Contacts of the strand formed by residues 82 - 86 (chain C) in PDB entry 3DM6
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 THR 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C TYR* 5.3 0.2 - - - -
60C TYR* 3.8 3.2 - - - -
61C ARG* 2.9 40.2 + - + +
63C LEU* 3.8 17.7 - - + -
81C GLY* 1.3 79.5 - - - +
83C ASP* 1.3 63.9 + - - +
96C ARG* 2.8 30.1 + - + +
97C ALA 3.3 18.2 - - - +
98C ASN* 3.7 21.1 - - - +
99C ILE* 4.4 4.5 - - - +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 5.2 0.2 - - + -
21C GLY* 3.4 23.5 - - - +
52C TYR* 2.8 27.9 + - - +
57C SER* 3.1 20.6 + - - -
59C THR* 3.5 22.9 + - - -
60C TYR 3.4 4.4 + - - -
82C THR* 1.3 76.7 + - - +
84C LEU* 1.3 80.3 + - - +
85C VAL* 3.9 1.4 - - - +
96C ARG* 3.2 14.8 - - - +
97C ALA 3.1 28.3 + - - +
99C ILE* 3.7 14.0 - - + +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR 4.3 0.2 - - - -
20C VAL* 3.3 7.3 - - - +
21C GLY* 3.1 25.1 + - - +
22C SER* 4.3 8.3 - - - +
59C THR* 3.8 26.7 - - + +
83C ASP* 1.3 89.0 + - - +
85C VAL* 1.3 63.2 + - - +
86C SER* 4.3 0.7 - - - -
94C THR* 3.8 23.6 - - + +
95C VAL* 3.2 14.4 - - - +
96C ARG* 3.9 31.4 - - + +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 3.8 13.2 - - + -
19C THR 3.2 15.3 - - - +
20C VAL* 3.7 10.1 - - + -
38C PHE* 3.7 15.7 - - + -
83C ASP 3.9 6.7 - - - +
84C LEU* 1.3 79.3 - - - +
86C SER* 1.3 62.3 + - - +
87C ILE* 5.5 0.2 - - - +
93C VAL 4.3 0.3 - - - +
94C THR* 3.7 3.1 - - - +
95C VAL* 2.7 38.9 + - - +
97C ALA* 4.5 7.4 - - + +
99C ILE* 3.9 25.6 - - + -
136C PHE* 3.7 30.7 - - + -
140C LEU* 5.7 0.2 - - - +
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 3.2 6.4 - - - +
19C THR* 2.6 51.4 + - - +
24C PRO* 5.7 1.2 - - - +
84C LEU 5.6 0.3 - - - -
85C VAL* 1.3 73.4 - - - +
87C ILE* 1.3 69.2 + - - +
88C PRO* 3.8 1.3 - - - -
91C PRO 5.8 0.2 - - - -
93C VAL 3.5 11.0 - - - -
94C THR* 3.1 23.1 + - - +
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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