Contacts of the strand formed by residues 61 - 67 (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 ASN 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B TYR* 3.2 22.1 - - - +
29B THR 3.4 9.1 - - - +
30B ASN* 4.8 0.2 - - - +
60B SER* 1.3 77.6 - - - +
62B VAL* 1.3 60.5 + - - +
63B THR* 4.2 1.6 + - - -
268B GLY* 5.7 0.9 - - - -
1U NAG 1.4 67.6 + - + +
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Residues in contact with VAL 62 (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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28B TYR* 3.4 6.2 - - - -
29B THR* 2.9 60.4 + - + +
30B ASN 4.4 7.4 - - - +
31B SER* 4.1 22.4 - - - +
56B LEU* 5.0 9.0 - - + -
60B SER* 5.0 1.1 - - - -
61B ASN* 1.3 79.4 - - - +
63B THR* 1.3 61.9 + - - +
91B TYR* 5.4 5.8 - - + -
216B LEU* 4.8 7.6 - - + -
266B TYR* 4.5 13.5 - - + -
267B VAL 3.4 18.4 - - - +
268B GLY* 4.1 14.1 - - - +
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Residues in contact with THR 63 (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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26B PRO* 5.0 8.3 - - + -
27B ALA 3.7 11.2 - - - +
28B TYR* 3.9 20.5 - - + -
61B ASN 5.1 1.4 + - - -
62B VAL* 1.3 74.6 - - - +
64B TRP* 1.3 65.8 + - - +
65B PHE* 3.6 32.0 - - + -
265B TYR 4.0 0.5 - - - +
266B TYR* 3.2 8.2 - - - +
267B VAL* 3.0 36.7 + - - -
269B TYR* 5.8 3.5 - - - -
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Residues in contact with TRP 64 (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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26B PRO* 5.4 0.9 - - - +
27B ALA* 3.0 44.4 + - + +
28B TYR 4.3 12.8 - - - -
29B THR* 4.3 15.5 - - + -
63B THR* 1.3 76.5 - - - +
65B PHE* 1.3 96.4 + - - +
66B HIS* 3.2 41.2 + + - -
80B ASP* 5.1 0.5 - - - +
214B ARG* 4.0 40.2 - - + -
215B ASP* 4.2 20.4 - - - -
264B ALA* 4.0 9.0 - - + +
265B TYR 3.7 3.1 - - - -
266B TYR* 3.6 33.8 + + + -
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Residues in contact with PHE 65 (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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26B PRO* 6.1 3.1 - - + -
63B THR* 3.6 36.1 - - + -
64B TRP* 1.3 82.1 - - - +
66B HIS* 1.3 65.7 + - - +
80B ASP* 4.0 17.5 - - + +
82B PRO* 3.8 31.0 - - + -
84B LEU* 4.1 20.0 - - + -
264B ALA* 3.4 4.9 - - - -
265B TYR* 2.9 74.7 + + + +
267B VAL* 4.0 18.8 - - + -
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Residues in contact with HIS 66 (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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24B LEU* 6.5 0.4 - - + -
27B ALA* 4.9 8.3 - - + +
64B TRP* 3.2 52.0 + + - -
65B PHE* 1.3 79.1 - - - +
67B ALA* 1.3 56.7 + - - +
68B ILE* 3.7 26.2 - - + +
78B ARG* 2.8 32.0 - - + +
80B ASP* 3.4 22.5 + - - +
242B LEU* 5.6 0.2 - - - +
263B ALA 3.7 4.9 + - - +
264B ALA* 5.0 4.4 - - + +
265B TYR* 5.5 4.0 - - - -
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Residues in contact with ALA 67 (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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66B HIS* 1.3 73.8 - - - +
68B ILE* 1.3 57.7 + - - +
77B LYS 4.4 2.0 - - - -
78B ARG 3.8 6.1 - - - +
79B PHE* 4.6 18.6 - - + +
100B ILE* 4.8 5.2 - - + -
242B LEU* 4.7 13.7 - - + -
260B ALA* 4.6 2.7 - - + -
261B GLY 2.8 32.2 - - - +
262B ALA* 2.8 14.6 - - - -
263B ALA* 2.9 25.0 + - + +
265B TYR* 6.5 0.4 - - + -
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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