Contacts of the helix formed by residues 131 - 140 (chain C) in PDB entry 3R2W
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 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C VAL* 6.1 1.6 - - + -
101C LYS* 3.7 36.8 - - + -
127C PHE 2.9 15.9 + - - -
128C LEU* 2.9 13.8 + - + -
130C LEU* 1.3 77.1 - - - +
132C VAL* 1.3 64.5 + - - +
133C GLN 3.1 1.3 - - - -
134C GLN* 3.1 23.3 + - - +
135C ILE* 3.2 26.9 + - + +
148C LEU* 5.5 8.1 - - + -
241C ILE* 3.5 16.7 - - + +
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Residues in contact with VAL 132 (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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128C LEU* 3.2 17.5 + - + +
129C ASP* 3.5 14.1 - - - +
131C THR* 1.3 74.8 - - - +
133C GLN* 1.3 62.7 + - + +
135C ILE* 3.9 9.3 - - - +
136C GLU* 3.0 44.3 + - - +
148C LEU* 5.6 5.6 - - + -
167C TYR* 3.7 41.7 - - + -
170C CYS* 5.4 3.4 - - - -
172C VAL* 4.3 20.5 - - + +
174C ILE* 5.5 8.7 - - + -
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Residues in contact with GLN 133 (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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125C ASN* 3.2 24.2 - - - +
129C ASP 2.7 27.5 + - - +
130C LEU* 3.8 9.5 - - - +
131C THR 3.1 0.2 - - - -
132C VAL* 1.3 82.5 - - + +
134C GLN* 1.3 59.0 + - - +
136C GLU* 3.6 21.9 - - - +
137C HIS* 3.5 16.6 + - - +
400C LEU* 5.3 6.9 - - - +
402C ALA* 3.3 11.3 - - - +
403C GLY* 3.3 28.9 - - - +
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Residues in contact with GLN 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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101C LYS* 5.1 3.8 - - - +
130C LEU* 3.1 21.3 + - - +
131C THR* 3.1 22.8 + - - +
133C GLN* 1.3 76.5 - - - +
135C ILE* 1.3 67.3 + - + +
137C HIS* 3.4 3.6 + - - +
138C LEU* 3.2 36.7 + - + +
244C LEU 5.7 2.1 + - - +
246C ALA 4.3 6.9 + - - +
247C THR* 3.5 26.8 + - - +
248C VAL* 5.0 2.5 + - + +
402C ALA 3.7 5.8 - - - -
404C SER* 3.3 41.8 - - - +
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Residues in contact with ILE 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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99C VAL* 4.6 27.8 - - + -
131C THR* 3.2 22.7 - - + +
132C VAL* 3.9 7.0 - - - +
134C GLN* 1.3 75.4 - - + +
136C GLU* 1.3 65.6 + - - +
138C LEU* 3.3 9.0 + - + +
139C ASN* 3.0 36.1 + - - +
146C VAL* 3.5 32.1 - - + +
148C LEU* 4.7 17.9 - - + +
172C VAL* 3.7 18.8 - - + -
248C VAL* 5.6 6.3 - - + -
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Residues in contact with GLU 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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132C VAL* 3.0 31.1 + - - +
133C GLN* 3.6 23.7 - - - +
135C ILE* 1.3 76.7 - - - +
137C HIS* 1.3 58.5 + - + +
139C ASN* 3.1 1.7 + - - +
140C LYS* 2.8 34.0 + - + +
170C CYS* 3.3 27.2 - - - -
171C ARG* 4.4 28.1 - - + +
172C VAL* 4.4 6.2 - - + +
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Residues in contact with HIS 137 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C GLN 3.5 13.8 + - - +
134C GLN 3.4 5.8 + - - +
135C ILE 3.3 0.8 - - - -
136C GLU* 1.3 79.4 - - - +
138C LEU* 1.3 60.6 + - + +
140C LYS* 3.9 4.3 + - - +
141C THR* 2.6 49.3 + - + +
402C ALA* 3.6 32.9 - - + +
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Residues in contact with LEU 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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134C GLN* 3.2 25.5 + - + +
135C ILE* 3.3 9.1 + - + +
136C GLU 3.2 0.4 - - - -
137C HIS* 1.3 88.2 - - + +
139C ASN* 1.3 66.7 + - - +
141C THR* 3.7 2.7 - - - -
142C TYR* 3.3 34.6 - - + -
144C THR* 3.6 12.0 - - + +
146C VAL* 6.4 1.6 - - + -
247C THR* 5.8 2.7 - - - +
248C VAL* 4.4 28.9 - - + +
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Residues in contact with ASN 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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135C ILE* 3.0 30.7 + - - +
136C GLU 3.6 2.7 - - - +
138C LEU* 1.3 77.0 - - - +
140C LYS* 1.3 57.5 + - - +
141C THR 2.9 10.8 + - - -
142C TYR 3.3 9.5 + - - -
143C ASN 3.4 5.7 + - - -
144C THR* 3.0 29.8 + - - +
145C ASP* 4.3 4.9 + - - +
146C VAL* 3.5 29.4 + - - +
171C ARG* 2.8 54.9 + - - +
172C VAL* 4.6 1.0 - - - +
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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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136C GLU* 2.8 20.0 + - + +
137C HIS* 3.9 5.1 + - - +
139C ASN* 1.3 69.6 - - - +
141C THR* 1.3 67.9 + - - +
171C ARG* 3.7 20.6 - - + +
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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