Contacts of the helix formed by residues 426 - 445 (chain I) 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 ASP 426 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I ASP* 5.4 0.2 + - - -
424I THR 3.3 2.8 + - - -
425I ALA* 1.3 74.2 - - - +
427I SER* 1.3 59.2 + - - +
428I LEU* 3.2 3.8 - - - -
429I LEU* 3.0 18.7 + - + +
430I LYS* 3.0 25.5 + - - +
81K ASN* 3.2 30.2 + - - +
82K VAL* 5.6 1.4 - - - +
136K LEU* 4.1 22.6 - - - +
139K ASN* 5.9 0.3 - - - +
140K TYR* 3.5 36.8 - - + +
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Residues in contact with SER 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I PHE* 3.9 19.8 - - - +
418I TYR* 4.1 2.0 - - - -
419I LEU* 3.3 28.4 - - - +
423I ASP* 5.2 0.2 + - - -
424I THR* 3.2 34.4 + - - -
425I ALA 3.0 2.1 + - - -
426I ASP* 1.3 74.3 - - - +
428I LEU* 1.3 61.4 + - - +
430I LYS* 3.2 13.6 + - - +
431I VAL* 2.9 32.9 + - - +
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Residues in contact with LEU 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I LEU* 3.7 34.1 - - + +
426I ASP* 3.2 1.3 - - - -
427I SER* 1.3 81.8 + - - +
429I LEU* 1.3 61.4 + - + +
431I VAL* 3.1 10.4 + - + +
432I ILE* 2.9 49.5 + - + +
469I PHE* 5.0 6.1 - - + -
470I ILE* 6.4 1.6 - - + -
473I TYR* 3.4 49.4 - - + +
479I SER* 6.1 0.7 - - - +
482I VAL* 5.4 1.3 - - + -
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Residues in contact with LEU 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426I ASP* 3.0 22.6 + - - +
428I LEU* 1.3 78.6 - - + +
430I LYS* 1.3 59.9 + - - +
432I ILE* 3.6 24.2 - - + +
433I HIS* 2.9 29.8 + - - +
481I ALA* 5.7 2.5 - - + -
80K PRO* 4.2 27.8 - - + +
81K ASN* 3.8 31.6 - - + +
140K TYR* 3.4 24.7 + - + +
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Residues in contact with LYS 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I ARG* 4.3 14.1 - - - +
415I PHE* 3.0 53.9 - - + -
425I ALA 4.9 2.7 - - - +
426I ASP 3.0 16.0 + - - +
427I SER* 3.4 13.9 - - - +
428I LEU 3.2 0.2 - - - -
429I LEU* 1.3 74.8 - - - +
431I VAL* 1.3 59.4 + - - +
433I HIS* 4.4 2.9 - - + -
434I TYR* 2.9 42.6 + - - +
28K LEU* 3.6 26.4 - - + +
139K ASN* 4.5 4.8 + - - +
140K TYR* 3.5 34.8 + - + +
142K ASN* 6.0 2.0 - - - +
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Residues in contact with VAL 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I TRP* 2.7 34.7 + - + +
415I PHE* 3.8 3.6 - - + +
416I LYS* 3.6 37.5 - - + +
419I LEU* 4.9 6.5 - - + -
427I SER 2.9 17.9 + - - +
428I LEU* 3.1 14.6 + - + +
430I LYS* 1.3 75.9 - - - +
432I ILE* 1.3 55.6 + - + +
435I SER* 2.4 37.5 + - - +
469I PHE* 4.7 13.0 - - + -
470I ILE* 4.2 15.0 - - + -
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Residues in contact with ILE 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I LEU* 2.9 36.1 + - + +
429I LEU* 3.6 30.3 - - + +
430I LYS 3.3 0.2 - - - -
431I VAL* 1.3 77.6 - - + +
433I HIS* 1.3 63.2 + - - +
435I SER* 3.7 5.0 - - - -
