Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 2HZA
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 SER 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLN* 4.3 21.9 + - - +
78A HIS 4.8 0.9 - - - -
79A HIS* 3.4 27.6 + - - +
80A ASP 3.4 2.9 - - - +
81A LEU* 1.3 80.1 - - - +
83A VAL* 1.3 63.9 + - - +
84A ALA* 3.8 11.6 + - - -
85A THR* 4.6 2.6 + - - -
99A ALA* 6.0 0.3 - - - +
100A VAL 3.9 4.2 + - - -
101A LEU* 4.1 9.8 - - - +
102A LYS* 5.1 2.3 - - - +
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Residues in contact with VAL 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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53A PHE* 4.0 3.6 - - + -
82A SER* 1.3 76.7 + - - +
84A ALA* 1.3 70.2 + - + +
100A VAL* 2.9 31.6 + - + +
101A LEU 4.0 3.8 - - - -
102A LYS* 3.7 40.8 - - + +
88B VAL* 4.3 28.0 - - + -
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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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82A SER* 3.8 6.2 + - - -
83A VAL* 1.3 88.1 - - + +
85A THR* 1.3 63.9 + - - +
98A ILE 4.1 0.5 - - - +
100A VAL* 2.9 30.8 + - + +
86B LEU* 4.4 18.0 - - + +
88B VAL* 6.0 2.2 - - + -
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Residues in contact with THR 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 GLN* 3.0 28.9 + - - +
82A SER* 4.6 2.8 + - - -
84A ALA* 1.3 77.0 + - - +
86A LEU* 1.3 71.2 + - - +
87A HIS* 3.8 3.8 + - + +
97A GLU* 4.0 28.9 - - + +
98A ILE 3.4 14.8 - - - +
99A ALA* 3.6 8.8 - - + +
86B LEU* 4.8 2.7 - - - -
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Residues in contact with LEU 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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85A THR* 1.3 74.9 - - - +
87A HIS* 1.3 67.2 + - - +
88A VAL* 4.6 10.3 - - + -
96A LEU 3.9 0.3 - - - +
97A GLU* 3.4 2.9 - - - -
98A ILE* 2.9 44.2 + - + +
84B ALA* 4.5 19.1 - - + +
85B THR 4.8 1.8 - - - -
86B LEU* 3.9 45.7 - - + +
98B ILE* 4.6 2.0 - - + +
100B VAL* 3.8 27.1 - - + -
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Residues in contact with HIS 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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60A TYR* 3.1 24.4 + + - -
85A THR* 3.8 4.3 + - + +
86A LEU* 1.3 79.5 - - - +
88A VAL* 1.3 71.9 + - - +
89A HIS* 3.1 18.7 + + - -
95A CYS* 3.1 10.4 - - + +
96A LEU 3.3 4.5 - - - -
97A GLU* 2.6 26.6 + - - +
302A NI 2.1 44.5 - - + +
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Residues in contact with VAL 88 (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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86A LEU* 4.6 10.3 - - + -
87A HIS* 1.3 81.9 - - - +
89A HIS* 1.3 68.2 + - - +
90A ILE* 3.0 6.9 + - - +
95A CYS* 3.7 0.3 - - - -
96A LEU* 2.8 51.9 + - + +
98A ILE* 5.9 0.2 - - + -
53B PHE* 4.5 18.2 - - + -
83B VAL* 4.4 22.4 - - + -
84B ALA* 6.1 1.8 - - + -
100B VAL* 4.0 31.2 - - + -
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Residues in contact with HIS 89 (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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87A HIS* 3.1 17.1 + + - -
88A VAL* 1.3 74.6 - - - +
90A ILE* 1.3 67.0 + - - +
91A ASN* 3.4 9.4 + - - +
94A ASP 4.0 1.1 - - - -
302A NI 2.0 45.5 - - + +
53B PHE* 5.4 0.5 - - - -
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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