Contacts of the helix formed by residues 125 - 141 (chain C) in PDB entry 3HUU
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 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN* 1.3 72.6 - - - +
126C ASN* 1.3 55.7 + - - +
127C ILE* 3.2 12.1 + - - +
128C ASP* 2.8 54.7 + - + +
129C ALA* 2.9 25.8 + - - +
281C LEU* 4.1 29.8 - - + +
282C ILE 4.3 3.4 + - - -
284C THR* 5.3 1.7 - - - +
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Residues in contact with ASN 126 (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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123C ASP* 3.4 27.7 + - - -
124C ASN* 3.0 20.9 + - - +
125C ASP* 1.3 70.1 - - - +
127C ILE* 1.3 66.8 + - - +
129C ALA* 3.7 8.8 - - - +
130C ALA* 3.1 24.4 + - - +
156C VAL* 3.6 20.1 - - - +
159C ASP* 3.7 25.2 + - + +
160C ARG* 2.7 46.6 + - + +
253C ILE* 4.9 1.7 - - - +
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Residues in contact with ILE 127 (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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112C LYS* 3.8 20.9 - - - +
125C ASP* 3.2 8.7 + - - +
126C ASN* 1.3 77.8 - - - +
128C ASP* 1.3 65.8 + - - +
131C TYR* 3.0 24.9 + - + +
159C ASP* 3.4 34.1 - - + +
162C VAL* 4.3 13.9 - - + -
163C GLY* 3.3 21.7 - - - +
166C GLN* 3.9 25.4 - - - +
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP* 2.8 43.8 + - + +
127C ILE* 1.3 83.5 - - - +
129C ALA* 1.3 58.0 + - - +
131C TYR* 3.1 7.6 + - - +
132C GLN* 2.8 39.9 + - + +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP 2.9 16.5 + - - +
126C ASN* 3.8 13.5 - - - +
127C ILE 3.3 0.4 - - - -
128C ASP* 1.3 75.8 - - - +
130C ALA* 1.3 58.0 + - - +
132C GLN* 3.4 6.0 + - - +
133C LEU* 3.0 27.7 + - - +
235C PHE* 4.2 9.4 - - + -
251C VAL* 4.3 13.2 - - + +
253C ILE* 5.7 0.4 - - + -
284C THR* 3.5 35.4 - - + +
286C ILE* 5.7 0.5 - - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASN 3.1 17.5 + - - +
127C ILE 3.8 3.4 - - - +
129C ALA* 1.3 73.4 - - - +
131C TYR* 1.3 61.9 + - - +
133C LEU* 3.8 1.1 - - - +
134C THR* 2.7 35.0 + - - +
147C PHE* 5.2 1.8 - - + -
160C ARG* 3.1 33.7 - - - +
163C GLY 4.4 1.3 - - - -
164C PHE* 4.0 7.0 - - + +
235C PHE* 3.7 21.7 - - + -
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Residues in contact with TYR 131 (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 ILE* 3.0 15.5 + - + +
128C ASP* 3.3 13.2 - - - +
130C ALA* 1.3 78.0 - - - +
132C GLN* 1.3 70.5 + - - +
134C THR* 3.2 2.9 + - - -
135C GLN* 2.9 43.2 + - - +
163C GLY 3.7 11.4 + - - +
166C GLN* 4.0 16.2 - - + -
167C TYR* 3.5 48.4 - + + -
170C ASP* 2.7 34.1 + - - +
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Residues in contact with GLN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ASP* 2.8 25.3 + - + +
129C ALA* 3.7 7.4 - - - +
131C TYR* 1.3 88.8 - - + +
133C LEU* 1.3 57.1 + - - +
135C GLN* 3.3 28.3 + - - +
136C TYR* 2.9 22.2 + - - +
284C THR* 5.7 2.9 - - - +
286C ILE* 3.4 19.0 - - + +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA 3.0 16.9 + - - +
130C ALA* 3.8 5.4 - - - +
131C TYR 3.3 0.2 - - - -
132C GLN* 1.3 73.2 - - - +
134C THR* 1.3 66.8 + - - +
136C TYR* 3.1 20.1 + - + +
137C LEU* 3.0 34.1 + - + +
205C ILE* 4.0 17.7 - - + -
233C ALA* 4.3 19.7 - - + -
234C THR 4.1 9.0 - - - +
235C PHE* 3.8 23.1 - - + -
249C THR* 4.7 5.2 - - + -
250C SER 5.3 0.9 - - - -
251C VAL* 3.7 28.9 - - + -
