Contacts of the helix formed by residues 133 - 145 (chain C) in PDB entry 4PJE
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 ASP 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C TYR* 2.6 36.3 + - - -
131C ALA* 3.6 2.7 - - - +
132C VAL* 1.3 90.7 - - + +
134C ASN* 1.3 60.1 + - - +
135C VAL* 3.1 5.3 + - - -
136C ALA* 2.8 31.9 + - - +
137C HIS* 2.9 27.0 + - - +
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Residues in contact with ASN 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ASP* 1.3 75.5 - - - +
135C VAL* 1.3 63.6 + - + +
137C HIS* 3.5 13.6 + - - +
138C THR* 3.1 27.3 + - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.9 16.4 - - + -
83C HIS* 3.7 42.2 - - + +
84C TYR* 3.7 45.1 - - + -
119C PHE* 4.1 0.4 - - + -
133C ASP* 3.1 7.5 + - - +
134C ASN* 1.3 76.6 - - + +
136C ALA* 1.4 64.2 + - - +
138C THR* 3.1 17.6 + - - -
139C ILE* 3.3 13.2 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 3.3 50.2 - - + +
120C LEU* 3.5 6.2 - - + +
131C ALA* 3.6 15.0 - - + -
132C VAL* 3.7 5.2 - - + +
133C ASP* 2.8 21.4 + - - +
135C VAL* 1.4 71.9 - - - +
137C HIS* 1.4 51.9 + - - +
139C ILE* 3.2 2.6 + - - +
140C LYS* 2.8 34.0 + - - +
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Residues in contact with HIS 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ALA* 3.5 10.9 - - + +
133C ASP 2.9 17.4 + - - +
134C ASN* 3.6 16.2 - - - +
135C VAL 3.2 0.4 - - - -
136C ALA* 1.4 76.2 - - - +
138C THR* 1.3 58.3 + - - +
140C LYS* 3.2 26.7 + - + +
141C GLN* 2.9 67.8 + - + +
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Residues in contact with THR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C HIS* 4.6 23.6 - - + +
134C ASN 3.1 15.1 + - - -
135C VAL* 3.1 11.8 + - - -
137C HIS* 1.3 77.2 - - - +
139C ILE* 1.3 65.4 + - + +
141C GLN* 3.4 11.4 + - - +
142C ALA* 3.2 20.5 + - + +
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ARG* 6.0 4.0 - - + -
80C LEU* 3.8 21.5 - - + -
83C HIS* 4.2 26.0 - - + +
92C TYR* 5.8 0.2 - - - +
119C PHE* 4.0 5.4 - - + -
120C LEU* 3.5 18.6 - - + -
135C VAL 3.3 12.7 + - - +
136C ALA 3.2 7.0 + - - +
138C THR* 1.3 76.6 - - + +
140C LYS* 1.4 63.5 + - - +
142C ALA* 3.0 9.3 + - + +
143C TRP* 2.9 58.4 + - + +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.0 17.0 - - + +
128C SER* 4.4 6.3 - - - -
129C TRP* 2.8 29.0 + - + +
131C ALA* 4.1 10.3 - - + +
136C ALA 2.8 17.2 + - - +
137C HIS* 3.4 35.9 - - - +
139C ILE* 1.4 71.9 - - - +
141C GLN* 1.4 59.5 + - + +
143C TRP* 3.3 3.2 + - - -
144C GLU* 2.7 75.7 + - - +
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Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C HIS* 2.9 54.8 + - + +
138C THR* 3.7 9.8 - - - +
139C ILE 3.3 0.2 - - - -
140C LYS* 1.4 77.0 - - + +
142C ALA* 1.3 61.6 + - - +
144C GLU* 4.1 4.9 - - - +
145C ALA* 3.4 22.2 + - - +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C THR* 3.2 8.9 + - + +
139C ILE* 3.0 13.7 + - + +
141C GLN* 1.3 79.0 - - - +
143C TRP* 1.3 70.0 + - + +
145C ALA* 3.5 18.1 + - - +
146C ASN* 4.2 4.2 + - - +
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Residues in contact with TRP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLU* 4.3 18.6 + - + +
92C TYR* 3.9 15.9 - - - -
112C TYR* 3.6 41.1 - + - -
120C LEU* 3.6 25.8 - - + -
129C TRP* 3.5 43.3 - + + +
139C ILE* 2.9 34.9 + - + +
140C LYS 3.9 2.7 - - - +
142C ALA* 1.3 81.6 - - + +
144C GLU* 1.3 62.4 + - - +
145C ALA 3.3 1.0 + - - -
146C ASN* 3.3 23.4 + - - +
149C GLU* 4.8 18.6 + - - +
150C LEU* 4.2 7.3 - - + +
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU 4.9 0.4 - - - -
128C SER* 3.4 12.1 - - - -
129C TRP* 2.8 34.3 + - + +
140C LYS* 2.7 60.6 + - - +
141C GLN* 4.1 5.2 - - - +
143C TRP* 1.3 70.3 - - - +
145C ALA* 1.3 57.8 + - - +
146C ASN 3.1 6.9 + - - -
147C GLN* 4.3 5.5 + - - +
150C LEU* 3.8 26.0 - - + +
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLN 3.4 12.1 + - - +
142C ALA* 3.5 15.3 - - - +
143C TRP 3.2 1.2 - - - -
144C GLU* 1.3 75.6 - - - +
146C ASN* 1.3 57.4 + - - +
147C GLN* 3.6 4.8 + - - +
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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