Contacts of the helix formed by residues 454 - 465 (chain A) in PDB entry 1Y8B
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 LEU 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLU* 5.2 1.5 + - - -
452A GLY 2.4 13.4 + - - -
453A PHE* 1.3 79.0 - - - +
455A ASP* 1.3 51.7 + - - +
456A ARG* 2.5 16.4 + - + -
457A THR* 2.5 67.6 + - + +
458A GLY 3.6 1.6 + - - -
481A TRP* 4.7 4.9 - - + -
482A ILE* 5.2 10.1 - - + -
485A TYR* 4.5 15.0 - - + -
506A LYS* 3.8 29.2 - - + +
507A GLY 3.3 14.8 - - - +
508A MET* 4.6 19.3 - - + -
509A TRP* 6.1 1.3 - - + -
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 3.0 21.9 - - - +
273A ASP* 2.6 48.8 - - - +
425A MET* 3.5 8.0 - - - +
427A GLU 3.7 16.6 + - - +
428A GLU* 3.5 13.4 - - + +
452A GLY 3.6 3.0 + - - +
453A PHE* 3.1 23.3 - - - -
454A LEU* 1.3 77.0 - - - +
456A ARG* 1.3 60.4 + - - +
457A THR 3.1 0.4 - - - -
458A GLY* 3.0 13.5 + - - +
459A ASP* 3.2 11.1 + - - +
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ASP* 4.8 6.7 + - - +
427A GLU 4.5 0.6 + - - -
428A GLU* 3.7 13.2 - - - +
429A ARG* 3.2 54.1 - - + +
432A SER* 3.1 31.6 + - - -
433A LEU* 4.9 2.4 - - - +
454A LEU* 2.5 16.5 + - + +
455A ASP* 1.3 76.3 - - - +
457A THR* 1.3 56.3 + - - +
460A GLU* 2.8 41.4 + - + +
481A TRP* 4.0 25.6 - - + +
485A TYR* 2.7 55.0 - - + +
576A LEU* 4.3 20.8 + - - +
577A LEU* 6.0 0.2 - - - +
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Residues in contact with THR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU* 2.5 54.9 + - + +
456A ARG* 1.3 73.6 - - - +
458A GLY* 1.3 56.4 + - - -
460A GLU* 4.8 0.9 - - - -
461A MET* 2.8 55.6 - - + +
479A THR* 6.0 6.3 - - + -
481A TRP* 3.8 18.5 - - + -
482A ILE* 5.2 1.0 - - + +
509A TRP* 5.2 13.9 - - + -
580A PRO* 5.9 1.1 - - + -
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU 3.6 2.8 + - - -
455A ASP* 3.0 8.8 + - - +
457A THR* 1.3 81.5 - - - +
459A ASP* 1.3 60.2 + - - +
461A MET* 4.2 1.0 - - - +
462A HIS* 3.5 17.8 + - - +
465A MET* 6.1 0.3 - - - +
637A ILE* 5.4 9.4 - - - -
640A GLN* 5.4 10.6 + - - -
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Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 2.7 35.6 + - - +
428A GLU* 3.4 28.2 - - + +
429A ARG* 4.3 10.7 - - - +
430A ARG* 3.4 18.0 + - - -
455A ASP 3.2 10.3 + - - +
458A GLY* 1.3 75.0 - - - +
460A GLU* 1.3 74.8 + - - +
461A MET 3.0 1.1 - - - -
462A HIS* 2.6 26.3 + - - +
463A SER* 3.5 5.0 + - - -
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.1 5.0 - - - +
68A HIS* 5.3 3.3 - - - -
429A ARG* 2.5 62.9 + - + +
456A ARG* 2.8 31.0 + - + +
457A THR* 4.8 1.6 - - - -
459A ASP* 1.3 85.6 + - - +
461A MET* 1.3 62.4 + - + +
463A SER* 3.3 18.3 + - - -
464A VAL* 3.3 19.6 + - + +
481A TRP* 5.4 10.3 - - + -
578A THR 5.8 2.7 - - - +
579A ILE* 6.2 3.6 - - + -
580A PRO* 5.5 7.9 - - + -
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Residues in contact with MET 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A THR* 2.8 51.9 + - + +
458A GLY 4.2 2.2 - - - +
459A ASP 2.8 3.6 + - - -
460A GLU* 1.3 72.7 - - + +
462A HIS* 1.3 58.4 + - - +
463A SER 2.6 6.0 + - - -
464A VAL* 2.8 9.8 + - + +
465A MET* 2.4 69.1 + - + +
481A TRP* 6.2 0.2 - - + -
580A PRO* 4.6 31.6 - - + +
581A VAL* 5.9 0.2 - - - -
582A ALA 5.9 2.0 - - - +
583A GLU* 5.4 9.0 - - + -
641A HIS* 6.3 1.1 - - + -
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Residues in contact with HIS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.9 20.6 - - - +
65A ASP* 5.3 2.3 - - - +
458A GLY 3.5 13.2 + - - +
459A ASP* 2.6 22.5 + - - +
461A MET* 1.3 72.8 - - - +
463A SER* 1.3 58.0 + - - +
465A MET* 4.0 17.9 + - - +
466A GLU* 5.0 2.1 + - - +
644A ASN* 5.4 4.2 + - - -
706A GLY* 5.5 13.0 - - - -
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.6 24.9 + - - +
64A LEU* 5.3 6.9 - - - +
65A ASP* 5.2 20.8 - - - +
68A HIS* 4.2 25.4 + - - +
459A ASP* 3.5 3.7 + - - -
460A GLU* 3.3 16.4 + - - -
461A MET 2.6 4.8 + - - -
462A HIS* 1.3 78.0 - - - +
464A VAL* 1.3 59.9 + - - +
465A MET 3.2 4.0 + - - -
466A GLU 4.6 0.5 + - - -
467A ALA* 4.2 13.3 + - - +
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS* 3.4 30.3 - - + +
81A TYR* 4.2 0.7 - - - +
460A GLU* 3.4 22.9 - - + +
461A MET* 2.8 14.3 + - + +
463A SER* 1.3 72.2 - - - +
465A MET* 1.3 58.8 + - - +
466A GLU 3.7 0.4 - - - -
467A ALA* 4.2 10.3 - - + -
579A ILE* 3.6 44.9 - - + -
580A PRO* 4.3 15.7 - - + -
581A VAL* 3.0 27.4 - - + +
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Residues in contact with MET 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A GLY 6.1 0.4 - - - +
461A MET* 2.4 61.6 + - + +
462A HIS* 4.0 13.7 - - - +
463A SER 3.2 1.8 - - - -
464A VAL* 1.3 74.0 - - - +
466A GLU* 1.3 65.8 + - + +
467A ALA 3.4 1.5 + - - -
581A VAL* 3.9 10.7 - - - +
583A GLU* 5.0 19.0 - - + +
641A HIS* 4.1 14.6 - - + -
644A ASN* 3.4 52.3 - - + +
645A TRP* 5.6 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
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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