Contacts of the helix formed by residues 111 - 116 (chain A) in PDB entry 3DEW
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.5 7.9 - - + -
24A TYR* 4.8 4.0 - - + +
110A THR* 1.3 88.3 - - - +
112A CYS* 1.3 61.0 + - - +
113A PHE 3.1 1.3 + - - -
114A ALA* 3.7 5.8 + - + +
115A ALA* 3.6 14.0 + - - +
205A BME 3.7 20.7 + - + +
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU 5.4 1.1 - - - -
53A TYR* 4.0 19.5 - - + -
54A ALA* 4.1 12.8 - - - -
57A LEU* 3.2 25.6 - - + -
105A GLU* 4.3 0.9 - - - -
110A THR* 3.0 10.2 + - - +
111A PRO* 1.3 77.1 - - - +
113A PHE* 1.3 65.0 + - - +
115A ALA* 3.8 1.6 - - - -
116A ILE* 3.0 22.1 + - + +
117A VAL* 3.4 6.2 + - - +
205A BME 2.0 48.0 - - - -
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Residues in contact with PHE 113 (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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105A GLU* 3.3 34.7 + - + +
106A LEU* 3.6 32.5 - - + -
109A PRO* 3.6 16.6 - - + -
110A THR 2.9 13.0 + - - +
112A CYS* 1.3 77.0 - - - +
114A ALA* 1.3 68.7 + - + +
117A VAL* 3.1 30.4 + - + -
118A SER* 2.8 55.4 + - - -
121A ILE* 5.3 0.2 - - + -
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Residues in contact with ALA 114 (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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110A THR 4.4 0.6 + - - -
111A PRO* 3.7 7.1 + - + +
112A CYS 3.4 0.2 - - - -
113A PHE* 1.3 88.8 - - + +
115A ALA* 1.3 58.1 + - - +
118A SER* 4.3 5.3 - - - -
119A PRO* 3.2 20.3 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A PRO 3.6 8.6 + - - +
112A CYS 3.5 1.7 + - - +
113A PHE 3.2 0.6 - - - -
114A ALA* 1.3 80.5 - - - +
116A ILE* 1.3 66.5 + - + +
119A PRO* 3.6 12.2 - - - +
205A BME 3.8 31.0 - - + +
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Residues in contact with ILE 116 (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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54A ALA* 3.9 20.9 - - + +
57A LEU* 4.0 15.5 - - + +
58A GLN* 3.8 28.7 - - + +
61A PHE* 3.9 29.6 - - + -
112A CYS* 3.0 14.5 + - + +
114A ALA 3.5 0.2 - - - -
115A ALA* 1.3 88.4 - - + +
117A VAL* 1.3 67.1 + - + +
118A SER 3.6 0.7 - - - -
119A PRO* 3.7 3.8 - - - +
120A ALA* 3.3 24.4 + - - +
205A BME 3.7 24.9 - - - -
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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