Contacts of the strand formed by residues 92 - 98 (chain C) in PDB entry 5DG4
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 VAL 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C TRP* 3.5 4.8 - - - -
89C GLU* 2.9 42.0 + - + +
90C GLY 3.3 0.2 - - - -
91C ASP* 1.3 88.7 - - - +
93C LEU* 1.3 63.5 + - - +
94C VAL* 3.6 13.3 + - + +
107C LYS* 3.8 32.5 - - + -
108C GLN 3.8 7.6 - - - +
109C TRP* 4.1 23.6 - - + -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLN* 3.6 20.4 - - - +
49C PHE* 3.9 20.0 - - + -
64C PHE* 4.1 4.5 - - + -
66C VAL* 4.1 11.9 - - + -
86C VAL* 3.5 26.9 - - + -
87C THR 3.6 7.0 - - - +
88C TRP* 3.6 36.8 - - + -
92C VAL* 1.3 69.5 - - - +
94C VAL* 1.3 58.3 + - - +
106C TRP* 3.7 26.1 - - + -
107C LYS* 3.2 5.0 - - - -
108C GLN* 2.8 48.6 + - - +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU 3.5 1.9 - - - +
86C VAL* 3.2 5.2 - - - -
87C THR* 2.8 49.3 + - - +
89C GLU* 3.8 35.0 - - + +
92C VAL* 3.7 26.5 - - + +
93C LEU* 1.3 78.2 - - - +
95C CYS* 1.3 68.0 - - - +
96C VAL* 4.2 11.8 + - + -
106C TRP 3.6 6.7 - - - +
107C LYS* 4.1 20.6 - - + -
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Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 5.5 1.6 - - - -
72C GLU* 5.5 0.4 - - - -
84C ALA* 4.5 7.2 - - - -
85C LEU 3.3 4.5 - - - -
86C VAL* 4.0 16.2 - - + -
93C LEU 4.2 0.2 + - - -
94C VAL* 1.3 74.2 - - - +
96C VAL* 1.3 70.8 + - - +
97C GLN* 3.8 25.4 - - - -
105C GLY* 3.1 3.8 - - - -
106C TRP* 2.8 78.0 + - + +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS 3.5 1.6 - - - +
84C ALA* 3.3 4.0 - - - -
85C LEU* 3.0 47.2 + - + +
94C VAL* 4.2 14.1 - - + -
95C CYS* 1.3 77.8 - - - +
97C GLN* 1.3 61.2 + - - +
98C LYS* 4.5 30.5 - - + +
104C ARG 3.8 5.8 - - - +
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 4.9 6.5 + - - -
72C GLU* 3.2 31.0 + - - +
74C THR* 4.7 6.3 - - - +
82C VAL* 3.9 14.6 - - + +
83C LYS 3.7 3.6 - - - -
84C ALA* 4.3 2.2 - - + -
95C CYS* 3.8 18.9 - - - -
96C VAL* 1.3 74.5 - - - +
98C LYS* 1.3 65.0 + - - +
99C GLY 3.6 1.9 + - - -
101C LYS 4.5 2.9 - - - +
104C ARG* 2.9 67.7 + - - +
105C GLY* 3.7 12.8 + - - -
106C TRP* 4.7 11.4 - - - +
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLU* 5.7 3.4 - - - +
81C HIS 4.5 0.2 - - - +
82C VAL* 3.3 6.0 - - - -
83C LYS* 2.8 61.4 + - + +
96C VAL* 4.5 26.3 - - + +
97C GLN* 1.3 71.5 - - - +
99C GLY* 1.3 57.5 + - - +
101C LYS 5.7 0.2 - - - -
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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