436I LYS* 3.2 48.0 + - + +
470I ILE* 5.6 3.1 - - + -
479I SER* 5.6 1.1 - - - +
481I ALA* 3.8 29.2 - - + +
482I VAL* 4.6 14.6 - - + -
485I LEU* 4.8 9.2 - - + -
80K PRO* 5.9 4.9 - - + -
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Residues in contact with HIS 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I LEU 2.9 18.3 + - - +
430I LYS* 3.7 6.5 - - - +
431I VAL 3.2 0.2 - - - -
432I ILE* 1.3 79.1 - - - +
434I TYR* 1.3 74.4 + + + +
436I LYS* 3.3 7.1 + - - +
437I VAL* 2.9 54.4 + - + +
28K LEU* 3.7 35.9 - - + +
32K TYR* 4.3 11.7 - + + -
77K MET* 4.0 16.7 - - + +
78K PRO* 3.9 33.4 - - + +
140K TYR* 4.4 9.0 - + + +
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Residues in contact with TYR 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I LEU* 5.9 2.0 - - + +
381I GLN* 5.6 4.5 - - - -
408I SER* 4.9 12.1 - - - +
411I SER* 4.7 15.7 - - - -
412I TRP* 3.5 29.2 - - + -
415I PHE* 3.6 34.0 - + - -
430I LYS* 2.9 37.9 + - + +
433I HIS* 1.3 84.5 - + - +
435I SER* 1.3 60.6 + - - +
437I VAL* 3.8 13.3 - - + +
438I ILE* 3.0 35.2 + - - +
28K LEU* 3.8 35.9 + - + +
31K ASN* 4.3 18.4 + - + -
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Residues in contact with SER 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I TRP* 2.4 45.3 + - - +
431I VAL* 2.4 14.1 + - - +
432I ILE 3.7 4.5 - - - -
434I TYR* 1.3 78.5 - - - +
436I LYS* 1.3 56.9 + - - +
438I ILE* 3.3 5.0 + - - +
439I ILE* 2.9 36.0 + - - +
466I VAL* 4.8 12.8 - - - -
470I ILE* 4.6 0.7 - - - +
485I LEU* 3.7 24.9 - - - +
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Residues in contact with LYS 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I ILE* 3.2 35.7 + - + +
433I HIS* 3.8 4.7 - - - +
435I SER* 1.3 76.9 - - - +
437I VAL* 1.3 60.2 + - + +
439I ILE* 3.8 5.9 - - - +
440I SER* 2.9 31.2 + - - -
481I ALA* 4.4 6.5 - - - -
484I GLN* 3.7 19.9 + - - +
485I LEU* 3.6 45.5 - - + +
488I ASP* 6.0 1.2 - - - +
78K PRO* 5.5 11.9 - - + -
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Residues in contact with VAL 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408I SER* 5.3 4.7 - - - +
433I HIS* 2.9 46.4 + - + +
434I TYR* 3.8 15.9 - - + +
435I SER 3.3 0.4 - - - -
436I LYS* 1.3 78.2 - - + +
438I ILE* 1.3 59.0 + - + +
440I SER* 3.3 2.7 + - - -
441I LEU* 2.9 32.5 + - + +
31K ASN 5.9 0.7 - - - +
32K TYR* 3.6 23.3 - - + -
35K ASP* 3.0 35.5 - - + +
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Residues in contact with ILE 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I PHE* 3.6 29.7 - - + -
408I SER* 3.4 48.9 - - - +
409I THR* 4.0 8.1 - - - +
412I TRP* 4.1 13.7 - - + -
434I TYR* 3.0 22.4 + - + +
435I SER* 3.8 4.7 - - - +
437I VAL* 1.3 77.2 - - + +
439I ILE* 1.3 62.0 + - + +
441I LEU* 3.1 13.4 + - + +
442I ILE* 3.0 33.7 + - + +
462I THR* 4.6 12.8 - - + -
463I ILE* 5.5 2.7 - - + -
466I VAL* 6.1 3.8 - - + -
