Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 5M64
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 GLU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE 5.2 0.5 - - - +
25A ARG* 5.8 3.8 - - - +
31A GLN* 3.9 20.7 + - + +
32A ILE 5.5 0.2 + - - -
78A HIS* 2.9 26.7 + - - -
79A ILE* 1.3 85.0 - - - +
81A LEU* 1.3 63.8 + - - +
82A PRO* 4.5 0.2 - - - +
358A ASP* 5.0 0.9 - - - +
359A VAL* 4.0 11.7 - - - +
393A SER* 3.7 12.1 + - - -
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Residues in contact with LEU 81 (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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79A ILE* 4.2 13.9 - - + +
80A GLU* 1.3 84.5 + - - +
82A PRO* 1.3 76.9 - - + +
83A VAL* 3.9 15.1 - - - +
85A CYS* 4.8 10.3 - - + -
357A MET 3.9 15.9 - - - +
358A ASP 3.3 27.4 + - - +
359A VAL 4.5 0.2 - - - +
360A LEU* 4.2 25.8 - - + -
389A VAL* 4.4 23.1 - - + -
393A SER* 4.7 4.0 - - - +
430A ILE* 5.4 10.3 - - + -
434A VAL* 5.1 5.2 - - + -
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Residues in contact with PRO 82 (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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80A GLU 4.5 0.4 - - - +
81A LEU* 1.3 91.6 - - + +
83A VAL* 1.3 72.6 + - + +
84A PRO* 4.6 2.1 - - - +
393A SER* 4.2 16.4 - - - +
396A ILE* 3.7 44.9 - - + +
397A ARG* 5.8 2.5 - - - +
400A ASN* 6.2 2.0 - - - +
427A PHE* 5.5 0.7 - - + -
430A ILE* 4.9 8.3 - - + -
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Residues in contact with VAL 83 (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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81A LEU* 3.9 18.2 - - - +
82A PRO* 1.3 90.0 - - + +
84A PRO* 1.3 74.3 - - + +
85A CYS* 3.3 4.4 + - - +
317A SER* 4.2 20.9 - - - +
318A THR* 5.1 10.8 - - + -
357A MET 4.4 0.2 - - - +
358A ASP* 5.8 0.7 - - - -
427A PHE* 3.8 43.7 - - + +
430A ILE* 5.1 12.1 - - + +
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Residues in contact with PRO 84 (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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82A PRO 4.6 1.6 - - - +
83A VAL* 1.3 86.9 - - + +
85A CYS* 1.3 62.0 + - - +
86A TYR* 4.9 0.7 - - - -
317A SER* 3.1 34.2 + - - +
318A THR* 5.0 10.3 - - + -
321A LYS* 3.8 24.0 - - + -
356A PHE* 3.9 23.6 - - + -
357A MET 3.7 7.2 - - - +
358A ASP* 3.3 23.8 - - - +
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Residues in contact with CYS 85 (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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81A LEU* 4.8 6.1 - - + -
83A VAL* 3.3 5.2 + - + +
84A PRO* 1.3 75.2 - - - +
86A TYR* 1.3 94.6 + - - +
88A PRO* 6.3 0.4 - - - -
317A SER* 5.1 0.2 - - - -
356A PHE* 3.2 12.0 - - - +
357A MET* 3.0 37.1 + - + +
430A ILE* 6.3 1.8 - - + -
431A GLN* 2.9 36.1 - - - +
434A VAL* 3.4 32.1 - - + -
435A ASN* 5.2 1.1 - - - -
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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