Contacts of the helix formed by residues 526 - 534 (chain E) 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 ASN 526 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510E PRO 4.1 6.6 - - - +
511E ILE* 4.3 13.8 - - + +
521E ASN 4.7 0.2 + - - -
522E LYS 5.6 3.0 - - - +
523E ILE* 3.3 17.3 + - - +
524E TYR* 2.9 16.5 - - - +
525E LYS* 1.3 74.5 - - - +
527E LYS* 1.3 72.3 + - - +
528E THR* 3.0 27.7 + - - -
529E ASN* 3.6 16.5 + - - +
530E PHE* 3.3 10.6 + - - +
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Residues in contact with LYS 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E SER* 3.3 22.4 - - - +
509E SER* 2.6 33.6 + - - +
510E PRO 3.3 13.0 + - - +
511E ILE 2.2 44.9 + - - +
512E LEU* 3.7 18.2 - - + -
525E LYS 3.4 0.8 + - - -
526E ASN* 1.3 77.2 + - - +
528E THR* 1.3 58.9 + - - +
530E PHE* 3.3 8.9 - - - +
531E TYR* 2.8 55.3 + - + +
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Residues in contact with THR 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E ASN* 3.0 19.0 + - - -
527E LYS* 1.3 76.6 - - - +
529E ASN* 1.3 64.4 + - - +
531E TYR* 2.9 11.9 + - + +
532E SER* 2.8 25.6 + - - -
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Residues in contact with ASN 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E THR* 5.9 3.3 - - - +
523E ILE* 2.7 46.4 + - - +
524E TYR* 3.2 27.1 - - + -
526E ASN* 3.6 17.7 + - - +
528E THR* 1.3 79.2 - - - +
530E PHE* 1.3 60.9 + - - +
532E SER* 2.4 27.8 + - - +
533E LEU 3.3 3.1 + - - -
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Residues in contact with PHE 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E LEU* 5.4 7.9 - - + -
190E LEU* 3.6 40.6 - - + +
277E CYS* 6.0 1.1 - - - -
279E PHE* 4.9 2.2 - + - -
478E PHE* 3.5 43.1 - + - -
512E LEU* 3.6 25.4 - - + -
514E PHE* 4.3 13.9 - + - -
516E ILE* 5.9 0.9 - - + -
524E TYR* 3.7 12.2 - - + +
526E ASN 3.3 15.3 + - - +
527E LYS 3.3 8.5 - - - +
528E THR 3.1 0.2 - - - -
529E ASN* 1.3 80.7 - - - +
531E TYR* 1.3 75.4 + + - +
533E LEU* 3.3 37.1 - - + +
534E LEU* 4.0 4.2 + - + +
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Residues in contact with TYR 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477E LYS* 4.7 8.0 + - - -
478E PHE* 4.2 19.9 - + - -
512E LEU* 6.0 0.8 - - + +
527E LYS* 2.8 38.9 + - + +
528E THR* 2.9 12.3 + - + +
530E PHE* 1.3 99.5 - + - +
532E SER* 1.3 60.9 + - - +
533E LEU 3.1 1.6 - - - -
534E LEU* 3.0 41.6 + - + +
538E PRO* 3.5 42.8 - - + +
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Residues in contact with SER 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E THR* 6.1 1.4 - - - +
187E LYS* 4.4 7.5 - - - -
524E TYR* 4.3 5.5 + - - -
528E THR 2.8 11.0 + - - -
529E ASN* 2.4 34.6 + - - +
531E TYR* 1.3 74.7 - - - +
533E LEU* 1.3 63.1 + - - +
534E LEU 3.4 7.5 - - - +
535E ILE* 5.1 0.7 - - - +
199L HIS* 4.5 13.7 + - - -
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Residues in contact with LEU 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E PRO* 5.5 2.7 - - + -
186E LEU* 4.2 19.1 - - + -
187E LYS* 3.7 39.0 - - + +
190E LEU* 3.8 17.9 - - + -
191E ASN* 2.6 31.5 + - - +
524E TYR* 3.5 32.3 - - + +
529E ASN 3.4 7.9 - - - +
530E PHE* 3.3 40.4 - - + +
532E SER* 1.3 79.7 + - - +
534E LEU* 1.3 59.2 + - - +
535E ILE* 3.7 4.3 + - - +
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Residues in contact with LEU 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E LEU* 4.0 24.5 - - + +
191E ASN* 3.3 15.7 - - - +
194E ASN* 5.9 0.9 - - + +
478E PHE* 5.7 8.1 - - + +
479E PHE* 3.7 33.0 - - + -
530E PHE* 4.3 5.2 - - + +
531E TYR* 3.0 38.5 + - + +
532E SER* 3.4 7.4 - - - +
533E LEU* 1.3 77.8 - - - +
535E ILE* 1.3 61.6 + - - +
536E GLU 4.5 6.7 - - - +
537E ARG 4.0 7.2 - - - +
538E PRO* 3.9 33.3 - - + +
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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