Contacts of the helix formed by residues 123 - 127 (chain B) in PDB entry 1YM4
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 TYR 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 2.6 23.0 + - - -
122B ALA* 1.3 78.4 - - - +
124B ALA* 1.3 66.9 + - - +
125B GLU 3.2 2.8 + - - +
126B ILE* 3.3 8.0 + - - +
135B PRO* 4.1 0.7 - - - -
138B ASP* 5.1 4.7 - - - -
193B ILE* 3.5 23.0 - - + +
196B GLU* 3.5 55.3 + - + +
197B TRP* 3.1 27.2 + - - +
198B TYR 4.1 4.0 - - - -
199B TYR* 3.5 26.0 - + - -
347B ARG* 3.5 50.2 + - + +
350B LYS* 5.5 0.9 - - - -
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Residues in contact with ALA 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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123B TYR* 1.3 73.4 - - - +
125B GLU* 1.3 64.2 + - - +
127B ALA* 2.7 22.2 + - - +
131B ASP* 3.4 33.5 - - + +
133B LEU 4.5 0.9 - - - +
134B GLU* 5.2 0.7 - - - -
135B PRO* 3.6 33.3 - - + +
138B ASP* 4.8 2.7 + - - +
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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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123B TYR* 3.2 1.6 - - - +
124B ALA* 1.3 78.3 - - - +
126B ILE* 1.3 58.1 + - + +
127B ALA 3.6 4.3 + - - +
131B ASP* 4.1 15.6 + - - +
195B ARG* 2.7 40.4 + - - +
196B GLU 3.3 22.8 - - - +
197B TRP* 3.9 14.1 - - + -
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Residues in contact with ILE 126 (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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34B GLY 4.2 5.6 - - - +
35B SER* 4.5 2.9 - - - -
36B SER* 3.1 23.9 + - - +
37B ASN* 4.8 0.9 - - - +
122B ALA* 3.8 7.2 - - + -
123B TYR 3.5 0.4 - - - +
124B ALA 3.1 0.4 - - - -
125B GLU* 1.3 79.0 - - + +
127B ALA* 1.3 60.0 + - - +
128B ARG* 4.1 8.4 + - - +
197B TRP* 3.1 58.8 - - + +
198B TYR* 3.6 37.9 - - + +
5Y ALA* 4.0 25.2 - - + +
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Residues in contact with ALA 127 (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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36B SER* 3.9 21.1 - - - +
37B ASN* 3.7 9.6 - - - +
124B ALA* 2.7 24.4 + - - +
125B GLU 3.3 2.5 - - - +
126B ILE* 1.3 75.7 - - - +
128B ARG* 1.3 66.9 + - - +
129B PRO 3.7 0.7 - - - -
130B ASP* 3.2 26.6 - - - +
131B ASP 3.9 0.3 + - - -
133B LEU* 3.9 21.8 - - + +
135B PRO* 4.9 0.2 - - + -
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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