Contacts of the strand formed by residues 81 - 87 (chain A) in PDB entry 2P3Z
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLU* 3.8 33.7 + - - +
74A VAL 3.3 6.3 - - - +
75A GLU* 3.7 24.9 - - + -
79A ARG 3.6 6.7 + - - +
80A GLN* 1.3 79.9 - - - +
82A GLY* 1.3 59.8 + - - +
83A PHE* 6.0 1.1 - - - -
147A LEU* 3.6 6.7 - - - +
150A LYS* 3.4 23.6 + - - +
392A GLU* 5.5 2.9 + - - -
395A ARG* 4.4 8.3 + - - +
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLU* 3.3 5.9 - - - +
74A VAL 2.8 31.8 + - - +
81A THR* 1.3 74.1 - - - +
83A PHE* 1.3 61.9 + - - -
143A ALA 3.9 6.7 - - - -
146A ASP* 3.2 13.2 - - - -
147A LEU* 3.6 24.4 - - - +
150A LYS* 4.5 1.1 - - - -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.4 4.5 - - + -
72A VAL 3.0 17.3 - - - +
73A GLU* 4.0 13.7 - - + +
81A THR* 6.0 1.3 - - - -
82A GLY* 1.3 75.1 - - - +
84A ALA* 1.3 83.1 + - - +
85A VAL* 4.1 2.9 - - + -
143A ALA* 3.8 6.0 + - - -
146A ASP* 2.9 32.2 + - - +
150A LYS* 4.0 5.8 - - - -
334A TYR* 4.0 10.0 + - - -
368A LEU* 3.7 21.5 - - + -
391A VAL* 3.5 34.1 - - + -
392A GLU* 3.3 10.5 - - - -
393A LEU* 3.3 56.3 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.5 1.2 - - - +
72A VAL 3.1 27.9 + - - -
83A PHE* 1.3 81.3 - - - +
85A VAL* 1.3 69.5 + - - +
139A CYS* 3.2 12.6 - - - +
142A LEU* 3.3 35.7 - - + -
143A ALA 3.6 6.5 - - - +
334A TYR* 3.4 19.3 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY* 4.1 11.9 - - - -
69A THR* 4.2 7.9 - - + -
70A LEU 3.2 8.3 - - - +
71A ILE* 3.8 20.6 - - + -
83A PHE* 4.1 9.6 - - + -
84A ALA* 1.3 84.5 - - - +
86A SER* 1.3 63.6 + - - +
139A CYS* 3.7 2.8 - - - -
142A LEU* 4.8 7.3 - - - +
304A GLY* 5.3 2.3 - - - -
334A TYR* 3.7 16.8 + - + +
364A PHE* 3.9 32.6 - - + -
367A ILE* 4.1 22.2 - - + -
368A LEU* 4.1 12.3 - - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 4.2 9.8 - - - -
69A THR* 3.4 9.2 - - - +
70A LEU* 2.9 31.1 + - - +
85A VAL* 1.3 77.7 - - - +
87A THR* 1.3 69.6 + - - +
135A ASN* 3.5 19.1 + - - +
139A CYS* 3.7 14.3 - - - -
304A GLY* 2.7 31.8 + - - -
305A TRP* 3.7 6.4 - - - +
364A PHE* 6.1 0.9 - - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.2 19.3 + - - -
31A ASP* 3.4 23.0 + - - +
32A TYR 4.7 0.2 + - - -
67A LEU* 4.0 22.7 - - + +
68A GLY 3.5 12.3 - - - +
86A SER* 1.3 78.4 + - - +
88A ALA* 1.4 66.7 + - - +
132A LEU* 4.8 0.7 - - - +
135A ASN* 3.0 28.1 + - - +
305A TRP* 3.9 25.4 + - + +
125B TYR* 5.0 8.5 - - + -
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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