Contacts of the strand formed by residues 263 - 269 (chain B) in PDB entry 6ZGI
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 ALA 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B HIS* 3.7 2.4 + - - +
67B ALA* 2.9 34.2 + - + +
95B THR 3.9 5.4 - - - -
96B GLU* 4.2 7.2 - - + -
100B ILE* 3.7 30.3 - - + -
101B ILE* 3.7 17.0 - - + -
186B PHE* 4.1 9.7 - - - -
262B ALA* 1.3 77.7 - - - +
264B ALA* 1.3 64.2 + - - +
265B TYR* 5.9 0.7 - - - -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 4.0 10.5 - - + +
65B PHE 3.4 11.7 - - - +
66B HIS* 5.0 4.5 - - + +
94B SER* 3.6 4.0 + - - -
95B THR* 2.9 47.5 + - - +
101B ILE* 4.3 1.6 - - - +
186B PHE* 4.5 9.6 - - + -
263B ALA* 1.3 76.9 - - - +
265B TYR* 1.3 67.2 + - - +
266B TYR* 4.0 14.6 - - - +
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 2.9 71.0 + + + +
66B HIS 5.5 2.9 - - - -
67B ALA* 6.5 0.4 - - + -
80B ASP* 3.4 24.2 + - + -
81B ASN* 3.9 3.8 - - - -
82B PRO* 3.8 19.1 + - - +
84B LEU* 5.0 4.6 - - + +
92B PHE* 3.5 29.6 - + + -
93B ALA 3.2 13.2 - - - +
94B SER* 4.4 3.1 - - - -
101B ILE* 4.2 17.9 - - + -
240B THR* 4.0 22.2 + - + -
242B LEU* 4.3 14.8 - - + -
263B ALA 5.9 0.7 - - - -
264B ALA* 1.3 78.2 - - - +
266B TYR* 1.3 67.2 + - - +
267B VAL* 4.1 6.3 - - + -
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.9 21.1 - - + -
62B VAL* 4.5 11.7 - - + -
63B THR 3.2 6.1 - - - +
64B TRP* 3.6 43.4 + + + -
91B TYR* 3.7 3.7 - - + +
92B PHE* 3.6 5.4 - - - -
93B ALA* 2.9 46.5 + - + +
95B THR* 3.8 36.8 + - + +
186B PHE* 5.9 0.5 - - - -
212B LEU* 6.0 0.2 - - - +
214B ARG* 4.8 1.6 - - - -
215B ASP 3.9 11.1 + - - -
216B LEU* 3.8 48.6 + - + -
264B ALA* 4.0 4.3 - - + +
265B TYR* 1.3 79.4 - - - +
267B VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 267 (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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62B VAL* 3.4 7.5 - - - +
63B THR* 3.0 34.7 + - - +
65B PHE* 4.0 24.0 - - + -
84B LEU* 4.1 15.7 - - + -
90B VAL* 4.1 19.5 - - + -
91B TYR* 3.6 2.5 - - - -
92B PHE* 4.2 11.7 - - + -
238B PHE* 4.3 10.5 - - + -
265B TYR* 4.1 12.8 - - + -
266B TYR* 1.3 80.3 - - - +
268B GLY* 1.3 63.1 + - - +
269B TYR* 4.5 22.5 - - + +
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Residues in contact with GLY 268 (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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56B LEU* 4.1 10.3 - - - -
61B ASN 5.7 1.6 - - - -
62B VAL* 4.1 16.9 - - - +
90B VAL* 3.7 7.4 - - - +
91B TYR* 2.9 36.4 + - - +
267B VAL* 1.3 75.0 - - - +
269B TYR* 1.3 69.3 + - - -
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Residues in contact with TYR 269 (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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56B LEU* 3.6 16.0 - - - +
57B PRO* 4.0 8.0 - - - +
63B THR* 5.8 3.4 - - - -
84B LEU* 4.2 6.9 - - - +
85B PRO* 3.3 48.7 + - + +
87B ASN* 3.8 35.0 - - + +
88B ASP 5.9 0.2 - - - +
89B GLY 3.9 10.8 - - - +
90B VAL* 4.2 11.9 - - + -
267B VAL* 4.5 16.5 - - + +
268B GLY* 1.3 79.3 - - - -
270B LEU* 1.3 65.2 + - - +
271B GLN* 4.6 7.1 - - + +
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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