 2.8 59.6 + - + +
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Residues in contact with VAL 431 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412J TRP* 3.2 24.2 + - + +
416J LYS* 4.1 24.7 - - + +
419J LEU* 3.7 17.7 - - + -
427J SER 2.4 31.6 + - - +
428J LEU* 3.9 9.0 - - + +
429J LEU 3.4 0.2 - - - -
430J LYS* 1.3 67.6 - - - +
432J ILE* 1.3 56.7 + - - +
435J SER* 2.5 40.4 + - - +
469J PHE* 3.8 17.7 - - + -
470J ILE* 3.8 28.3 - - + -
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Residues in contact with ILE 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428J LEU* 2.9 45.7 + - + +
429J LEU* 4.2 3.1 - - - +
431J VAL* 1.3 74.9 - - + +
433J HIS* 1.3 62.3 + - - +
435J SER* 3.8 0.5 - - - -
436J LYS* 3.1 45.9 + - + +
470J ILE* 4.8 0.7 - - + -
481J ALA* 4.3 22.7 - - + +
482J VAL* 3.9 17.5 - - + +
485J LEU* 3.7 28.5 - - + -
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Residues in contact with HIS 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429J LEU* 2.8 28.1 + - + +
430J LYS* 3.6 13.2 - - + +
431J VAL 3.2 0.2 - - - -
432J ILE* 1.3 76.9 - - - +
434J TYR* 1.3 91.0 + + - +
436J LYS* 3.0 8.0 + - - +
437J VAL* 2.8 48.3 + - + +
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Residues in contact with TYR 434 (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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377J LEU* 5.3 3.1 - - - +
381J GLN* 6.5 0.7 - - - -
408J SER* 4.6 7.0 - - - +
411J SER* 3.6 41.2 + - - -
412J TRP* 3.6 23.3 - - + -
415J PHE* 4.2 11.6 - + - -
430J LYS* 2.8 64.1 + - + +
433J HIS* 1.3 94.1 - + - +
435J SER* 1.3 61.7 + - - +
437J VAL* 3.6 18.4 - - + +
438J ILE* 2.9 33.7 + - + +
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Residues in contact with SER 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412J TRP* 3.1 18.5 + - - -
431J VAL* 2.5 28.5 + - - +
432J ILE 3.8 1.1 - - - -
434J TYR* 1.3 76.4 - - - +
436J LYS* 1.3 57.9 + - - +
438J ILE* 3.3 11.0 + - - +
439J ILE* 2.9 30.3 + - - +
463J ILE* 5.7 0.2 - - - +
466J VAL* 3.8 21.3 - - - +
485J LEU* 3.7 26.6 - - - +
489J LEU* 4.6 2.2 - - - +
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Residues in contact with LYS 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432J ILE* 3.1 28.1 + - + +
433J HIS* 3.0 6.5 + - - +
435J SER* 1.3 72.9 - - - +
437J VAL* 1.3 60.4 + - - +
439J ILE* 3.3 16.0 - - + +
440J SER* 2.9 26.3 + - - -
481J ALA 6.0 0.2 - - - -
484J GLN* 5.4 1.9 - - - +
485J LEU* 3.6 19.8 - - + +
488J ASP* 2.0 41.0 + - - +
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Residues in contact with VAL 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408J SER* 4.5 17.7 - - - +
433J HIS* 2.8 46.8 + - + +
434J TYR* 3.6 20.9 - - + +
435J SER 3.3 0.2 - - - -
436J LYS* 1.3 75.7 - - - +
438J ILE* 1.3 57.2 + - - +
440J SER* 3.2 11.1 + - - -
441J LEU* 2.9 32.2 + - + +
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Residues in contact with ILE 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405J PHE* 3.6 29.8 - - + -
408J SER* 4.7 10.8 - - - +
409J THR* 4.6 4.3 - - - +
412J TRP* 4.4 20.4 - - + -
434J TYR 2.9 21.9 + - - +
435J SER* 3.5 7.2 - - - +
437J VAL* 1.3 74.4 - - - +
439J ILE* 1.3 58.6 + - - +
441J LEU* 3.0 13.8 + - + +
442J ILE* 2.9 34.0 + - + +
462J THR* 3.8 25.1 - - + -
463J ILE* 3.7 28.9 - - + -
466J VAL* 5.2 2.7 - - + -
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Residues in contact with ILE 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435J SER 2.9 14.5 + - - +
436J LYS* 3.2 35.6 + - + +
438J ILE* 1.3 76.4 - - - +
440J SER* 1.3 56.6 + - - +
443J VAL* 2.8 54.4 + - + +
485J LEU* 4.2 0.4 - - + -
488J ASP* 3.9 21.3 - - + +
489J LEU* 3.7 28.9 - - + -
492J LEU* 3.7 21.8 - - + -
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Residues in contact with SER 440 (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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436J LYS 2.9 13.3 + - - -
437J VAL* 3.2 13.2 + - - -
439J ILE* 1.3 79.2 - - - +
441J LEU* 1.3 61.2 + - - +
442J ILE 3.4 0.3 + - - -
443J VAL* 5.2 1.1 - - - -
444J ASN* 3.3 30.8 + - - +
445J ASN* 4.9 0.5 + - - -
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Residues in contact with LEU 441 (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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401J PHE* 3.5 23.9 - - + -
404J LEU* 4.0 36.1 - - + +
405J PHE* 3.7 27.8 - - + -
408J SER* 3.7 26.7 - - - +
437J VAL* 2.9 22.1 + - + +
438J ILE* 3.0 15.2 + - + +
440J SER* 1.3 76.6 - - - +
442J ILE* 1.3 58.5 + - + +
445J ASN* 2.9 28.4 + - - +
454J ASN* 4.0 0.2 - - - +
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Residues in contact with ILE 442 (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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401J PHE* 5.8 0.2 - - + -
405J PHE* 5.5 0.2 - - + -
438J ILE* 2.9 25.0 + - + +
440J SER 3.2 0.2 - - - -
441J LEU* 1.3 81.2 - - + +
443J VAL* 1.3 61.4 + - - +
444J ASN 3.2 1.3 - - - -
445J ASN 2.9 14.0 + - - -
446J PHE* 3.3 19.7 - - + -
454J ASN* 2.7 47.8 + - - +
459J VAL* 4.5 19.1 - - + -
463J ILE* 3.7 37.0 - - + -
492J LEU* 3.7 24.0 - - + -
496J LEU* 3.9 6.1 - - + -
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Residues in contact with VAL 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439J ILE* 2.8 33.4 + - + +
440J SER* 5.2 1.3 - - - -
442J ILE* 1.3 72.2 - - - +
444J ASN* 1.3 56.7 + - + +
445J ASN 3.2 3.6 + - - -
446J PHE* 3.6 24.9 + - + -
447J HIS* 3.7 15.8 + - + +
492J LEU* 3.7 25.4 - - + -
495J ASN* 5.0 8.5 - - - +
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Residues in contact with ASN 444 (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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397J ARG* 5.1 0.9 + - - -
440J SER* 3.3 27.1 + - - +
442J ILE 3.2 0.8 - - - -
443J VAL* 1.3 77.0 - - - +
445J ASN* 1.3 70.3 + - - +
446J PHE 3.7 1.1 - - - -
447J HIS* 3.9 24.7 + - - +
450J SER* 4.0 4.7 + - - -
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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
------------------------------------------------------------
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