Contacts of the helix formed by residues 125 - 130 (chain A) in PDB entry 3QEM
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 MET 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR* 6.6 0.2 - - + -
123A THR* 3.6 10.3 - - + +
124A ARG* 1.3 78.6 - - - +
126A SER* 1.3 56.5 + - - +
127A ILE* 3.3 6.1 + - + +
128A TYR* 3.8 21.4 + - + -
139A ARG* 2.6 36.3 + - - +
144A TYR* 4.1 19.3 - - + -
171A HIS* 6.3 1.1 - - + +
172A GLU* 3.2 44.6 - - + +
273A ARG* 4.3 13.9 - - - +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 1.3 71.8 - - - +
127A ILE* 1.3 65.0 + - - +
128A TYR 3.2 2.7 - - - -
129A SER* 3.1 20.1 + - - -
130A ASP* 4.1 1.2 + - - +
139A ARG* 4.0 5.2 - - - +
143A PRO* 3.8 4.3 - - - +
145A SER* 3.0 26.1 + - - -
171A HIS* 3.6 15.1 + - - -
172A GLU* 2.8 33.0 + - - -
175A ALA* 3.5 22.7 - - - -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.3 4.6 - - + +
126A SER* 1.3 77.5 - - - +
128A TYR* 1.3 73.6 + - + +
129A SER 3.1 5.2 + - - -
130A ASP* 3.1 23.6 + - - +
133A ILE* 4.5 4.6 - - + +
134A HIS* 3.7 15.0 - - + +
171A HIS* 3.6 20.7 + - + +
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Residues in contact with TYR 128 (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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103A THR* 3.5 14.3 - - + +
104A PRO* 3.5 30.2 - - + +
105A THR* 2.6 31.4 + - - -
123A THR* 4.3 12.1 - - + -
125A MET* 3.8 24.9 + - + -
126A SER 3.2 1.2 - - - -
127A ILE* 1.3 86.3 - - + +
129A SER* 1.3 57.5 + - - +
130A ASP 3.2 2.8 + - - -
134A HIS* 3.8 42.8 - + - +
137A PHE* 3.7 51.4 - + + +
139A ARG* 3.9 15.7 - - - +
364A ASP 4.7 2.6 - - - +
366A ASP* 4.9 1.7 - - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.1 15.7 + - - -
127A ILE 3.1 1.6 + - - -
128A TYR* 1.3 77.9 - - - +
130A ASP* 1.3 57.5 + - - +
131A LYS* 3.4 7.0 + - - +
139A ARG* 3.2 11.1 + - - +
143A PRO* 3.8 7.8 - - - +
145A SER* 6.1 0.2 - - - -
364A ASP* 3.3 33.9 - - - +
366A ASP* 2.7 36.8 + - - -
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 4.1 2.4 + - - +
127A ILE* 3.1 16.9 + - - +
128A TYR 3.2 0.4 - - - -
129A SER* 1.3 75.1 - - - +
131A LYS* 1.3 59.0 + - - +
132A SER* 3.0 23.1 + - - -
133A ILE* 3.1 24.4 + - + +
134A HIS* 2.8 29.0 + - - +
171A HIS* 5.1 10.4 + - + -
175B TYR* 5.9 0.2 - - - -
180B GLN* 5.4 4.5 + - - -
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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
------------------------------------------------------------
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