Contacts of the strand formed by residues 72 - 76 (chain Z) in PDB entry 6MGP
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 PHE 72 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C ARG* 3.8 12.3 - - - -
152C VAL* 3.5 31.9 - - + -
227C GLN* 4.1 8.3 - - - -
67Z GLN 5.2 2.5 - - - -
68Z CYS* 3.5 30.5 - - + +
69Z LYS* 3.1 21.1 + - - +
70Z GLY 3.5 8.5 + - - +
71Z VAL* 1.3 83.7 - - + +
73Z ARG* 1.3 62.7 + - - +
86Z CYS* 3.9 15.0 - - + -
87Z ASP 3.4 10.8 - - - +
99Z CYS* 3.2 24.2 - - - -
100Z SER 3.5 22.0 - - - -
101Z MET* 3.9 8.7 - - - -
102Z CYS* 3.5 24.7 - - - -
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Residues in contact with ARG 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z CYS* 3.2 14.4 - - - +
70Z GLY 5.7 0.4 - - - +
71Z VAL 4.0 0.2 + - - -
72Z PHE* 1.3 78.1 - - - +
74Z THR* 1.3 64.0 + - - +
75Z ARG 3.5 0.4 - - - -
86Z CYS* 3.2 1.0 - - - -
87Z ASP* 2.9 61.0 + - - +
88Z CYS 3.8 7.9 + - - -
89Z THR* 3.9 26.9 - - - +
90Z PRO* 3.3 28.9 - - - +
206Z GOL 4.6 6.9 + - - -
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Residues in contact with THR 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z CYS* 3.7 27.2 + - - +
73Z ARG* 1.3 75.2 - - - +
75Z ARG* 1.3 60.9 + - - +
76Z LYS 3.6 21.5 - - - +
77Z GLU* 3.7 36.7 + - + +
84Z ALA* 4.9 3.8 - - + -
85Z GLU 4.0 1.8 - - - +
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Residues in contact with ARG 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Z ARG 3.3 4.6 + - - -
74Z THR* 1.3 74.5 - - - +
76Z LYS* 1.3 63.4 + - + +
77Z GLU* 4.4 0.4 - - - -
85Z GLU* 3.0 33.7 + - - +
86Z CYS 4.8 4.7 - - - -
87Z ASP* 4.0 35.9 - - - +
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Residues in contact with LYS 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Z THR* 3.6 4.5 - - - +
75Z ARG* 1.3 82.5 - - + +
77Z GLU* 1.3 86.8 + - - +
79Z SER* 4.6 2.1 + - - +
82Z SER* 3.4 28.7 + - - -
83Z ASN 2.8 24.5 + - - -
84Z ALA* 3.2 5.5 - - - +
85Z GLU* 2.8 64.5 + - - +
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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