Contacts of the helix formed by residues 557 - 567 (chain A) in PDB entry 4DAY
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 557 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A TRP* 3.7 4.8 - - - +
551A THR* 3.5 19.2 - - - +
556A PHE* 1.3 76.3 - - - +
558A VAL* 1.3 59.9 + - - +
559A PRO* 3.4 11.9 - - - +
560A GLU* 3.0 44.8 + - - +
561A MET* 2.8 28.1 + - - +
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Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 3.8 30.3 - - - +
526A GLY* 3.3 20.0 - - - +
527A ILE* 3.2 37.5 - - + -
528A TRP* 3.6 24.9 - - + +
547A ASP* 4.7 2.0 - - - +
557A SER* 1.3 72.9 - - - +
559A PRO* 1.4 66.3 - - + +
561A MET* 3.0 8.9 + - + +
562A LYS* 3.0 39.3 + - + +
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Residues in contact with PRO 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLY* 4.2 8.3 - - - +
557A SER* 3.4 12.6 - - - +
558A VAL* 1.4 94.8 - - + +
560A GLU* 1.3 59.6 + - + +
562A LYS* 3.1 17.1 + - + -
563A GLN* 2.9 33.7 + - - +
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A THR* 5.3 1.1 - - - +
555A GLY 3.7 7.8 - - - +
556A PHE* 3.5 22.7 - - + -
557A SER* 3.0 44.0 + - - +
559A PRO* 1.3 72.9 - - + +
561A MET* 1.3 54.8 + - - +
563A GLN* 3.4 8.3 + - - +
564A SER* 2.8 36.2 + - - -
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Residues in contact with MET 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 4.4 8.1 - - - +
528A TRP* 4.0 9.2 - - + -
556A PHE* 4.3 0.8 - - - -
557A SER 2.8 14.4 + - - +
558A VAL* 3.0 13.5 - - + +
560A GLU* 1.3 75.5 - - - +
562A LYS* 1.3 95.2 + - - +
564A SER* 2.7 24.5 + - - +
565A LYS* 3.7 19.7 + - - +
571A TYR* 5.0 5.1 - - + -
574A PHE* 3.3 40.8 - - + -
1228C PHE* 3.6 32.1 - - + -
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Residues in contact with LYS 562 (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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523A SER* 4.5 8.1 + - - -
558A VAL* 3.0 40.2 + - + +
559A PRO* 3.1 16.5 + - + +
561A MET* 1.3 107.6 - - - +
563A GLN* 1.3 71.5 + - - +
565A LYS* 3.2 33.9 + - - +
566A LYS* 3.2 20.1 + - - +
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Residues in contact with GLN 563 (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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559A PRO* 2.9 38.0 + - - +
560A GLU* 4.1 7.5 + - - +
562A LYS* 1.3 87.6 - - - +
564A SER* 1.3 54.5 + - - +
565A LYS 2.7 15.7 + - - -
566A LYS* 3.2 38.9 + - + +
567A ASP* 3.7 5.9 + - - +
570A GLN* 4.8 0.9 - - - +
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Residues in contact with SER 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PHE* 3.9 13.0 - - - -
560A GLU 2.8 16.7 + - - -
561A MET* 2.7 21.8 + - - -
563A GLN* 1.3 75.5 - - - +
565A LYS* 1.3 56.4 + - - +
567A ASP 2.8 16.0 - - - +
570A GLN* 3.4 31.9 - - - -
571A TYR* 2.9 33.8 + - - +
574A PHE* 3.8 8.1 - - - +
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Residues in contact with LYS 565 (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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561A MET* 3.8 28.3 - - - +
562A LYS* 3.2 38.2 + - - +
563A GLN 2.7 3.2 + - - -
564A SER* 1.3 77.4 - - - +
566A LYS* 1.3 72.9 + - - +
567A ASP 2.8 11.0 + - - -
568A PRO* 3.8 3.6 - - - +
571A TYR* 3.9 28.7 - - + +
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Residues in contact with LYS 566 (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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562A LYS* 3.2 25.1 + - - +
563A GLN* 3.4 32.5 - - + +
565A LYS* 1.3 76.8 - - - +
567A ASP* 1.3 59.0 + - + +
568A PRO* 3.9 6.1 - - - +
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Residues in contact with ASP 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A GLN 3.7 4.0 + - - +
564A SER 2.8 28.1 - - - +
565A LYS 3.3 3.4 - - - -
566A LYS* 1.3 78.6 - - + +
568A PRO* 1.3 64.9 - - - +
569A LEU* 3.1 31.8 + - - +
570A GLN* 3.3 33.1 + - + -
571A TYR 3.3 4.0 + - - -
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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