Contacts of the helix formed by residues 556 - 564 (chain A) in PDB entry 5DO7
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 PRO 556 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ARG* 3.8 2.0 - - - +
555A MET* 1.3 91.4 - - + +
557A ILE* 1.3 76.6 + - + +
558A PRO* 3.1 12.2 - - + +
559A PHE* 3.4 20.8 + - + +
560A LYS 3.7 1.7 + - - -
433B PHE* 3.4 24.7 - - + +
434B LEU 3.8 14.8 - - - +
436B PHE* 4.6 6.5 - - + -
441B ILE* 3.5 28.8 - - + -
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Residues in contact with ILE 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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555A MET 3.6 2.4 + - - -
556A PRO* 1.3 73.8 - - + +
558A PRO* 1.3 74.5 - - + +
560A LYS* 2.8 36.0 + - - +
561A ILE* 3.5 6.2 + - + +
524C VAL* 3.9 27.5 - - + +
529C ILE* 4.3 27.6 - - + -
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Residues in contact with PRO 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PRO* 3.1 16.6 - - + +
557A ILE* 1.3 94.1 - - + +
559A PHE* 1.3 83.8 + - + +
561A ILE* 2.8 29.3 + - + +
562A ILE* 3.1 18.2 + - + +
433B PHE* 5.5 9.0 - - + -
533C VAL* 6.4 1.8 - - + -
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Residues in contact with PHE 559 (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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544A VAL* 4.1 17.8 - - + +
555A MET* 3.4 19.9 - - + +
556A PRO* 3.9 16.4 - - + +
557A ILE 3.4 0.2 - - - -
558A PRO* 1.3 86.4 - - + +
560A LYS* 1.3 65.8 + - - +
562A ILE* 2.8 17.5 + - + +
563A SER* 2.8 22.9 + - - -
430B THR* 3.9 24.2 - - + -
433B PHE* 3.3 26.5 - + + -
434B LEU* 3.1 50.9 - - + -
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Residues in contact with LYS 560 (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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552A ILE* 4.2 14.6 - - + +
553A GLN* 3.6 28.4 + - - +
555A MET* 3.5 28.8 + - + +
556A PRO 3.7 1.2 + - - -
557A ILE* 2.8 22.6 + - - +
559A PHE* 1.3 78.2 - - - +
561A ILE* 1.3 58.5 + - + +
563A SER* 2.3 29.5 + - - +
564A TYR* 3.2 23.8 - - + +
523C ILE* 4.2 24.3 + - + +
524C VAL* 6.2 1.7 - - + +
525C GLN* 5.8 2.4 + - - -
648C LEU* 5.5 6.6 - - + +
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Residues in contact with ILE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ILE* 4.3 3.1 - - + +
558A PRO* 2.8 26.8 + - + +
560A LYS* 1.3 68.8 - - - +
562A ILE* 1.3 79.7 + - + +
564A TYR* 3.1 22.6 + - - +
565A PHE* 3.5 27.7 - - + -
520C LEU* 4.3 31.2 - - + -
523C ILE* 4.4 13.2 - - + +
524C VAL* 3.7 31.9 - - + -
529C ILE* 6.4 0.4 - - + -
533C VAL* 5.2 12.1 - - + -
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Residues in contact with ILE 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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544A VAL* 4.6 17.3 - - + -
558A PRO* 3.4 19.3 - - + +
559A PHE* 2.8 27.3 + - + +
561A ILE* 1.3 79.8 - - + +
563A SER* 1.3 69.2 + - - +
565A PHE* 2.5 32.2 + - + +
566A THR* 3.7 9.9 + - + -
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Residues in contact with SER 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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544A VAL* 3.6 27.1 - - - +
545A GLY* 4.0 7.4 - - - -
552A ILE* 3.3 29.0 - - - +
555A MET* 4.9 0.4 - - - -
559A PHE 2.8 14.2 + - - -
560A LYS* 2.3 28.2 + - - -
562A ILE* 1.3 71.7 - - - +
564A TYR* 1.3 54.8 + - - -
565A PHE 2.8 10.6 + - - -
566A THR* 2.4 34.5 + - - +
569A LYS* 3.8 6.6 - - - +
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Residues in contact with TYR 564 (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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552A ILE* 5.1 2.2 - - + -
560A LYS* 3.2 34.5 - - + +
561A ILE 3.1 7.1 + - - +
562A ILE 2.8 2.8 + - - -
563A SER* 1.3 80.6 + - - +
565A PHE* 1.3 65.4 + - + +
566A THR 3.4 0.4 - - - -
569A LYS* 3.6 25.0 + - - -
570A TYR* 2.5 39.8 + - - +
630A PHE* 5.5 0.5 - - - -
523C ILE* 3.4 43.8 - - + +
637C LEU* 4.7 5.6 - - + +
641C VAL* 3.7 22.7 + - + +
644C ILE* 3.6 30.3 - - + +
648C LEU* 3.0 34.0 - - - +
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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