Contacts of the helix formed by residues 132 - 146 (chain C) in PDB entry 1R4N
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 PRO 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ASN* 6.0 0.2 - - - +
130C GLN 4.3 2.9 - - - +
131C LEU* 1.3 94.3 - - + +
133C GLU* 1.3 73.1 + - - +
134C SER* 4.2 11.0 - - - +
135C THR* 3.0 18.0 + - - +
136C SER* 2.9 15.3 + - - -
433C ASP* 4.5 2.9 - - - +
436C HIS* 4.5 18.8 - - + +
442C TYR* 4.1 21.8 - - - +
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Residues in contact with GLU 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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131C LEU 4.0 0.8 + - - -
132C PRO* 1.3 69.4 - - - +
134C SER* 1.3 70.0 + - - +
136C SER* 2.7 21.8 + - - -
137C LEU* 3.0 24.4 + - + +
402C TYR* 3.5 23.3 + - + +
430C ARG* 2.7 33.4 + - - +
433C ASP* 3.6 45.2 + - + +
434C ARG* 4.8 2.4 + - - -
437C LYS* 5.8 7.7 - - + +
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLU* 3.9 7.8 + - - -
132C PRO* 4.2 10.1 - - - +
133C GLU* 1.3 78.9 - - - +
135C THR* 1.3 75.5 + - - -
137C LEU* 3.9 5.3 + - - +
138C ARG* 3.2 22.7 + - - +
437C LYS* 5.9 9.0 - - - -
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Residues in contact with THR 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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109C PRO* 4.2 19.5 - - + -
110C GLU* 2.4 37.6 + - + +
113C LEU* 4.6 8.7 - - + -
131C LEU* 4.2 21.1 - - + -
132C PRO* 3.0 22.7 + - - +
133C GLU 2.8 3.2 + - - -
134C SER* 1.3 82.4 + - - +
136C SER* 1.3 65.7 + - - +
138C ARG* 3.3 2.7 + - - +
139C LEU* 2.8 24.8 + - + +
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Residues in contact with SER 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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131C LEU* 3.4 34.9 + - - +
132C PRO 2.9 8.2 + - - -
133C GLU* 2.7 18.1 + - - -
135C THR* 1.3 71.5 - - - +
137C LEU* 1.3 60.3 + - - -
139C LEU* 3.7 1.7 - - - +
140C ALA* 2.8 31.5 + - - +
152C ILE* 4.1 24.5 - - - +
398C LEU* 4.0 7.4 - - - -
402C TYR* 6.5 1.1 - - - -
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Residues in contact with LEU 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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133C GLU* 3.0 25.0 + - + +
134C SER* 4.2 4.3 - - - +
136C SER* 1.3 82.4 - - - +
138C ARG* 1.3 64.1 + - - +
140C ALA* 3.4 1.7 + - - +
141C ASP* 3.2 22.3 + - - +
398C LEU* 3.8 26.8 - - + +
399C ALA* 4.9 4.0 - - - +
402C TYR* 3.5 51.6 - - + -
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Residues in contact with ARG 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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110C GLU* 2.9 27.8 + - - -
113C LEU* 2.7 50.1 + - + +
114C ASP* 2.8 33.3 + - - +
134C SER 3.2 18.0 + - - +
135C THR* 3.7 4.3 - - - +
137C LEU* 1.3 80.9 - - - +
139C LEU* 1.3 58.1 + - - +
141C ASP* 3.6 5.4 - - - +
142C VAL* 3.2 28.5 + - + +
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Residues in contact with LEU 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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36C ILE* 4.5 11.4 - - + -
109C PRO* 6.0 2.5 - - + -
113C LEU* 3.6 34.1 - - + +
120C PHE* 4.0 17.0 - - + -
126C VAL* 4.7 0.4 - - + -
