Contacts of the helix formed by residues 131 - 147 (chain C) in PDB entry 4QOZ
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 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C GLU* 3.2 15.3 + - - +
130C THR* 1.3 75.7 + - - +
132C GLU* 1.3 64.7 + - - +
133C SER* 2.8 39.9 + - - -
134C VAL* 3.1 18.0 + - + +
135C LEU* 3.1 22.5 + - - +
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Residues in contact with GLU 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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130C THR 3.1 7.3 + - - +
131C ASP* 1.3 73.1 + - - +
133C SER* 1.3 56.8 + - - +
135C LEU* 3.8 18.6 - - - +
136C MET* 2.9 57.5 + - + +
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Residues in contact with SER 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 ASP* 2.8 15.5 + - - -
132C GLU* 1.3 76.2 - - - +
134C VAL* 1.3 66.2 + - - +
136C MET* 3.4 5.4 + - - +
137C ARG* 3.0 31.6 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A U 6.0 0.7 - - - +
129C GLU* 4.0 18.6 - - + +
131C ASP* 3.1 26.3 + - + +
133C SER* 1.3 79.6 - - - +
135C LEU* 1.3 55.7 + - - +
137C ARG* 3.3 33.3 + - - +
138C ARG* 2.9 68.5 + - - +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLU* 3.9 25.1 - - + +
130C THR* 3.9 22.0 - - - +
131C ASP 3.1 14.3 + - - +
132C GLU* 3.8 23.8 - - - +
134C VAL* 1.3 74.7 - - - +
136C MET* 1.3 62.1 + - + +
138C ARG* 3.2 5.2 + - - +
139C GLN* 2.9 31.0 + - - +
174C LYS* 3.4 42.6 - - + +
175C PHE* 3.9 24.5 - - + -
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Residues in contact with MET 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLU* 2.9 49.4 + - + +
133C SER* 3.6 6.7 - - - +
134C VAL 3.3 0.2 - - - -
135C LEU* 1.3 76.6 - - + +
137C ARG* 1.3 66.4 + - - +
139C GLN* 3.3 14.8 + - + +
140C LYS* 3.0 23.1 + - - +
174C LYS* 5.7 3.8 - - - +
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Residues in contact with ARG 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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9A U 3.7 23.8 + - - -
10A C 3.5 27.5 + - - -
133C SER* 3.0 25.4 + - - +
134C VAL* 3.7 41.5 + - - +
136C MET* 1.3 75.3 - - - +
138C ARG* 1.3 69.9 + - - +
140C LYS* 3.1 12.4 + - - +
141C GLN* 3.0 36.1 + - + +
180C ARG* 3.3 35.4 - - - +
183C TRP* 6.1 1.2 - - - -
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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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129C GLU* 4.0 10.3 + - - +
134C VAL* 2.9 44.1 + - + +
135C LEU* 3.7 3.8 - - - +
137C ARG* 1.3 82.1 - - + +
139C GLN* 1.3 65.3 + - - +
141C GLN* 3.2 12.1 + - - +
142C ILE* 3.0 28.6 + - - +
174C LYS* 3.0 33.0 + - + +
176C LYS 2.8 24.7 + - - -
178C TYR* 3.4 34.1 + - - +
179C SER 5.0 0.8 + - - -
180C ARG* 6.0 0.6 - - - +
183C TRP* 3.6 55.5 - - + +
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Residues in contact with GLN 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 LEU 2.9 17.2 + - - +
136C MET* 3.8 14.1 - - + +
138C ARG* 1.3 76.4 - - - +
140C LYS* 1.3 58.0 + - - +
142C ILE* 3.3 24.0 + - - +
143C ASN* 2.8 65.1 + - - +
146C LYS* 5.6 2.8 - - - +
174C LYS* 2.7 40.1 + - - +
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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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11A U 4.8 12.3 + - - +
