Contacts of the strand formed by residues 94 - 98 (chain B) 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 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.0 27.4 - - + -
85B VAL 3.3 18.8 - - - +
86B SER* 3.4 12.9 + - - +
93B VAL* 1.3 81.1 + - - +
95B VAL* 1.3 67.9 + - - +
143B GLN* 5.8 0.5 - - - +
144B THR* 4.8 3.5 - - - +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP 3.3 0.5 - - - +
84B LEU* 3.0 11.7 - - - -
85B VAL* 2.6 44.6 + - + +
93B VAL* 4.7 0.9 - - + -
94B THR* 1.3 80.6 - - - +
96B ARG* 1.3 70.1 + - - +
97B ALA* 4.0 4.5 - - + -
136B PHE* 3.6 30.1 - - + -
139B SER* 4.7 5.2 - - - +
140B LEU* 3.8 31.0 - - + +
143B GLN* 3.2 16.2 - - + +
144B THR* 4.0 18.4 - - + -
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 2.7 55.7 + - - +
61B ARG* 3.4 44.4 - - - +
82B THR* 3.4 29.1 + - + -
83B ASP* 3.1 26.2 + - - +
84B LEU* 4.0 16.5 - - + +
95B VAL* 1.3 72.2 - - - +
97B ALA* 1.3 62.5 + - - +
139B SER* 3.7 5.7 - - - -
143B GLN* 2.6 43.1 + - - +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 4.6 1.1 - - + -
82B THR* 3.4 5.9 - - - -
83B ASP 2.9 27.0 + - - +
85B VAL* 4.1 11.4 - - + -
95B VAL* 4.0 7.4 - - + -
96B ARG* 1.3 76.8 - - - +
98B ASN* 1.3 70.2 + - - +
99B ILE* 3.2 5.4 - - - +
136B PHE* 3.7 33.7 - - + -
139B SER* 4.5 9.4 - - - -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.5 21.1 - - - +
63B LEU* 4.5 5.8 - - + +
80B LEU* 5.9 0.2 - - + -
81B GLY 3.5 7.0 - - - +
82B THR* 3.7 14.4 - - - +
97B ALA* 1.3 75.7 - - - +
99B ILE* 1.3 64.1 + - - +
133B LEU* 3.4 35.0 - - + +
134B GLU* 2.3 57.8 + - - +
136B PHE* 5.7 2.3 + - - +
139B SER* 4.9 1.9 + - - -
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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