Contacts of the helix formed by residues 119 - 123 (chain B) in PDB entry 2EX4
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 GLY 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.3 22.6 - - - +
118B CYS* 1.3 80.9 - - - +
120B LEU* 1.3 65.2 + - - -
121B GLN* 3.0 18.6 - - - -
122B ASP* 2.9 16.7 + - - +
123B PHE* 3.1 9.6 + - - +
1402B SAH 3.4 1.1 - - - -
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Residues in contact with LEU 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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69B CYS* 4.0 12.1 - - + -
70B GLY 4.1 2.2 - - - +
91B VAL* 3.7 33.7 - - + -
119B GLY* 1.3 71.6 - - - -
121B GLN* 1.3 58.8 + - - +
122B ASP 3.1 0.2 - - - -
123B PHE* 3.0 11.8 + - + -
135B ILE* 4.5 3.4 - - + -
138B VAL* 4.0 32.3 - - + +
139B ILE* 6.1 0.7 - - - -
142B LEU* 4.1 21.8 - - + -
150B PHE* 3.4 40.0 - - + -
153B ARG* 3.0 20.8 + - - -
1402B SAH 2.9 31.2 + - + +
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Residues in contact with GLN 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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13B TYR* 3.6 44.1 - - + +
93B ILE* 5.3 1.6 - - - +
119B GLY* 3.9 11.7 - - - -
120B LEU* 1.3 82.8 + - - +
122B ASP* 1.3 80.4 + - - +
123B PHE 3.5 0.2 - - - -
142B LEU* 4.0 6.2 - - + +
146B HIS* 3.7 43.3 + - + +
153B ARG* 3.5 14.8 + - - +
1402B SAH 3.1 23.6 + - - -
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Residues in contact with ASP 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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118B CYS* 3.6 16.4 - - - -
119B GLY* 2.9 12.4 + - - +
121B GLN* 1.3 102.1 + - - +
123B PHE* 1.3 59.7 + - - +
124B THR* 4.0 4.5 + - - -
153B ARG* 4.6 1.1 - - - -
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Residues in contact with PHE 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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67B LEU* 3.8 27.6 - - + -
91B VAL* 4.0 25.1 - - + -
116B PHE* 3.5 51.8 - + + -
118B CYS* 4.0 13.0 - - + -
119B GLY 3.5 13.2 - - - +
120B LEU* 3.0 13.0 + - + +
121B GLN 3.5 0.2 - - - -
122B ASP* 1.3 79.6 - - - +
124B THR* 1.3 62.7 + - - +
125B PRO* 3.7 27.4 - - + +
130B TYR* 4.9 2.2 - - - -
150B PHE* 3.9 13.9 - + + -
153B ARG* 2.7 30.2 + - - -
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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