Contacts of the helix formed by residues 129 - 149 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 4.2 24.9 - - + +
127D GLY* 3.0 16.0 + - - +
128D VAL* 1.3 76.9 - - - +
130D ASP* 1.3 67.8 + - - +
131D GLU* 3.3 25.3 + - - +
132D VAL* 3.3 19.5 + - - +
133D LEU* 3.0 24.6 + - - +
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.3 21.2 + - - +
114D SER* 3.6 10.2 + - - -
120D LYS* 3.8 21.6 + - - +
124D ASP* 5.0 3.0 + - - -
129D THR* 1.3 74.1 - - - +
131D GLU* 1.3 73.4 - - - +
133D LEU* 3.2 9.5 + - - +
134D ASP* 2.8 32.4 + - - +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D THR* 3.3 19.0 + - - +
130D ASP* 1.3 87.1 + - - +
132D VAL* 1.3 55.4 + - + +
134D ASP* 3.1 9.5 + - - +
135D ALA* 2.7 34.8 + - - +
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLU* 4.8 0.9 - - + -
144C VAL* 4.1 29.4 - - + +
147C LYS* 3.6 41.5 - - + +
148C HIS* 4.5 4.9 - - + +
127D GLY 4.0 13.0 - - - +
128D VAL* 4.9 5.8 - - + -
129D THR* 3.3 23.6 + - - +
131D GLU* 1.3 73.0 - - + +
133D LEU* 1.3 70.1 + - - +
135D ALA* 2.9 9.0 + - - +
136D ALA* 2.7 21.9 + - - +
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Residues in contact with LEU 133 (chain D).
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* 4.6 13.2 - - + -
140C PHE* 5.2 4.6 - - + -
110D ARG* 3.4 39.5 - - + +
113D TRP* 4.3 28.5 - - + -
114D SER* 4.5 2.0 - - - +
120D LYS* 5.6 8.3 - - + -
123D LEU* 6.1 6.1 - - + -
128D VAL* 4.2 25.3 - - + +
129D THR 3.0 19.3 + - - +
130D ASP* 3.3 13.7 - - - +
132D VAL* 1.3 76.0 - - - +
134D ASP* 1.3 53.5 + - - +
136D ALA* 3.1 7.9 + - + +
137D MET* 2.8 41.5 + - + +
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Residues in contact with ASP 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.7 10.1 + - - -
130D ASP* 2.8 24.0 + - - +
131D GLU* 3.3 11.1 - - - +
133D LEU* 1.3 70.2 - - - +
135D ALA* 1.3 66.1 + - - +
137D MET* 3.2 2.1 + - - +
138D GLN* 2.9 32.3 + - - +
168D TYR* 2.5 47.4 + - - -
171D ARG* 5.8 3.1 - - - +
172D LEU* 3.5 12.9 - - + +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLU* 4.2 18.2 - - + +
147C LYS* 4.3 15.7 - - + +
66D LYS* 6.2 0.4 - - - +
131D GLU 2.7 16.1 + - - +
132D VAL* 2.9 11.9 + - - +
134D ASP* 1.3 74.2 - - - +
136D ALA* 1.3 60.7 + - - +
138D GLN* 2.9 19.3 + - - +
139D ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PHE* 3.7 28.1 - - + +
143C GLU* 3.8 24.1 - - + +
144C VAL* 4.0 15.3 - - + +
132D VAL 2.7 15.2 + - - +
133D LEU* 3.4 10.3 - - - +
135D ALA* 1.3 69.3 - - - +
137D MET* 1.3 55.6 + - - +
139D ALA* 3.3 3.1 + - - +
140D PHE* 2.7 35.5 + - - +
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Residues in contact with MET 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PHE* 4.5 14.1 - - - -
106D VAL* 3.7 24.0 - - + +
107D LEU* 3.8 26.0 - - + +
110D ARG* 3.6 36.3 - - + -
113D TRP* 5.4 4.0 - - - -
133D LEU* 2.8 22.1 + - + +
134D ASP 3.4 7.4 - - - +
136D ALA* 1.3 69.6 - - - +
138D GLN* 1.3 69.0 + - - +
140D PHE* 2.6 17.9 + - - -
141D ILE* 2.7 28.8 + - + +
168D TYR* 3.4 21.8 - - + +
172D LEU* 3.9 8.3 - - + -
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 3.3 51.1 + - + +
134D ASP* 2.9 21.7 + - - +
135D ALA* 2.9 27.2 - - - +
137D MET* 1.3 74.7 - - - +
139D ALA* 1.3 62.2 + - - +
141D ILE* 3.7 0.9 - - - +
142D LEU* 2.8 32.0 + - + +
171D ARG 5.3 0.6 + - - -
172D LEU* 3.5 36.5 + - + +
173D PHE* 4.1 17.0 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ALA* 4.1 17.3 - - + +
143C GLU* 3.6 27.1 - - + +
135D ALA 3.0 10.3 + - - +
136D ALA 3.4 8.3 - - - +
138D GLN* 1.3 81.9 - - - +
140D PHE* 1.3 64.9 + - - +
142D LEU* 4.0 7.0 - - - +
143D GLU* 3.2 26.6 + - - +
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Residues in contact with PHE 140 (chain D).
