Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 2HW6
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 ARG 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.0 41.2 + - - -
83A GLN* 6.0 0.4 - - - +
118A THR* 3.7 18.4 + - - -
119A ARG* 3.6 42.3 - - - +
44B PHE* 5.5 1.8 - - - -
50B LEU* 5.8 0.2 - - - +
62B LYS* 4.5 3.4 - - - +
79B ILE* 3.3 31.1 - - + +
80B ILE 3.2 15.7 - - - +
81B GLU* 4.3 5.6 - - - -
82B LYS* 3.5 5.2 - - - +
115B GLU* 3.4 5.4 - - - +
116B ASP* 2.9 34.7 + - - +
118B THR* 1.3 88.8 + - - +
120B PHE* 1.3 64.7 + - - +
121B TYR* 2.6 32.7 + - + -
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Residues in contact with PHE 120 (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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78B LYS 3.6 0.6 - - - +
79B ILE* 3.2 8.3 - - - +
80B ILE* 2.9 40.8 + - + +
82B LYS* 3.6 26.2 - - + -
87B SER* 3.5 34.3 - - - -
88B ARG* 3.8 24.7 - - + -
91B VAL* 3.8 24.5 - - + -
92B PHE* 5.6 2.2 - - + -
113B PHE* 3.5 29.8 - + + -
114B PHE 3.6 1.8 - - - -
115B GLU* 3.1 31.4 - - + -
119B ARG* 1.3 74.1 - - - +
121B TYR* 1.3 63.9 + - - +
122B LEU* 4.1 4.0 - - + -
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Residues in contact with TYR 121 (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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118A THR* 4.3 2.1 + - - -
44B PHE* 3.6 49.8 - + + +
77B VAL* 4.4 3.1 - - + -
78B LYS 3.6 2.9 - - - -
79B ILE* 3.5 35.9 - - + -
112B GLU 3.8 0.2 - - - +
113B PHE* 3.5 5.9 - - - -
114B PHE* 2.6 70.3 + + + +
116B ASP* 2.8 39.3 + - - -
119B ARG* 2.6 42.4 + - + -
120B PHE* 1.3 72.3 - - - +
122B LEU* 1.3 64.1 + - - +
123B VAL* 3.7 3.8 + - + +
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Residues in contact with LEU 122 (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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77B VAL* 3.2 3.1 - - - +
78B LYS* 2.7 45.8 + - + +
80B ILE* 3.8 29.2 - - + -
91B VAL* 4.1 7.6 - - + -
94B GLU* 5.0 10.3 - - - +
95B VAL* 4.1 15.0 - - + -
98B LEU* 4.3 12.1 - - + -
110B LEU* 3.8 13.5 - - + -
112B GLU 3.9 0.4 - - - -
113B PHE* 3.6 27.8 - - + -
120B PHE* 4.2 3.6 - - + -
121B TYR* 1.3 71.2 - - - +
123B VAL* 1.3 63.2 + - - +
124B PHE* 3.4 33.4 + - + -
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Residues in contact with VAL 123 (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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44B PHE* 5.0 4.5 - - + -
48B TYR* 3.6 44.4 - - + +
75B TYR* 3.7 34.8 - - + -
76B ALA 4.1 1.8 - - - -
77B VAL* 4.1 16.8 - - + +
110B LEU* 3.5 3.9 - - - +
111B ILE* 2.7 36.5 + - + -
112B GLU* 2.8 29.3 + - + +
113B PHE 6.0 0.2 - - - -
114B PHE* 5.8 2.7 - - + +
121B TYR* 4.7 5.6 - - + +
122B LEU* 1.3 70.5 - - - +
124B PHE* 1.3 53.9 + - - +
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Residues in contact with PHE 124 (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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63B VAL* 6.2 0.2 - - + -
75B TYR* 3.2 9.2 - - - +
76B ALA* 2.8 42.2 + - + +
78B LYS* 4.1 16.8 - - + -
94B GLU* 5.7 1.3 - - - -
98B LEU* 4.0 16.6 - - + -
108B LEU* 3.7 33.9 - - + -
109B GLU 3.2 25.8 - - - +
110B LEU* 3.6 18.6 - - + -
111B ILE* 4.0 3.4 - - - -
122B LEU* 3.4 50.7 - - + -
123B VAL* 1.3 73.2 - - - +
125B GLU* 1.3 67.0 + - - +
190B CYS* 6.2 0.4 - - + -
191B ASP 5.2 9.6 - - - -
192B PHE* 4.4 16.4 - + - -
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Residues in contact with GLU 125 (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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75B TYR* 4.5 5.6 - - - -
76B ALA* 4.0 5.2 - - - +
108B LEU* 3.6 22.1 - - + +
109B GLU* 3.0 42.7 + - - +
111B ILE* 3.4 19.1 - - + +
124B PHE* 1.3 77.1 - - - +
126B LYS* 1.3 62.5 + - - +
127B LEU* 3.8 11.8 + - + +
188B LYS* 2.7 39.0 + - - +
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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