Contacts of the helix formed by residues 129 - 148 (chain C) in PDB entry 3AP3
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 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASP* 3.5 33.0 - - + +
127C GLY* 3.2 11.7 + - - +
128C VAL* 1.3 75.2 - - - +
130C ASP* 1.3 65.4 + - - +
131C GLU* 3.1 30.5 + - - +
132C VAL* 3.1 13.9 + - - +
133C LEU* 2.8 28.2 + - - +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.9 9.4 + - - +
114C SER* 3.8 17.7 + - - -
120C LYS* 5.4 6.2 + - - -
124C ASP* 4.3 6.8 + - - +
129C THR* 1.3 73.2 - - - +
131C GLU* 1.3 63.5 - - + +
133C LEU* 2.9 13.0 + - - +
134C ASP* 2.6 46.4 + - - +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C THR* 3.1 23.0 + - - +
130C ASP* 1.3 85.6 + - + +
132C VAL* 1.3 66.6 - - + +
134C ASP* 4.0 5.0 - - - +
135C ALA* 2.9 24.6 + - - +
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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
----------------------------------------------------------
127C GLY 3.4 23.8 - - - +
128C VAL* 4.5 5.6 - - + -
129C THR* 3.1 16.9 + - - +
131C GLU* 1.3 75.9 - - + +
133C LEU* 1.3 65.9 + - - +
135C ALA* 3.1 8.2 + - + +
136C ALA* 2.8 21.7 + - - +
143D GLU 4.2 1.1 - - - +
144D VAL* 4.0 29.8 - - + +
147D LYS* 3.9 28.5 - - + +
148D HIS* 4.0 17.7 - - + +
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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
----------------------------------------------------------
110C ARG* 3.3 36.6 - - + +
113C TRP* 4.2 30.3 - - + -
114C SER* 4.5 2.7 - - - +
123C LEU* 5.0 11.4 - - + -
128C VAL* 4.3 24.7 - - + +
129C THR 2.8 20.6 + - - +
130C ASP* 3.0 16.8 - - - +
132C VAL* 1.3 75.5 - - - +
134C ASP* 1.3 58.2 + - - +
136C ALA* 3.0 9.8 + - - +
137C MET* 2.8 34.6 + - + +
102D ILE* 4.6 9.4 - - + -
140D PHE* 6.2 1.3 - - + -
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Residues in contact with ASP 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 2.8 27.1 + - - -
130C ASP* 2.6 22.6 + - - +
131C GLU* 4.0 4.5 - - - +
133C LEU* 1.3 69.6 - - - +
135C ALA* 1.3 54.9 + - - +
137C MET* 3.0 3.3 + - - +
138C GLN* 2.7 41.5 + - - +
168C TYR* 2.9 23.6 + - - -
171C ARG* 5.8 3.1 - - - +
172C LEU* 3.4 21.2 - - + +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C GLU 2.9 15.9 + - - +
132C VAL* 3.1 13.4 + - - +
134C ASP* 1.3 77.0 - - - +
136C ALA* 1.3 63.1 + - - +
138C GLN* 3.2 19.0 + - - +
139C ALA* 3.0 22.2 + - - +
143D GLU* 4.5 17.6 - - + +
147D LYS* 5.0 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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132C VAL 2.8 14.8 + - - +
133C LEU* 3.3 10.1 - - - +
135C ALA* 1.3 69.6 - - - +
137C MET* 1.3 67.7 + - - +
139C ALA* 3.0 5.9 + - - +
140C PHE* 2.8 23.6 + - - +
140D PHE* 3.7 40.5 - - + +
143D GLU* 4.1 13.6 - - + +
144D VAL* 4.1 12.3 - - + -
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Residues in contact with MET 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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106C VAL* 3.7 43.3 - - + +
107C LEU* 4.4 10.3 - - + +
109C MET* 6.0 0.4 - - - -
110C ARG* 3.7 23.8 - - + -
113C TRP* 5.1 6.1 - - - -
133C LEU* 2.8 23.0 + - + +
134C ASP 3.2 6.5 - - - +
136C ALA* 1.3 70.5 - - - +
138C GLN* 1.3 63.8 + - - +
140C PHE* 3.0 8.0 + - + +
141C ILE* 3.0 42.0 + - + +
168C TYR* 3.4 18.8 - - + +
172C LEU* 3.8 15.5 - - + -
140D PHE* 4.5 16.2 - - - -
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Residues in contact with GLN 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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66C LYS* 3.2 38.1 - - + +
134C ASP* 2.7 21.5 + - - +
135C ALA* 3.2 21.9 - - - +
137C MET* 1.3 71.7 - - - +
139C ALA* 1.3 65.1 + - - +
141C ILE* 4.2 0.2 - - - -
142C LEU* 3.0 34.2 + - + +
171C ARG 4.8 2.4 + - - -
172C LEU* 3.2 44.1 + - + +
173C PHE* 3.9 16.4 - - + -
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Residues in contact with ALA 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 ALA 3.0 9.3 + - - +
136C ALA 3.0 8.7 + - - +
138C GLN* 1.3 78.1 - - - +
140C PHE* 1.3 62.4 + - - +
142C LEU* 3.4 8.7 - - - +
143C GLU* 3.1 31.9 + - - +
139D ALA* 4.0 17.5 - - + +
143D GLU* 3.7 28.7 - - + +
