Contacts of the strand formed by residues 2082 - 2087 (chain B) in PDB entry 6D1U
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 THR2082 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B THR* 3.9 7.1 - - - +
2078B VAL* 3.9 19.4 - - + +
2079B ALA* 2.8 30.1 + - + +
2080B ALA 3.6 3.8 + - - -
2081B GLY* 1.3 80.2 + - - +
2083B GLU* 1.3 72.6 + - - +
2084B SER 4.1 0.3 + - - -
2103B LYS 3.9 0.9 - - - +
2104B ILE* 3.7 0.3 - - - -
2105B CYS* 2.8 31.7 + - - +
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Residues in contact with GLU2083 (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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51B GLN* 5.7 1.4 + - - -
55B THR* 4.6 4.7 - - + +
2082B THR* 1.3 82.9 - - - +
2084B SER* 1.3 72.7 + - - +
2085B MET* 5.8 1.1 - - + +
2100B LYS* 5.2 3.8 + - - -
2102B THR* 3.7 31.8 + - + +
2103B LYS 3.5 7.4 - - - +
2104B ILE* 4.1 25.1 - - + +
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Residues in contact with SER2084 (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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2075B TRP* 3.7 24.9 - - - -
2078B VAL* 3.2 37.0 - - - +
2082B THR 4.1 0.4 + - - -
2083B GLU* 1.3 75.0 - - - +
2085B MET* 1.3 62.0 + - - +
2102B THR* 3.2 7.3 - - - -
2103B LYS 2.8 32.7 + - - -
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Residues in contact with MET2085 (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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2075B TRP* 4.2 1.5 - - - -
2083B GLU* 5.8 0.9 - - + +
2084B SER* 1.3 76.5 - - - +
2086B GLN* 1.3 88.1 + - - +
2087B LEU* 4.1 14.1 - - + +
2100B LYS* 3.9 33.7 - - + +
2101B VAL 3.2 12.8 - - - +
2102B THR* 4.2 5.6 - - + -
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Residues in contact with GLN2086 (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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2073B LEU* 3.9 29.0 - - + +
2074B CYS* 2.7 29.6 + - - +
2075B TRP* 3.3 31.6 - - + -
2085B MET* 1.3 88.6 - - - +
2087B LEU* 1.3 66.5 + - - +
2100B LYS* 3.5 4.3 - - - -
2101B VAL* 2.8 30.1 + - - +
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Residues in contact with LEU2087 (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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2073B LEU* 4.0 15.8 - - - +
2085B MET* 4.5 13.2 - - + -
2086B GLN* 1.3 79.0 + - - +
2088B CYS* 1.3 66.2 + - - +
2089B PRO* 3.6 1.4 - - - +
2097B PRO 3.8 16.2 - - - +
2098B SER* 4.1 16.4 - - - +
2099B GLU 3.5 13.2 - - - +
2100B LYS* 4.9 2.0 - - + -
2101B VAL* 4.1 1.3 - - - -
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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