Contacts of the strand formed by residues 131 - 135 (chain H) in PDB entry 1I43
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 SER 131 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H SER* 3.3 10.1 - - - -
129H ALA* 3.5 1.8 - - - +
130H GLU* 1.3 81.8 - - - +
132H THR* 1.3 61.2 + - - +
275H SER* 3.4 2.1 - - - -
276H GLY 3.0 29.7 + - - +
278H LEU* 4.4 15.4 - - - +
281H VAL* 3.1 31.8 - - - +
285H ARG* 3.4 18.5 + - - -
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Residues in contact with THR 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H GLU* 3.0 48.7 + - - +
123H ILE* 3.7 19.5 - - + +
124H SER* 2.9 30.1 + - - -
131H SER* 1.3 74.6 + - - +
133H LEU* 1.3 70.2 + - - +
134H LEU* 4.5 3.1 - - + -
273H CYS* 4.4 8.7 - - - -
274H ILE 3.2 9.9 - - - +
275H SER* 3.0 24.2 + - - +
281H VAL* 4.5 0.2 - - - -
285H ARG* 3.8 3.5 + - - -
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H GLU* 4.0 2.7 - - - +
132H THR* 1.3 73.2 - - - +
134H LEU* 1.3 67.0 + - - +
135H MET* 3.6 36.3 + - + +
272H GLY 3.9 0.2 - - - +
273H CYS* 3.8 3.3 - - - -
274H ILE* 2.7 38.8 + - + +
281H VAL* 3.9 16.6 - - + +
284H ILE* 3.8 19.7 - - + -
285H ARG* 3.8 50.9 - - + +
288H HIS* 4.1 19.7 - - + -
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H THR* 4.3 10.7 - - + +
119H LEU* 3.5 45.8 - - + +
120H GLU* 3.5 43.0 + - + +
123H ILE* 4.2 13.5 - - + -
132H THR* 4.5 1.8 - - + -
133H LEU* 1.3 79.4 - - - +
135H MET* 1.3 64.7 + - - +
259H ALA* 5.2 2.0 - - + -
271H ALA* 4.4 12.1 - - + -
272H GLY 3.3 18.4 - - - +
273H CYS* 4.6 3.4 - - - -
288H HIS* 4.0 11.3 + - - -
295H LEU* 4.1 25.6 + - + +
303H ILE* 4.7 0.9 - - + -
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Residues in contact with MET 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H LEU* 3.6 36.1 - - + +
134H LEU* 1.3 73.2 - - - +
136H ALA* 1.3 62.6 + - - +
137H SER 3.2 6.5 - - - +
140H CYS* 3.6 20.2 - - + +
141H ALA* 3.5 28.5 - - - -
144H VAL* 3.4 37.2 - - + -
271H ALA* 4.0 0.3 - - - +
272H GLY* 3.0 24.3 + - - -
274H ILE* 3.8 11.2 - - + -
284H ILE* 4.1 0.4 - - + -
288H HIS* 3.4 24.7 - - + +
293H GLY 3.6 5.8 - - - +
295H LEU* 3.3 21.3 - - - +
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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