Contacts of the strand formed by residues 106 - 112 (chain B) in PDB entry 1HXD
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 ALA 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B SER 3.3 13.0 + - - +
81B VAL* 3.5 13.2 - - + -
82B ALA* 3.1 23.8 + - - +
93B TYR* 5.8 0.2 - - - -
94B LEU* 5.0 2.6 - - - +
104B GLY 3.3 5.1 + - - +
105B ASP* 1.3 73.8 - - - +
107B CYS* 1.3 66.1 + - - +
108B ILE* 5.8 0.2 - - + -
133B LEU* 5.3 1.1 - - + -
134B SER 3.4 12.6 - - - +
135B MET* 4.6 7.0 - - + -
243B ILE* 4.0 27.8 - - + -
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Residues in contact with CYS 107 (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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82B ALA* 3.1 8.7 - - + +
84B LEU* 3.1 36.3 - - - -
90B THR* 4.0 22.8 - - - +
93B TYR* 3.4 21.3 - - + -
94B LEU* 3.5 20.6 - - + -
106B ALA* 1.3 77.9 - - - +
108B ILE* 1.3 66.3 + - - +
133B LEU* 3.4 3.3 - - - +
134B SER 3.0 29.6 + - - +
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Residues in contact with ILE 108 (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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67B LEU* 3.6 26.2 - - + -
72B ILE* 5.6 5.8 - - + -
81B VAL* 3.8 22.9 - - + -
82B ALA 2.8 7.3 + - - +
83B VAL* 3.2 17.1 - - + +
84B LEU* 2.5 33.8 + - - +
90B THR* 4.4 1.6 - - - -
106B ALA* 5.8 0.4 - - + -
107B CYS* 1.3 78.9 - - - +
109B ALA* 1.4 54.4 + - - +
131B LEU* 3.9 26.7 - - + -
132B TYR 3.3 20.9 - - - +
133B LEU* 3.8 14.8 - - + -
235B ARG* 6.3 0.2 - - - +
239B ALA* 4.5 13.7 - - + -
243B ILE* 5.2 9.4 - - + -
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Residues in contact with ALA 109 (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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67B LEU* 3.7 12.4 - - - +
84B LEU* 2.7 17.3 - - + +
87B ILE* 4.6 8.5 - - + -
90B THR* 3.8 20.1 - - + +
108B ILE* 1.4 72.7 - - - +
110B GLU* 1.4 62.5 + - - +
111B TYR 3.7 21.8 - - - +
112B GLN* 4.4 3.1 - - + -
130B ASN 5.1 0.5 - - - +
132B TYR* 3.4 25.7 + - + +
235B ARG* 4.5 3.6 + - - -
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Residues in contact with GLU 110 (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 LEU* 3.2 20.2 - - + +
67B LEU* 2.5 46.2 + - + +
83B VAL* 5.9 1.1 - - + -
84B LEU 2.9 9.3 + - - +
85B PRO* 3.1 15.8 + - + +
109B ALA* 1.4 73.0 - - - +
111B TYR* 1.3 61.2 + - - +
126B PRO 3.4 4.7 - - - +
127B PHE* 3.1 33.4 - - + -
128B GLY* 2.8 34.0 + - - -
132B TYR* 3.4 7.0 - - - -
235B ARG* 2.8 30.5 + - - +
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Residues in contact with TYR 111 (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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45B ASP* 4.5 5.1 + - - -
46B TRP* 3.3 49.2 - + - -
85B PRO 2.7 11.5 + - - +
86B VAL* 3.7 21.3 - - + -
87B ILE 3.2 22.2 + - - +
109B ALA* 3.3 8.1 - - - +
110B GLU* 1.3 84.5 - - - +
112B GLN* 1.3 69.3 + - - +
113B GLN* 2.3 57.1 + - + +
125B SER 2.8 29.8 - - - -
126B PRO* 5.0 0.2 - - + -
127B PHE* 3.5 15.3 - + + -
132B TYR* 4.1 1.8 - - - -
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Residues in contact with GLN 112 (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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87B ILE* 2.8 4.9 - - + +
88B ASP 3.5 11.7 - - - +
89B SER* 3.5 1.4 - - - -
90B THR* 2.9 39.9 + - + +
109B ALA* 4.4 6.1 - - + -
111B TYR* 1.3 81.8 - - - +
113B GLN* 1.3 66.2 + - - +
115B GLY* 3.9 8.9 + - - +
123B TRP* 4.1 1.4 - - - -
125B SER* 3.4 44.9 + - - +
132B TYR* 3.7 16.7 - - + +
501B BTN 3.0 45.7 + - - +
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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