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Residues in contact with ILE 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I SER 2.9 21.5 + - - +
436I LYS* 4.0 5.2 - - - +
438I ILE* 1.3 77.0 - - + +
440I SER* 1.3 57.9 + - - +
442I ILE* 3.1 15.8 + - + +
443I VAL* 2.9 29.5 + - + +
463I ILE* 4.5 10.5 - - + -
466I VAL* 4.4 11.9 - - + -
485I LEU* 3.8 25.8 - - + -
488I ASP* 3.1 31.2 - - - +
489I LEU* 4.2 16.8 - - + +
492I LEU* 3.7 25.1 - - + -
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Residues in contact with SER 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LYS 2.9 19.6 + - - -
437I VAL* 3.6 5.4 - - - -
438I ILE 3.3 0.2 - - - -
439I ILE* 1.3 75.6 - - - +
441I LEU* 1.3 59.5 + - - +
443I VAL* 3.2 11.0 + - - +
444I ASN* 2.9 29.6 + - - +
35K ASP* 4.0 16.2 + - - -
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Residues in contact with LEU 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I PHE* 3.5 26.0 - - + -
404I LEU* 4.0 32.8 - - + +
405I PHE* 5.3 3.8 - - + -
408I SER* 4.7 11.7 - - - +
437I VAL* 2.9 20.0 + - + +
438I ILE* 3.1 18.4 + - + +
440I SER* 1.3 74.8 - - - +
442I ILE* 1.3 61.1 + - - +
444I ASN* 3.6 8.6 + - + +
445I ASN* 3.0 32.0 + - - +
34K ASN 4.4 2.0 - - - +
35K ASP* 3.3 37.4 + - + +
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Residues in contact with ILE 442 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I PHE* 5.1 3.8 - - + -
405I PHE* 5.1 9.6 - - + -
438I ILE* 3.0 24.0 + - + +
439I ILE* 3.3 15.5 - - - +
441I LEU* 1.3 75.1 - - + +
443I VAL* 1.3 59.0 + - - +
445I ASN 3.0 5.9 + - - -
446I PHE* 3.0 46.9 + - + -
454I ASN* 3.8 23.6 - - + +
459I VAL* 5.3 9.0 - - + -
463I ILE* 4.1 24.7 - - + -
492I LEU* 3.8 22.4 - - + -
496I LEU* 5.7 4.9 - - + -
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Residues in contact with VAL 443 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I ILE* 2.9 27.2 + - + +
440I SER* 3.2 13.0 + - - +
442I ILE* 1.3 75.5 - - - +
444I ASN* 1.3 61.6 + - - +
446I PHE* 3.1 44.8 + - + +
447I HIS* 3.9 6.4 + - - -
488I ASP* 5.0 8.3 - - - +
492I LEU* 5.0 1.8 - - + -
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Residues in contact with ASN 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440I SER* 2.9 16.9 + - - +
441I LEU* 4.0 10.3 - - + +
442I ILE 3.3 0.2 - - - -
443I VAL* 1.3 77.5 - - - +
445I ASN* 1.3 65.7 + - - +
446I PHE 3.3 0.9 - - - -
447I HIS* 3.0 39.9 + - - -
450I SER* 4.0 0.9 + - - -
35K ASP 6.1 3.4 - - - -
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Residues in contact with ASN 445 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I ARG* 5.6 0.9 + - - -
401I PHE* 3.2 39.0 - - - -
441I LEU* 3.0 20.5 + - - +
442I ILE 3.0 7.9 + - - +
444I ASN* 1.3 82.8 - - - +
446I PHE* 1.3 52.8 + - - +
447I HIS 3.1 6.9 + - - -
450I SER* 2.9 37.8 + - - +
451I GLU* 3.7 1.2 - - - -
453I PHE* 3.5 15.8 - - + -
454I ASN* 2.3 37.4 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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