286C ILE* 3.8 18.1 - - + +
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Residues in contact with THR 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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130C ALA 2.7 22.7 + - - -
131C TYR 3.7 3.6 - - - -
133C LEU* 1.3 76.7 - - - +
135C GLN* 1.3 56.7 + - - +
137C LEU* 3.2 10.4 + - - +
138C TYR* 2.8 27.4 + - - +
145C ILE* 4.1 13.8 - - + +
147C PHE* 5.8 0.2 - - - -
164C PHE* 3.4 44.1 - - + +
167C TYR* 3.6 28.5 - - + -
168C CYS* 4.6 3.1 - - - -
173C ILE* 6.0 0.2 - - + -
205C ILE* 4.1 6.1 - - + +
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Residues in contact with GLN 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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131C TYR* 2.9 26.6 + - + +
132C GLN* 3.3 28.7 + - - +
134C THR* 1.3 73.1 - - - +
136C TYR* 1.3 66.2 + - - +
138C TYR* 3.2 2.6 + - - +
139C HIS* 3.0 24.7 + - + +
167C TYR* 3.5 37.1 + - + +
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Residues in contact with TYR 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 GLN 2.9 14.3 + - - +
133C LEU* 3.2 13.5 - - + +
135C GLN* 1.3 79.9 - - - +
137C LEU* 1.3 75.3 + - + +
139C HIS* 3.4 13.3 + + - +
140C LEU* 3.3 53.8 + - + +
249C THR* 4.0 16.4 - - + -
286C ILE* 3.5 28.3 - - + -
288C GLU* 2.5 47.9 + - + +
292C THR* 3.8 11.9 + - - -
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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 LEU* 3.0 16.9 + - + +
134C THR* 3.6 6.3 - - - +
136C TYR* 1.3 91.9 - - + +
138C TYR* 1.3 66.0 + - - +
140C LEU* 3.0 17.8 + - + -
142C HIS* 3.1 38.6 + - + +
145C ILE* 4.4 5.8 - - + -
203C VAL* 4.2 16.8 - - + -
205C ILE* 3.6 37.7 - - + -
233C ALA* 4.5 10.5 - - + -
249C THR* 5.4 0.2 - - + -
292C THR* 3.9 26.5 - - + -
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Residues in contact with TYR 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 THR 2.8 14.3 + - - +
135C GLN 3.5 5.4 - - - +
137C LEU* 1.3 74.3 - - - +
139C HIS* 1.3 60.3 + - - +
141C GLY* 2.9 17.3 + - - -
142C HIS 3.5 12.8 - - - -
143C ARG* 2.9 61.5 + - - -
145C ILE* 4.9 2.6 - - + +
167C TYR* 3.2 37.9 - + + +
171C VAL* 3.9 34.3 + - + +
173C ILE* 4.3 11.2 - - + +
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Residues in contact with HIS 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 GLN* 3.0 13.1 + - + +
136C TYR* 3.4 17.5 - + - +
138C TYR* 1.3 81.3 - - + +
140C LEU* 1.3 70.3 + - + +
141C GLY* 3.1 1.3 + - - -
294C LYS* 5.4 3.1 - - - +
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Residues in contact with LEU 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 TYR* 3.4 55.2 - - + +
137C LEU* 3.0 12.5 + - + +
139C HIS* 1.3 87.6 - - + +
141C GLY* 1.3 56.8 + - - +
142C HIS* 3.6 16.2 - - + -
288C GLU* 5.3 0.4 - - - +
292C THR* 3.8 21.8 - - - -
293C THR* 3.9 20.0 - - - +
294C LYS* 3.6 22.3 - - + +
295C ILE* 3.0 32.5 + - - +
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Residues in contact with GLY 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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138C TYR 2.9 10.5 + - - -
139C HIS 3.1 2.0 - - - -
140C LEU* 1.3 79.7 - - - +
142C HIS* 1.3 62.3 + - - +
143C ARG* 3.5 20.7 + - - +
295C ILE* 3.0 25.1 - - - +
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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