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Residues in contact with PHE 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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102C ILE* 4.0 22.0 - - + -
103C ILE* 5.2 0.9 - - + -
106C VAL* 3.4 47.6 - - + -
136C ALA 2.8 15.1 + - - +
137C MET* 3.0 11.8 + - + +
139C ALA* 1.3 69.4 - - - +
141C ILE* 1.3 83.2 + - + +
143C GLU* 3.0 15.4 + - - +
144C VAL* 3.2 24.4 + - + +
113D TRP* 5.2 5.8 - + - -
133D LEU* 5.8 3.8 - - + -
136D ALA* 3.7 43.0 - - + +
137D MET* 4.5 15.9 - - + -
140D PHE* 3.9 25.3 - + + +
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 5.1 4.7 - - + -
103C ILE* 4.0 32.1 - - + -
106C VAL* 4.7 2.9 - - + -
107C LEU* 4.9 7.4 - - + -
137C MET* 3.0 34.7 + - + +
138C GLN 4.3 1.3 - - - +
140C PHE* 1.3 89.1 - - + +
142C LEU* 1.3 53.4 - - - +
144C VAL* 2.9 9.0 + - - +
145C ILE* 2.8 63.3 + - + +
169C LEU* 4.9 5.4 - - + -
172C LEU* 4.2 22.7 - - + -
173C PHE* 4.5 16.4 - - + -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 4.9 14.6 - - + -
65C GLY* 4.0 25.8 - - - +
66C LYS* 3.4 25.8 - - + +
68C MET* 4.9 5.4 - - - -
70C LEU* 4.4 14.1 - - + -
138C GLN* 3.0 32.8 + - + +
139C ALA* 3.4 8.1 - - - +
141C ILE* 1.3 76.8 - - - +
143C GLU* 1.3 65.2 + - + +
145C ILE* 3.1 8.1 + - + +
146C ALA* 2.7 27.5 + - - +
173C PHE* 3.8 18.8 - - + -
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Residues in contact with GLU 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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64C TYR* 3.3 25.0 + - - -
139C ALA* 3.1 14.9 + - - +
140C PHE 3.0 7.9 + - - +
142C LEU* 1.3 77.5 - - - +
144C VAL* 1.3 55.2 + - - +
146C ALA* 3.0 5.3 + - - +
147C LYS* 2.7 70.0 + - + +
132D VAL* 4.8 0.9 - - - +
135D ALA* 4.2 8.4 - - + +
136D ALA* 3.8 19.5 - - + +
139D ALA* 3.6 25.1 - - + +
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Residues in contact with VAL 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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100C THR* 4.2 11.4 - - + -
102C ILE* 3.6 27.6 - - + -
103C ILE* 4.2 11.9 - - + -
140C PHE* 3.2 35.2 - - + +
141C ILE* 2.9 8.0 + - - +
143C GLU* 1.3 79.3 - - - +
145C ILE* 1.3 66.6 + - - +
146C ALA 2.9 0.2 + - - -
147C LYS 2.9 8.0 + - - -
148C HIS* 2.9 23.6 + - + +
128D VAL* 5.0 6.5 - - + -
132D VAL* 4.1 15.7 - - + -
136D ALA* 4.0 15.7 - - + -
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Residues in contact with ILE 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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70C LEU* 4.7 18.4 - - + -
72C PHE* 4.2 23.8 - - + -
95C ARG* 3.2 22.2 + - - +
103C ILE* 4.1 11.2 - - + -
141C ILE* 2.8 45.4 + - + +
142C LEU* 3.6 9.6 - - + +
144C VAL* 1.3 73.0 - - - +
146C ALA* 1.3 62.2 + - - +
148C HIS* 3.2 16.0 - - + -
155C LEU* 4.4 21.9 - - + +
156C CYS 4.2 20.4 - - - +
157C ASN* 4.2 10.5 - - + +
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Residues in contact with ALA 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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64C TYR* 4.1 31.6 - - + -
95C ARG* 3.3 17.2 + - - -
142C LEU 2.7 21.2 + - - +
143C GLU* 3.3 5.4 - - - +
145C ILE* 1.3 73.1 - - - +
147C LYS* 1.3 67.0 + - + +
149C GLY 3.8 4.7 - - - +
150C GLU 5.5 0.2 - - - -
151C PRO* 5.8 1.7 - - - +
155C LEU* 4.2 15.1 - - + +
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Residues in contact with LYS 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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64C TYR* 4.5 13.4 + - - -
143C GLU* 2.7 46.4 + - + +
146C ALA* 1.3 78.1 - - - +
148C HIS* 1.3 61.7 + - - +
149C GLY* 3.0 11.6 + - - +
132D VAL* 3.6 31.9 - - + +
135D ALA* 4.3 16.2 - - + +
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Residues in contact with HIS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 3.4 17.4 + - - -
96C CYS 3.4 18.7 + - - -
97C GLY* 4.1 2.9 - - - -
98C GLU* 3.6 30.6 + - - +
99C GLU 5.5 0.2 + - - -
100C THR* 4.2 19.2 - - + +
144C VAL* 2.9 23.1 + - + +
145C ILE* 3.2 32.3 - - - -
146C ALA 3.5 0.6 - - - -
147C LYS* 1.3 77.7 - - - +
149C GLY* 1.3 55.9 + - - +
156C CYS 4.9 1.0 + - - -
157C ASN* 4.4 3.8 + - - -
126D ALA 3.8 13.6 + - - +
127D GLY* 3.9 35.7 - - - +
128D VAL* 4.8 5.8 - - + +
132D VAL* 4.7 5.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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