Contacts of the helix formed by residues 129 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLY* 2.9 18.8 + - - +
128A VAL* 1.3 77.5 - - - +
130A ASP* 1.3 66.4 + - - +
131A GLU* 3.1 32.3 + - - +
132A VAL* 3.0 24.4 + - - +
133A LEU* 3.3 11.0 + - - +
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.1 8.3 + - - +
114A SER* 3.5 21.8 + - - -
129A THR* 1.3 73.6 - - - +
131A GLU* 1.3 72.5 + - - +
132A VAL 3.2 0.5 + - - -
133A LEU* 3.2 8.8 + - - +
134A ASP* 3.0 34.2 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 3.1 24.5 + - - +
130A ASP* 1.3 92.4 + - - +
132A VAL* 1.3 58.3 + - + +
134A ASP* 3.9 5.4 - - - +
135A ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 3.8 16.2 - - - +
128A VAL* 4.7 7.9 - - + -
129A THR* 3.0 23.2 + - - +
131A GLU* 1.3 75.5 - - + +
133A LEU* 1.3 56.2 + - - +
135A ALA* 2.9 8.3 + - - +
136A ALA* 2.7 34.7 + - - +
143B GLU* 4.4 0.6 - - - +
144B VAL* 3.5 45.5 - - + +
147B LYS* 3.9 30.1 - - + +
148B HIS* 4.3 3.6 - - + +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.8 33.2 - - + +
113A TRP* 4.5 24.2 - - + -
114A SER* 4.7 5.8 - - - +
128A VAL* 4.0 28.7 - - + +
129A THR 3.3 11.4 + - - +
130A ASP* 3.2 11.5 + - - +
132A VAL* 1.3 77.2 - - - +
134A ASP* 1.3 53.1 - - - +
136A ALA* 3.2 7.8 + - - +
137A MET* 2.7 42.3 + - + +
102B ILE* 4.3 21.5 - - + -
140B PHE* 4.9 5.1 - - + -
144B VAL* 5.8 2.0 - - + -
196C LYS* 6.2 1.1 - - - +
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.1 18.5 + - - -
130A ASP* 3.0 23.8 + - - +
131A GLU* 3.9 6.0 - - - +
133A LEU* 1.3 72.4 - - - +
135A ALA* 1.3 57.3 + - - +
137A MET* 2.9 2.6 + - - +
138A GLN* 2.8 38.7 + - - +
168A TYR* 2.5 43.8 + - - -
171A ARG* 5.9 2.3 - - - +
172A LEU* 3.6 14.3 - - + +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLU 3.0 19.7 + - - +
132A VAL* 2.9 9.0 + - - +
134A ASP* 1.3 73.6 - - - +
136A ALA* 1.3 62.3 + - - +
138A GLN* 3.2 20.3 - - - +
139A ALA* 3.3 23.6 + - - +
143B GLU* 3.7 25.0 - - + +
147B LYS* 4.8 11.2 - - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL 2.7 15.1 + - - +
133A LEU* 3.3 11.7 - - - +
135A ALA* 1.3 72.1 - - - +
137A MET* 1.3 58.7 + - - +
139A ALA* 3.8 2.1 + - - +
140A PHE 3.0 21.5 + - - -
140B PHE* 3.1 44.1 - - + +
143B GLU* 4.0 11.8 - - + +
144B VAL* 4.0 20.0 - - + -
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Residues in contact with MET 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.4 40.2 - - + +
107A LEU* 3.8 21.8 - - + -
110A ARG* 3.6 26.2 - - + -
113A TRP* 5.3 5.4 - - - -
133A LEU* 2.7 27.1 + - + +
134A ASP 2.9 6.5 + - - +
136A ALA* 1.3 70.3 - - - +
138A GLN* 1.3 66.8 + - - +
140A PHE* 2.9 5.8 + - - +
141A ILE* 2.8 36.2 + - + +
168A TYR* 3.3 21.8 - - + +
172A LEU* 4.0 9.0 - - + -
140B PHE* 4.2 16.8 - - - -
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS* 3.4 44.1 - - + +
134A ASP* 2.8 20.5 + - - +
135A ALA* 3.2 25.1 - - - +
137A MET* 1.3 73.7 - - - +
139A ALA* 1.3 65.6 + - - +
141A ILE* 3.2 1.7 + - - +
142A LEU* 2.8 31.0 + - + +
171A ARG 5.5 0.4 + - - -
172A LEU* 3.6 29.9 + - + +
173A PHE* 3.6 25.1 - - + -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 3.3 12.9 + - - +
136A ALA 3.9 2.9 - - - +
138A GLN* 1.3 79.3 - - - +
140A PHE* 1.3 64.9 + - - +
142A LEU* 3.7 9.6 - - - +
143A GLU* 3.2 27.4 + - - +
139B ALA* 3.6 34.1 - - + +
