Contacts of the helix formed by residues 114 - 122 (chain B) in PDB entry 3PU3
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 THR 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B SER 3.6 20.0 - - - +
112B GLN* 2.8 13.2 + - - +
113B LEU* 1.3 79.1 - - - +
115B LEU* 1.3 65.1 + - - +
116B GLY* 3.4 5.0 + - - -
117B TYR* 3.2 16.6 + - - +
118B MET* 3.0 25.1 + - - +
211B ILE* 3.7 7.6 - - - -
214B LYS* 5.7 8.7 - - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B EDO 3.2 28.5 - - - +
114B THR* 1.3 74.4 - - - +
116B GLY* 1.3 63.5 + - - +
118B MET* 3.5 1.9 + - + +
119B GLU* 2.9 35.6 + - - +
211B ILE* 3.8 11.0 - - + +
214B LYS* 4.8 26.2 - - + +
215B LEU* 3.5 25.1 - - + -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 3.2 7.7 + - - -
115B LEU* 1.3 77.6 - - - +
117B TYR* 1.3 51.8 + - - +
119B GLU* 2.9 13.3 + - - +
120B GLU* 2.7 36.5 + - - +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA* 4.1 13.0 - - - +
108B VAL* 3.4 31.3 - - + +
112B GLN* 3.6 30.1 - - + +
113B LEU* 3.7 13.9 - - + -
114B THR* 3.2 14.8 + - - +
116B GLY* 1.3 74.1 - - - +
118B MET* 1.3 68.7 + - - +
120B GLU* 3.1 4.4 + - - -
121B HIS* 2.9 68.7 + + + +
127B ILE* 3.8 23.3 - - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 4.0 14.8 - - + -
114B THR 3.0 18.9 + - - +
115B LEU* 3.8 7.6 - - + +
117B TYR* 1.3 78.9 - - - +
119B GLU* 1.3 54.5 + - - +
121B HIS* 5.5 0.2 - - - -
122B GLY* 2.6 36.1 + - - +
123B PHE* 3.5 49.0 + - + +
127B ILE* 4.0 24.9 - - + -
211B ILE* 4.1 16.4 - - + -
215B LEU* 3.8 26.2 - - + -
314B PHE* 5.4 5.2 - - + -
336B PHE* 5.6 1.1 - - + -
340B LEU* 3.5 18.0 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B EDO 3.5 25.0 + - - +
115B LEU* 2.9 31.7 + - - +
116B GLY* 2.9 13.3 + - - +
118B MET* 1.3 75.9 - - - +
120B GLU* 1.3 69.3 + - - +
121B HIS 3.3 0.3 + - - -
122B GLY* 3.5 6.1 + - - -
340B LEU* 4.8 9.2 - - + +
392B PRO* 5.8 2.8 - - - +
394B HIS* 5.3 10.5 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 2.7 15.8 + - - +
117B TYR* 3.4 4.9 - - - +
119B GLU* 1.3 75.7 - - - +
121B HIS* 1.3 90.8 + - + +
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Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 2.9 66.7 + + + +
118B MET* 5.5 0.2 - - - -
120B GLU* 1.3 99.9 - - + +
122B GLY* 1.3 61.4 + - - +
123B PHE* 3.4 3.2 + - - +
124B THR* 4.2 13.7 + - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B EDO 4.9 0.2 - - - -
118B MET 2.6 22.2 + - - -
119B GLU 3.5 6.7 + - - -
121B HIS* 1.3 70.9 - - - +
123B PHE* 1.3 70.2 + - - +
124B THR* 3.1 15.7 + - - +
340B LEU* 4.1 24.4 - - - +
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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