Contacts of the strand formed by residues 79 - 84 (chain B) in PDB entry 2Z9I
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA* 6.1 0.4 - - - -
78B PHE* 1.3 81.8 - - - +
80B VAL* 1.3 66.1 + - - +
81B VAL* 3.6 0.7 + - - +
92B VAL* 3.3 3.3 - - - +
93B ARG* 2.9 45.2 + - - +
95B GLN* 5.5 3.2 + - + +
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Residues in contact with VAL 80 (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 ILE* 4.2 19.3 - - + -
54B ALA* 2.9 46.8 - - + +
78B PHE* 4.4 6.1 - - + -
79B THR* 1.3 77.3 + - - +
81B VAL* 1.3 63.3 + - - +
82B GLY* 3.7 22.4 - - - +
83B ALA* 4.5 4.7 - - + +
91B VAL 4.0 6.3 - - - +
92B VAL* 4.0 13.7 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 16.2 - - + -
79B THR* 3.6 0.8 + - - +
80B VAL* 1.3 74.2 - - - +
82B GLY* 1.3 55.8 + - - +
91B VAL* 2.8 27.4 + - + +
92B VAL 4.0 4.5 - - - -
93B ARG* 3.5 38.8 - - + +
220B LEU 3.9 20.5 - - - +
221B ILE* 4.1 18.2 - - + +
224B GLY* 4.4 6.6 - - - -
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Residues in contact with GLY 82 (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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80B VAL* 3.5 8.5 - - - +
81B VAL* 1.3 78.2 - - - +
83B ALA* 1.3 61.3 + - - +
90B ALA* 3.5 1.7 - - - +
91B VAL* 2.8 30.4 + - - +
220B LEU* 3.8 23.3 - - - -
224B GLY 4.1 8.7 - - - -
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Residues in contact with ALA 83 (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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48B ASN* 3.1 23.1 - - - +
51B ILE* 4.2 9.9 - - + -
80B VAL* 4.5 5.8 - - + +
82B GLY* 1.3 74.4 - - - +
84B ASP* 1.3 60.2 + - - +
85B PRO* 3.9 7.5 - - + +
89B ILE 4.0 0.7 - - - -
90B ALA* 4.0 13.0 - - + +
220B LEU* 3.7 9.6 - - - +
224B GLY 4.7 3.2 + - - +
225B LYS* 5.4 1.6 - - - -
226B ALA 5.5 0.3 + - - -
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Residues in contact with ASP 84 (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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48B ASN* 3.8 1.7 - - - +
83B ALA* 1.3 76.7 - - - +
85B PRO* 1.3 68.8 - - - +
86B THR* 3.2 8.3 + - - +
87B SER* 2.8 21.0 + - - +
88B ASP* 3.0 17.8 + - - -
89B ILE 2.9 20.6 + - - +
216B ILE* 3.6 12.2 - - + +
220B LEU* 4.3 1.8 - - + -
226B ALA* 3.5 20.6 + - + +
228B HIS* 2.9 40.3 + - - -
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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