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* 6.5 0.4 - - + -
109C MET* 6.4 0.4 - - + -
113C TRP* 5.3 4.3 - + - -
133C LEU* 6.2 1.3 - - + -
136C ALA* 3.7 34.8 - - + +
137C MET* 4.5 15.7 - - - -
139C ALA* 4.7 0.9 - - - +
140C PHE* 3.9 31.2 - + + -
102D ILE* 4.2 19.7 - - + -
103D ILE* 5.0 1.3 - - - -
106D VAL* 3.6 46.9 - - + -
136D ALA 2.7 13.8 + - - +
137D MET* 2.6 18.8 + - - +
139D ALA* 1.3 74.5 - - - +
141D ILE* 1.3 73.8 + - + +
143D GLU* 3.5 4.5 + - - +
144D VAL* 3.3 35.0 + - + +
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PHE* 5.2 3.8 - - + -
103D ILE* 4.1 29.8 - - + -
106D VAL* 4.9 1.3 - - + -
107D LEU* 4.5 11.9 - - + -
137D MET* 2.7 42.3 + - + +
138D GLN 3.8 1.8 - - - +
140D PHE* 1.3 81.4 - - + +
142D LEU* 1.4 69.9 + - - +
144D VAL* 2.6 21.8 + - - +
145D ILE* 3.2 28.0 + - + -
169D LEU* 4.9 2.7 - - + -
172D LEU* 3.9 26.2 - - + -
173D PHE* 4.1 16.4 - - + -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D TYR* 4.0 26.2 - - + -
65D GLY* 3.8 19.5 - - - +
66D LYS* 3.6 29.6 - - + +
68D MET* 4.3 14.4 - - + -
70D LEU* 4.8 11.2 - - + -
138D GLN* 2.8 29.8 + - + +
139D ALA* 4.0 5.8 - - - +
141D ILE* 1.4 73.9 - - - +
143D GLU* 1.3 59.3 + - + +
145D ILE* 3.1 9.7 + - + +
146D ALA* 2.8 31.6 + - - +
155D LEU* 5.7 2.5 - - + -
173D PHE* 4.0 13.8 - - + -
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Residues in contact with GLU 143 (chain D).
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* 4.2 2.0 - - - +
135C ALA* 4.5 8.5 - - + +
136C ALA* 4.1 16.4 - - - +
139C ALA* 3.7 22.5 - - + +
64D TYR* 3.4 21.1 + - - -
139D ALA* 3.2 15.4 + - - +
140D PHE 3.6 8.5 - - - +
141D ILE 2.8 4.6 + - - -
142D LEU* 1.3 77.3 - - + +
144D VAL* 1.3 62.1 + - - +
146D ALA* 4.5 3.4 - - - -
147D LYS* 2.9 61.2 + - + +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 4.8 4.9 - - + -
132C VAL* 4.0 13.7 - - + -
136C ALA* 4.1 11.4 - - + -
100D THR* 3.8 22.0 - - + -
102D ILE* 3.7 25.6 - - + -
103D ILE* 4.2 7.2 - - + -
140D PHE* 3.3 39.7 - - + +
141D ILE* 2.6 13.6 + - - +
143D GLU* 1.3 70.7 - - - +
145D ILE* 1.3 56.4 + - - +
148D HIS* 2.9 43.9 + - + +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 4.6 16.4 - - + -
72D PHE* 4.0 17.9 - - + -
95D ARG* 2.5 38.1 + - - +
103D ILE* 4.1 12.6 - - + -
141D ILE* 3.2 24.7 + - + +
142D LEU* 3.1 9.4 + - + +
144D VAL* 1.3 72.9 - - - +
146D ALA* 1.3 56.4 + - - +
148D HIS* 3.1 11.0 - - - -
155D LEU* 3.7 34.1 - - + -
156D CYS 3.9 15.3 - - - +
157D ASN* 4.0 26.7 - - + +
173D PHE* 5.8 0.2 - - + -
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D TYR* 3.7 38.4 - - + -
95D ARG* 2.4 22.7 + - - -
142D LEU 2.8 19.2 + - - +
143D GLU 3.9 2.7 - - - +
145D ILE* 1.3 73.0 - - - +
147D LYS* 1.3 63.7 - - + +
149D GLY 3.4 3.8 - - - +
150D GLU 5.0 0.7 - - - -
151D PRO* 5.1 2.9 - - - +
155D LEU* 3.6 18.8 - - + +
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Residues in contact with LYS 147 (chain D).
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* 3.9 22.4 - - + +
135C ALA* 5.0 12.6 - - + +
64D TYR* 3.1 30.9 + - - -
143D GLU* 2.9 47.1 + - + +
146D ALA* 1.3 74.9 - - + +
148D HIS* 1.3 64.8 + - - +
149D GLY 3.1 9.7 + - - +
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Residues in contact with HIS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA 3.2 21.6 + - - +
127C GLY* 3.4 41.0 - - - +
128C VAL* 4.4 6.2 - - + +
132C VAL* 4.0 11.2 - - + +
95D ARG* 3.2 17.9 + - - -
96D CYS 3.8 12.7 + - - -
97D GLY* 4.6 1.8 - - - -
98D GLU* 3.7 31.2 + - - +
100D THR* 4.1 18.6 - - + +
144D VAL* 2.9 29.9 + - + +
145D ILE* 3.1 22.7 - - - -
147D LYS* 1.3 76.8 - - - +
149D GLY* 1.3 57.2 + - - +
156D CYS 5.1 0.6 + - - -
157D ASN* 4.6 3.4 + - - -
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 3.2 22.7 + - - +
97D GLY* 6.2 0.9 - - - -
98D GLU* 5.9 2.2 - - - -
146D ALA 3.4 5.9 - - - +
147D LYS 3.1 7.4 - - - +
148D HIS* 1.3 86.5 - - - +
150D GLU* 1.3 66.7 + - - -
151D PRO* 3.8 2.3 - - - +
278D SER* 6.3 2.7 - - - -
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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