Contacts of the strand formed by residues 126 - 132 (chain D) in PDB entry 1M7X
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 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D LEU* 1.3 76.3 - - - +
127D ALA* 1.3 60.2 + - - -
128D HIS* 4.1 2.0 + - - -
139D ARG 3.2 6.2 - - - +
140D PHE* 3.4 0.5 - - - -
141D SER* 3.0 38.7 + - - -
190D TYR* 4.1 2.5 - - - -
204D ASP* 3.0 24.7 + - - -
206D TYR* 4.0 12.2 - - - +
208D PHE* 4.8 0.4 - - - -
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU 4.1 0.8 + - - -
126D GLY* 1.3 72.7 - - - -
128D HIS* 1.3 68.6 + - - +
138D THR* 4.9 2.0 - - - +
139D ARG 3.2 6.3 - - - +
140D PHE* 3.8 28.5 - - + -
188D TYR* 3.9 18.1 + - + +
204D ASP* 3.9 1.8 + - - -
208D PHE* 4.1 8.7 - - + -
220D ILE* 4.4 17.4 - - + +
221D CYS 3.3 21.6 - - - +
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D TYR 3.0 23.3 + - - -
123D GLU 3.6 13.2 + - - +
124D THR* 3.7 18.4 - - - -
125D LEU 2.7 27.7 + - - -
126D GLY 4.2 2.0 - - - -
127D ALA* 1.3 77.2 + - - +
129D ALA* 1.3 70.7 + - - +
138D THR* 3.2 4.2 - - - -
139D ARG* 2.8 37.0 + - + +
141D SER* 5.6 0.2 - - - -
208D PHE* 3.3 17.1 - + - -
220D ILE* 6.3 0.4 - - - -
221D CYS 5.8 0.2 - - - -
222D GLY* 4.6 9.3 - - - -
223D LEU* 3.2 23.6 + - + +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D HIS* 1.3 84.1 - - - +
130D ASP* 1.3 64.3 + - - +
136D THR* 6.3 1.6 - - + -
137D GLY 3.6 10.8 - - - +
138D THR* 4.2 6.2 - - + +
184D ASN* 6.0 2.2 - - - +
222D GLY* 5.6 3.4 - - - -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D HIS 4.2 3.8 - - - +
129D ALA* 1.3 79.1 - - - +
131D THR* 1.3 94.0 + - - +
136D THR* 3.7 3.3 - - - +
137D GLY 3.2 25.8 + - - +
139D ARG* 3.3 31.6 + - + -
178D PHE* 3.6 19.1 - - + -
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP* 1.3 96.2 + - - +
132D MET* 1.3 81.8 + - - +
133D ASP 5.0 0.2 - - - +
134D GLY* 3.5 15.5 - - - +
135D VAL 3.1 28.7 - - - +
136D THR* 3.8 13.0 + - - +
178D PHE* 3.8 1.6 - - - -
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Residues in contact with MET 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D THR* 1.3 86.5 - - - +
133D ASP* 1.3 63.9 + - + +
134D GLY 2.9 3.8 - - - -
135D VAL* 2.6 37.9 + - + +
139D ARG* 3.3 30.3 - - - +
178D PHE* 3.4 33.0 - - + -
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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