Contacts of the strand formed by residues 82 - 87 (chain A) in PDB entry 4Z7Q
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 GLN 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASN* 3.3 4.9 - - - +
79A VAL 2.8 35.7 + - - +
80A GLY* 3.5 11.8 - - - +
81A SER* 1.3 80.2 - - - +
83A THR* 1.3 63.3 + - - +
84A LEU* 4.1 6.9 - - + +
115A VAL* 4.1 15.3 - - + +
116A LEU 3.4 7.6 - - - +
117A GLU* 2.9 34.4 + - + +
149A ASN* 3.4 45.9 + - - +
151A LEU* 4.5 4.2 - - - +
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Residues in contact with THR 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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76A THR* 3.9 22.0 - - + -
77A ARG 3.6 2.5 - - - +
78A ASN* 3.0 26.7 + - - +
82A GLN* 1.3 73.6 - - - +
84A LEU* 1.3 65.7 + - - +
85A GLN* 3.8 11.0 + - + +
114A ASN 3.9 0.2 - - - +
115A VAL* 3.3 4.5 - - - -
116A LEU* 2.8 58.8 + - + +
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Residues in contact with LEU 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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76A THR* 3.3 8.0 - - - +
77A ARG* 2.9 42.7 + - - +
79A VAL* 4.0 22.9 - - + -
82A GLN* 4.9 7.6 - - + +
83A THR* 1.3 73.0 - - - +
85A GLN* 1.3 62.2 + - - +
113A TRP* 3.7 15.5 - - + -
114A ASN 3.9 2.2 - - - -
115A VAL* 3.8 31.4 - - + -
149A ASN* 4.9 2.2 - - + -
211A ILE 4.0 21.1 - - - +
212A LEU* 3.9 17.0 - - + -
213A LEU* 4.1 24.0 - - + -
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Residues in contact with GLN 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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75A GLU 3.7 4.9 - - - +
76A THR* 4.7 9.3 + - + +
83A THR* 4.2 13.7 - - + +
84A LEU* 1.3 80.3 - - - +
86A THR* 1.3 63.7 + - - +
87A PHE* 3.4 33.7 - - + -
113A TRP* 3.1 11.9 - - - -
114A ASN* 2.9 47.3 + - - +
116A LEU* 3.5 37.8 - - - +
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Residues in contact with THR 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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74A ASP* 3.3 21.7 - - - +
75A GLU* 3.0 41.6 + - - +
85A GLN* 1.3 76.8 - - - +
87A PHE* 1.3 66.2 + - - +
88A LYS* 4.2 5.8 - - - -
111A GLN* 4.2 14.1 - - - +
112A HIS 3.7 3.6 - - - -
113A TRP* 3.7 23.6 - - + -
147A ARG* 3.7 21.3 - - - +
212A LEU* 4.4 11.4 - - + -
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Residues in contact with PHE 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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74A ASP* 3.4 14.4 - - + +
85A GLN* 3.4 51.8 - - + -
86A THR* 1.3 79.2 - - - +
88A LYS* 1.3 62.5 + - - +
89A ALA* 3.4 9.8 + - + +
111A GLN* 3.5 5.1 - - - +
112A HIS* 3.0 56.6 + - + +
113A TRP 4.5 0.2 - - - -
114A ASN* 4.2 11.4 - - + -
124A LYS* 3.6 39.5 - - + +
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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