Contacts of the strand formed by residues 81 - 86 (chain A) in PDB entry 2HTE
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 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO 3.8 0.2 - - - -
80A LYS* 1.3 82.5 - - + +
82A VAL* 1.3 65.6 + - - +
104A ASN* 3.0 34.5 + - + +
106A ASP* 4.8 0.8 + - - -
150A ASN* 3.6 24.5 + - - +
151A THR 3.6 16.9 + - - +
152A TYR* 3.4 27.7 - - + -
153A ASP* 2.8 39.1 + - - +
154A VAL 3.7 0.2 + - - -
183A LYS* 5.2 3.8 - - - +
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Residues in contact with VAL 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 MET* 3.9 22.4 - - + -
79A PRO* 4.5 7.2 - - + -
81A ASN* 1.3 79.2 + - - +
83A LEU* 1.3 67.3 + - - +
96A LEU* 3.5 35.7 - - + -
102A VAL* 4.2 19.5 - - + -
104A ASN 3.2 8.4 + - - +
105A ILE* 3.4 7.4 - - + +
106A ASP 3.0 24.9 + - - +
152A TYR* 3.6 6.4 - - - -
154A VAL* 3.3 24.7 - - + +
156A ILE* 4.3 6.1 - - + -
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Residues in contact with LEU 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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82A VAL* 1.3 75.9 - - - +
84A VAL* 1.3 78.4 + - - +
85A VAL* 3.8 19.1 - - + -
106A ASP* 3.3 24.5 - - + +
108A CYS* 4.2 7.0 - - + +
144A PHE* 3.7 31.4 - - + -
145A LEU* 3.8 25.1 - - + -
152A TYR* 3.5 25.6 - - + +
154A VAL 3.0 6.9 + - - +
155A ILE* 3.3 15.1 - - + +
156A ILE 2.9 26.0 + - - -
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Residues in contact with VAL 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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83A LEU* 1.3 76.3 - - - +
85A VAL* 1.3 67.2 + - - +
86A GLY 3.8 16.2 - - - +
87A GLY* 4.2 11.4 - - - +
92A ILE* 3.7 23.8 - - + -
93A ILE* 4.2 13.2 - - + -
96A LEU* 3.6 31.4 - - + -
105A ILE* 4.5 1.1 - - + -
106A ASP 2.8 13.9 + - - +
107A ILE* 3.3 14.0 - - + +
108A CYS 2.9 26.0 + - - -
156A ILE* 3.6 9.9 - - + +
158A ASP* 4.4 3.8 - - + -
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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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83A LEU* 3.8 28.3 - - + -
84A VAL* 1.3 69.9 - - - +
86A GLY* 1.3 64.2 - - - +
108A CYS* 3.7 4.9 - - + -
141A ALA* 3.3 34.1 - - + -
145A LEU* 4.6 10.1 - - + -
155A ILE* 4.2 12.6 - - + -
156A ILE 2.9 10.5 + - - +
157A VAL* 4.1 23.1 - - + -
158A ASP* 2.8 32.4 + - - +
159A SER* 5.0 4.7 - - - -
174A PHE* 4.4 6.3 - - + -
4000A MTA 4.6 3.8 - - + +
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Residues in contact with GLY 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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84A VAL* 3.8 0.7 - - - +
85A VAL* 1.3 76.7 - - - +
87A GLY* 1.3 65.3 + - - -
88A GLY 3.3 3.5 + - - -
107A ILE* 3.2 21.1 - - - +
108A CYS 2.8 13.8 + - - +
109A GLU* 3.6 3.3 - - - +
158A ASP 3.6 2.9 - - - -
159A SER* 4.5 1.1 - - - -
4000A MTA 3.4 35.5 + - - -
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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