12A U 2.8 26.7 + - - -
136C MET 3.0 13.3 + - - +
137C ARG* 3.1 13.0 + - - +
139C GLN* 1.3 77.2 - - - +
141C GLN* 1.3 63.5 + - + +
143C ASN* 3.3 10.5 + - + +
144C TYR* 3.0 60.8 + - + -
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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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11A U 5.7 3.0 + - - +
14A U 6.1 1.3 - - - +
137C ARG* 3.0 34.0 + - + +
138C ARG* 3.2 8.6 + - - +
140C LYS* 1.3 76.6 - - + +
142C ILE* 1.3 62.5 + - - +
144C TYR* 3.2 11.9 + - + +
145C GLY* 3.1 16.1 + - - -
180C ARG* 5.6 2.3 - - - +
183C TRP* 3.1 24.6 + - - +
184C ASP* 3.0 27.4 + - - +
187C ILE* 4.3 29.4 - - + +
190C TRP* 4.3 2.8 - - - -
191C LYS* 4.7 6.2 - - - +
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Residues in contact with ILE 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 ARG 3.0 25.8 + - - +
139C GLN* 3.6 28.0 - - - +
141C GLN* 1.3 73.5 - - - +
143C ASN* 1.3 56.1 + - - +
145C GLY* 2.7 22.2 + - - -
146C LYS* 2.9 43.2 + - + +
171C TPO 3.8 17.3 - - + -
172C PRO 3.9 18.6 - - - +
174C LYS* 4.2 11.4 - - + -
183C TRP* 4.1 8.7 - - + -
187C ILE* 4.4 14.4 - - + -
190C TRP* 3.4 12.2 - - + -
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Residues in contact with ASN 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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139C GLN* 2.8 53.4 + - - +
140C LYS* 3.5 9.6 - - + +
142C ILE* 1.3 73.4 - - - +
144C TYR* 1.3 65.8 + - + +
146C LYS* 3.7 8.8 - - - +
147C ASN* 2.8 40.1 + - - +
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Residues in contact with TYR 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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12A U 3.1 87.2 + + - +
14A U 3.6 40.6 + + - +
140C LYS* 3.0 52.0 + - + -
141C GLN* 3.4 13.9 - - + +
142C ILE 3.2 0.2 - - - -
143C ASN* 1.3 78.4 - - + +
145C GLY* 1.3 63.6 + - - +
147C ASN* 3.7 6.2 + - - +
148C THR* 3.7 10.0 + - - -
191C LYS* 3.9 14.1 + - - +
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Residues in contact with GLY 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 3.1 7.3 + - - -
142C ILE 2.7 14.6 + - - -
144C TYR* 1.3 73.5 - - - +
146C LYS* 1.3 58.9 + - - -
148C THR* 3.1 23.2 + - - -
151C TYR* 3.8 6.2 - - - +
190C TRP* 3.7 19.7 - - - -
191C LYS* 4.3 16.5 - - - +
194C LEU* 4.0 8.7 - - - +
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Residues in contact with LYS 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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139C GLN* 5.6 2.5 - - - +
142C ILE* 2.9 41.3 + - + +
143C ASN* 3.1 9.8 + - - +
145C GLY* 1.3 69.8 - - - +
147C ASN* 1.3 58.1 + - - +
148C THR 3.1 12.4 + - - +
151C TYR* 3.1 61.0 + - + +
152C ASP* 4.5 6.1 - - - +
160C ARG* 4.0 5.3 - - - +
171C TPO 3.1 34.9 + - - +
190C TRP* 3.9 4.0 - - + -
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Residues in contact with ASN 147 (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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12A U 4.1 18.6 + - - +
143C ASN* 2.8 30.1 + - - +
144C TYR 4.3 2.5 - - - +
145C GLY 3.2 1.6 - - - -
146C LYS* 1.3 77.5 - - - +
148C THR* 1.3 59.8 + - - +
152C ASP* 6.0 0.2 - - - -
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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