Contacts of the helix formed by residues 550 - 557 (chain A) in PDB entry 5YD6
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 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A PRO* 1.3 77.9 - - - +
551A TYR* 1.3 63.0 + - + +
553A SER* 2.6 28.3 + - - -
554A LYS* 3.6 29.7 + - - +
404B GLN* 5.2 11.0 + - - +
585B PRO* 3.6 35.6 - - + +
586B ALA* 5.1 1.2 - - - +
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Residues in contact with TYR 551 (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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496A MET* 2.7 45.9 + - + -
497A ASN 3.7 7.4 + - - -
498A ILE* 3.6 16.1 - - + +
499A ASP* 5.9 2.2 - - - -
502A ALA* 5.9 2.5 - - + -
539A VAL* 4.4 18.2 - - + -
549A PRO 5.8 0.9 - - - -
550A ASN* 1.3 79.8 - - - +
552A LEU* 1.3 56.4 + - - +
554A LYS* 3.4 13.8 + - + +
555A LEU* 2.9 64.2 + - + +
360C PRO* 5.2 12.1 - - + -
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Residues in contact with LEU 552 (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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532A VAL* 5.5 2.0 - - + +
535A LEU* 4.3 20.6 - - + -
536A LYS* 3.6 44.6 - - + -
539A VAL* 4.8 19.9 - - + +
549A PRO* 3.5 20.7 + - + +
550A ASN 3.2 0.2 - - - -
551A TYR* 1.3 76.3 - - - +
553A SER* 1.3 58.7 - - - +
555A LEU* 3.2 11.4 + - + +
556A LEU* 2.8 52.1 + - + +
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Residues in contact with SER 553 (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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549A PRO 4.0 3.6 + - - -
550A ASN* 2.6 25.4 + - - -
552A LEU* 1.3 77.3 - - - +
554A LYS* 1.3 54.2 + - - +
556A LEU* 3.4 8.1 + - - +
557A GLY* 2.7 31.7 + - - -
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Residues in contact with LYS 554 (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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496A MET* 3.6 23.7 - - + +
550A ASN* 3.6 26.9 + - - +
551A TYR* 3.4 16.5 + - + +
552A LEU 3.4 0.4 - - - -
553A SER* 1.3 79.3 + - - +
555A LEU* 1.3 63.2 + - - +
557A GLY* 3.5 7.9 + - - +
558A LYS* 3.6 15.2 + - - +
404B GLN* 5.9 1.0 + - - -
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Residues in contact with LEU 555 (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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496A MET* 4.0 8.3 - - + -
498A ILE* 3.6 44.6 - - + -
502A ALA* 4.8 2.9 - - + -
506A ILE* 3.6 27.5 - - + +
535A LEU* 4.2 16.8 - - + -
539A VAL* 3.8 20.4 - - + -
551A TYR* 2.9 44.3 + - + +
552A LEU* 3.2 11.0 + - - +
554A LYS* 1.3 71.5 - - - +
556A LEU* 1.3 62.7 + - - +
557A GLY 3.1 3.4 - - - -
558A LYS* 3.1 23.1 + - - +
559A LEU 4.3 0.7 + - - -
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Residues in contact with LEU 556 (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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506A ILE* 4.4 2.2 - - + -
509A LEU* 3.8 29.6 - - + -
532A VAL* 5.3 13.7 - - + -
535A LEU* 4.2 12.1 - - + -
536A LYS* 6.4 0.2 - - - -
552A LEU* 2.8 40.0 + - + +
553A SER* 3.9 6.1 - - - +
555A LEU* 1.3 71.9 - - - +
557A GLY* 1.3 59.3 + - - +
558A LYS 3.2 0.4 - - - -
559A LEU* 3.2 34.3 + - + +
560A PRO* 3.3 10.2 - - - +
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Residues in contact with GLY 557 (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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553A SER 2.7 16.1 + - - -
554A LYS* 3.8 7.9 - - - -
555A LEU 3.1 1.0 - - - -
556A LEU* 1.3 76.1 - - - +
558A LYS* 1.3 62.6 + - - +
559A LEU 3.2 0.9 - - - -
560A PRO* 3.4 14.4 - - - +
561A GLU* 3.4 22.5 - - - +
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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