Contacts of the helix formed by residues 109 - 115 (chain B) in PDB entry 2R1U
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 PRO 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.7 26.9 - - + +
105B ILE* 3.7 8.7 - - - +
106B CYS 3.3 16.8 - - - +
107B ALA 3.3 4.9 - - - -
108B GLY* 1.3 90.0 - - - +
110B THR* 1.3 56.3 + - - +
112B LEU* 2.9 31.2 + - + +
113B LEU 3.4 0.3 + - - -
124B THR 3.7 19.1 - - - +
125B THR* 3.8 11.0 - - + -
133B MET* 3.2 26.6 - - + +
154B THR* 3.9 9.2 - - + -
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Residues in contact with THR 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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79B ALA* 4.0 10.7 - - - +
83B SER* 3.8 5.5 + - - -
107B ALA* 2.7 25.1 + - + +
109B PRO* 1.3 77.5 - - + +
111B ALA* 1.3 57.5 + - - +
113B LEU* 3.2 8.0 + - - +
114B ALA* 3.1 24.8 + - - +
125B THR* 5.5 0.9 - - + -
129B ALA* 4.2 17.9 - - + +
132B LYS* 4.0 41.3 + - + +
133B MET* 3.8 24.2 - - + +
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Residues in contact with ALA 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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72B LEU* 4.1 13.5 - - + -
79B ALA 4.3 2.9 - - - +
82B LEU* 4.1 24.9 - - + -
83B SER* 3.2 21.8 - - - +
88B VAL* 5.6 0.4 - - + -
92B LEU* 5.0 0.9 - - + -
108B GLY* 3.0 14.7 + - - +
110B THR* 1.3 78.9 + - - +
112B LEU* 1.3 66.6 + - - +
114B ALA* 3.4 0.3 + - - +
115B HIS* 3.2 35.0 + - + -
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Residues in contact with LEU 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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72B LEU* 4.0 15.7 - - + -
92B LEU* 4.3 6.5 - - + -
102B ILE* 3.8 26.2 - - + +
104B ALA* 4.4 11.7 - - + +
108B GLY 4.6 0.7 - - - +
109B PRO* 2.9 28.8 + - + +
111B ALA* 1.3 77.7 - - - +
113B LEU* 1.3 59.7 + - - +
115B HIS 3.4 1.2 + - - -
116B GLU 3.0 4.0 + - - -
117B ILE* 2.8 51.5 + - + +
123B VAL* 5.7 0.2 - - + -
133B MET* 4.7 4.7 - - + -
139B TYR* 3.3 13.9 + - + +
152B ILE* 4.3 28.9 - - + -
154B THR* 4.6 6.5 - - + -
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Residues in contact with LEU 113 (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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109B PRO 3.4 2.0 + - - -
110B THR* 3.2 12.7 + - - +
112B LEU* 1.3 79.6 - - - +
114B ALA* 1.3 64.2 + - - +
116B GLU* 3.0 17.0 + - - +
119B PHE* 3.9 21.9 - - + -
132B LYS* 3.1 32.5 - - + +
133B MET* 3.7 16.6 - - - +
135B ASN* 4.3 13.2 - - + +
138B HIS* 4.1 15.3 - - + -
139B TYR* 3.3 23.4 + - + -
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Residues in contact with ALA 114 (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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83B SER* 3.6 43.2 - - - +
89B LYS* 4.9 2.6 + - - -
110B THR 3.1 7.8 + - - +
111B ALA 3.6 6.5 - - - +
112B LEU 3.3 0.2 - - - -
113B LEU* 1.3 80.0 - - - +
115B HIS* 1.3 62.6 + - + +
116B GLU* 3.7 5.0 + - - +
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Residues in contact with HIS 115 (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 LEU 2.9 23.4 + - - -
83B SER* 3.1 24.8 + - - -
85B SER 3.3 24.2 + - - -
88B VAL* 4.0 4.7 - - + +
89B LYS* 3.3 39.5 + - + +
92B LEU* 3.9 17.0 - - + -
93B LYS* 3.2 21.3 + - - -
111B ALA* 3.2 25.8 + - + +
113B LEU 3.2 0.2 - - - -
114B ALA* 1.3 78.4 + - - +
116B GLU* 1.3 68.5 + - - +
117B ILE* 3.3 18.8 + - + +
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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