Contacts of the strand formed by residues 128 - 132 (chain M) in PDB entry 5I2D
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 HIS 128 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73M GLU* 3.2 26.0 + - - -
81M ASN* 3.5 27.6 + - - +
108M GLU* 4.2 12.8 - - + -
109M VAL 3.8 6.5 + - - -
110M LYS* 3.4 26.0 + - - +
126M ASP 3.3 4.0 + - - +
127M LEU* 1.3 85.5 - - - +
129M ILE* 1.3 65.2 + - - +
130M ALA 3.7 18.4 - - - -
131M THR* 3.4 25.5 - - + +
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Residues in contact with ILE 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M GLU* 4.4 3.1 - - - +
78M ILE* 4.0 29.6 - - + +
81M ASN* 3.2 24.4 - - + +
82M LEU* 4.5 18.6 - - + -
85M LEU* 5.9 0.7 - - + -
101M LEU* 4.8 0.9 - - + -
109M VAL* 3.1 20.2 + - + +
110M LYS 3.3 34.8 - - - +
111M ALA* 3.7 6.3 - - + +
114M PHE* 3.7 27.4 - - + -
127M LEU* 4.1 9.9 - - + +
128M HIS* 1.3 82.3 - - - +
130M ALA* 1.3 68.2 + - + +
138M LEU* 5.0 5.4 - - + -
140M MET* 5.0 6.1 - - - -
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Residues in contact with ALA 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M VAL* 4.0 17.3 - - + -
73M GLU* 3.5 12.3 - - - +
78M ILE* 4.2 9.9 - - + -
109M VAL* 2.9 31.7 + - - +
128M HIS* 3.7 7.3 + - - -
129M ILE* 1.3 86.4 - - + +
131M THR* 1.3 60.5 + - - +
132M LEU* 4.1 1.1 - - + -
138M LEU* 4.0 24.5 - - + -
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Residues in contact with THR 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M GLY 4.2 0.2 - - - +
71M VAL* 3.6 5.9 - - - +
72M LYS* 3.2 43.6 + - + +
73M GLU* 2.8 23.0 + - - +
107M LYS 4.1 2.5 - - - -
108M GLU* 3.8 22.4 - - + +
128M HIS* 3.4 25.6 - - + +
130M ALA* 1.3 70.9 - - - +
132M LEU* 1.3 61.9 + - - +
133M GLU* 4.8 2.9 - - - +
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Residues in contact with LEU 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M GLY 3.8 2.0 - - - -
71M VAL* 3.9 22.7 - - + -
103M ALA* 3.4 38.6 - - + +
104M GLU* 3.7 9.4 - - - +
105M GLY 3.3 13.2 - - - +
106M PRO* 3.2 3.1 - - - +
107M LYS* 2.9 36.4 + - + +
109M VAL* 3.7 20.0 - - + -
130M ALA* 4.0 5.4 - - + +
131M THR* 1.3 81.6 - - - +
133M GLU* 1.3 62.3 + - - +
136M GLY 3.8 6.5 - - - +
138M LEU* 3.6 29.6 - - + +
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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