128C ALA* 4.0 18.4 - - + -
131C LEU* 4.2 8.7 - - + -
135C THR* 2.8 24.1 + - + +
136C SER* 3.7 2.0 - - - +
138C ARG* 1.3 70.1 - - - +
140C ALA* 1.3 55.0 + - - +
141C ASP 2.7 15.5 + - - -
142C VAL 3.1 0.7 + - - -
143C LEU* 2.9 49.1 + - + +
150C LEU* 3.7 25.8 - - + -
152C ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 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 SER 2.8 13.0 + - - +
137C LEU 3.9 2.2 - - - +
139C LEU* 1.3 71.6 - - - +
141C ASP* 1.3 55.2 + - - +
143C LEU* 4.8 0.2 - - - -
144C TRP* 3.2 24.0 + - - +
150C LEU* 3.2 27.5 - - + +
152C ILE* 4.5 0.2 - - + -
165C ILE* 3.7 10.9 - - + +
397C SER* 5.8 0.2 - - - -
398C LEU* 3.2 49.3 + - + +
399C ALA 5.8 0.4 + - - -
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Residues in contact with ASP 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 LEU 3.2 16.2 + - - +
138C ARG* 3.6 6.5 - - - +
139C LEU 2.7 0.8 + - - -
140C ALA* 1.3 77.8 - - - +
142C VAL* 1.3 73.7 + - - +
143C LEU 3.0 0.7 - - - -
144C TRP* 2.7 17.5 + - - +
145C ASN* 3.0 32.0 + - - -
399C ALA* 5.2 11.6 - - + +
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Residues in contact with VAL 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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113C LEU* 3.8 26.7 - - + +
117C PRO* 3.7 36.8 - - + +
120C PHE* 5.4 2.5 - - + -
138C ARG* 3.2 21.8 - - + +
139C LEU 3.1 4.2 + - - +
141C ASP* 1.3 82.7 + - - +
143C LEU* 1.3 63.8 + - + +
145C ASN* 3.5 6.4 + - - +
146C SER* 2.9 35.8 + - - +
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Residues in contact with LEU 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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120C PHE* 3.4 35.0 - - + -
126C VAL* 3.9 11.0 - - + -
139C LEU* 2.9 38.0 + - + +
140C ALA 4.7 1.1 - - - +
142C VAL* 1.3 78.3 - - + +
144C TRP* 1.3 64.0 + - - +
146C SER* 3.2 4.1 + - - -
147C GLN 3.0 4.3 + - - -
148C ILE* 2.9 59.6 + - + +
150C LEU* 3.2 43.5 - - + -
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Residues in contact with TRP 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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140C ALA 3.2 21.5 + - - +
141C ASP* 2.7 15.0 + - - +
143C LEU* 1.3 72.9 - - - +
145C ASN* 1.3 76.2 + - - +
147C GLN* 3.0 22.8 + - - +
148C ILE 4.7 4.3 - - - +
165C ILE* 3.6 23.6 - - + -
167C LYS* 3.9 55.3 - - + +
395C CYS 3.6 20.2 - - - -
397C SER* 3.2 45.1 - - - -
400C GLU* 5.1 5.8 - - - -
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Residues in contact with ASN 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 ASP* 3.0 37.2 + - - -
142C VAL* 3.9 7.4 - - - +
144C TRP* 1.3 87.5 - - - +
146C SER* 1.3 59.1 + - - +
147C GLN* 3.1 17.9 + - - +
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Residues in contact with SER 146 (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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117C PRO 5.3 2.6 + - - -
118C SER* 5.6 1.7 - - - -
120C PHE* 5.9 0.7 - - - -
121C CYS* 3.8 29.6 - - - -
142C VAL* 2.9 26.3 + - - +
143C LEU* 3.7 7.6 - - - -
144C TRP 3.2 0.4 - - - -
145C ASN* 1.3 75.6 - - - +
147C GLN* 1.3 71.1 + - - +
148C ILE* 3.5 15.7 + - - +
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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