Contacts of the helix formed by residues 118 - 122 (chain A) in PDB entry 5E1M
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.8 18.3 - - - +
117A CYS* 1.3 80.5 - - - +
119A LEU* 1.3 66.9 + - - -
120A GLN* 3.1 15.9 - - - -
121A ASP* 2.9 18.1 + - - +
122A PHE* 3.2 9.3 + - - +
301A SAH 3.3 11.4 - - - -
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Residues in contact with LEU 119 (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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68A CYS* 4.1 9.4 - - + -
69A GLY 4.1 2.9 - - - +
90A VAL* 3.8 32.8 - - + -
118A GLY* 1.3 70.8 - - - -
120A GLN* 1.3 59.3 + - - +
122A PHE* 3.0 11.8 + - + -
134A ILE* 4.7 2.7 - - + -
137A VAL* 4.0 33.7 - - + +
138A ILE* 6.0 0.9 - - - -
141A LEU* 4.0 22.2 - - + -
146A LEU* 6.5 0.2 - - + -
149A PHE* 3.4 42.8 - - + -
152A ARG* 3.0 21.1 + - - -
301A SAH 2.9 29.1 + - + +
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Residues in contact with GLN 120 (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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13A TYR* 3.5 32.3 - - + +
92A ILE* 4.6 7.7 - - - +
118A GLY* 4.0 10.7 - - - -
119A LEU* 1.3 80.7 + - - +
121A ASP* 1.3 63.6 + - - +
122A PHE 3.6 0.4 - - - -
141A LEU* 3.6 10.7 - - + +
145A HIS* 3.8 37.0 - - + +
152A ARG* 3.6 15.5 + - - +
301A SAH 3.0 24.8 + - - -
314A UNX 3.0 28.4 - - - -
323A UNX 2.9 22.9 - - - -
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Residues in contact with ASP 121 (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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117A CYS* 3.6 17.4 - - - -
118A GLY* 2.9 13.8 + - - +
120A GLN* 1.3 89.9 + - - +
122A PHE* 1.3 59.3 + - - +
123A THR* 4.0 3.7 + - - -
152A ARG* 4.6 1.3 - - - -
314A UNX 3.6 15.9 - - - -
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Residues in contact with PHE 122 (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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66A LEU* 4.0 18.2 - - + -
90A VAL* 4.0 25.6 - - + -
115A PHE* 3.5 54.1 - + + -
117A CYS* 4.0 11.0 - - + -
118A GLY 3.6 12.8 - - - +
119A LEU* 3.0 12.6 + - + +
120A GLN 3.6 0.6 - - - -
121A ASP* 1.3 77.6 - - - +
123A THR* 1.3 63.2 + - - +
124A PRO* 3.6 40.2 - - + +
129A TYR* 4.8 0.7 - - - -
149A PHE* 3.9 14.5 - + + -
152A ARG* 2.8 29.3 + - - -
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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