143B GLU* 4.1 10.3 - - + +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.2 17.3 - - + -
103A ILE* 5.4 0.9 - - + -
106A VAL* 3.8 44.4 - - + -
136A ALA 3.0 19.2 + - - +
137A MET* 2.9 8.7 + - - +
139A ALA* 1.3 76.7 - - - +
141A ILE* 1.3 70.9 + - + +
143A GLU* 3.4 4.0 + - - +
144A VAL* 3.3 35.7 + - + +
106B VAL* 6.4 1.3 - - + -
109B MET* 6.4 0.4 - - + -
113B TRP* 4.7 7.6 - + - -
133B LEU* 5.2 5.8 - - + -
136B ALA* 3.7 31.9 - - + +
137B MET* 4.5 16.4 - - - -
139B ALA* 4.6 0.2 - - - +
140B PHE* 3.6 29.4 - + + -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.0 4.9 - - + -
103A ILE* 4.1 29.6 - - + -
106A VAL* 4.8 5.2 - - + -
107A LEU* 4.5 11.9 - - + -
137A MET* 2.8 44.1 + - + +
138A GLN 3.8 2.2 - - - +
140A PHE* 1.3 80.9 - - + +
142A LEU* 1.3 67.4 + - - +
144A VAL* 2.9 16.9 + - - +
145A ILE* 3.1 33.5 + - + +
169A LEU* 4.8 3.4 - - + -
172A LEU* 4.2 10.1 - - + -
173A PHE* 4.1 25.4 - - + -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.9 24.9 - - + -
65A GLY* 3.7 23.6 - - - +
66A LYS* 3.5 28.7 - - + +
68A MET* 4.5 11.0 - - + -
70A LEU* 4.9 10.3 - - + -
138A GLN* 2.8 30.9 + - + +
139A ALA* 3.7 9.6 - - - +
141A ILE* 1.3 72.6 - - - +
143A GLU* 1.3 57.7 + - + +
145A ILE* 3.9 5.8 - - - +
146A ALA* 2.9 33.7 + - - +
155A LEU* 6.5 0.4 - - + -
173A PHE* 4.5 10.7 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 2.9 23.4 + - + -
139A ALA 3.2 14.2 + - - +
140A PHE 3.7 7.4 - - - +
142A LEU* 1.3 79.4 - - + +
144A VAL* 1.3 55.1 + - - +
146A ALA* 4.3 2.9 - - - -
147A LYS* 2.5 69.9 + - - +
132B VAL* 4.2 1.3 - - - +
135B ALA* 3.6 19.6 - - + +
136B ALA* 3.9 14.6 - - + +
139B ALA* 3.8 21.7 - - + +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 4.3 12.1 - - + -
102A ILE* 4.0 21.8 - - + -
103A ILE* 4.2 16.4 - - + -
140A PHE* 3.3 41.1 - - + +
141A ILE* 2.9 8.8 + - - +
143A GLU* 1.3 74.4 - - - +
145A ILE* 1.3 54.8 + - - +
148A HIS* 2.7 39.2 + - + +
128B VAL* 4.3 19.3 - - + -
132B VAL* 3.6 11.4 - - + -
133B LEU* 6.1 1.6 - - + -
136B ALA* 4.1 9.0 - - + -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 5.1 11.9 - - + -
72A PHE* 3.7 33.9 - - + -
95A ARG* 3.0 23.1 + - - +
103A ILE* 3.8 16.4 - - + -
141A ILE* 3.1 25.4 + - + +
142A LEU* 4.0 5.2 - - - +
144A VAL* 1.3 73.0 - - - +
146A ALA* 1.3 65.2 + - - +
147A LYS 3.2 0.2 + - - -
148A HIS* 3.1 19.9 + - - +
155A LEU* 4.3 19.7 - - + -
156A CYS* 3.6 26.9 - - - +
157A ASN* 3.7 11.4 - - + +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.6 36.3 - - + -
95A ARG* 3.1 16.8 + - - -
142A LEU 2.9 23.0 + - - +
143A GLU* 3.6 3.1 - - - +
145A ILE* 1.3 72.2 - - - +
147A LYS* 1.3 65.9 + - + +
149A GLY 3.6 4.9 - - - +
150A GLU 5.3 0.5 - - - -
151A PRO* 5.3 2.9 - - - +
155A LEU* 3.8 18.6 - - + +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.2 29.7 + - - -
143A GLU* 2.5 53.0 + - - +
146A ALA* 1.3 76.3 - - - +
148A HIS* 1.3 61.2 + - - +
149A GLY* 3.0 12.3 + - - +
127B GLY 4.2 0.5 - - - +
132B VAL* 3.5 27.2 - - + +
135B ALA* 4.2 13.7 - - + +
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Residues in contact with HIS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.2 17.3 + - - -
96A CYS 3.5 13.5 + - - -
97A GLY* 4.1 2.5 - - - -
98A GLU* 3.7 31.7 - - - +
100A THR* 4.3 13.4 - - + +
144A VAL* 2.7 23.0 + - + +
145A ILE* 3.1 36.1 + - - +
147A LYS* 1.3 72.6 - - - +
149A GLY* 1.3 55.3 + - - +
157A ASN* 4.4 3.2 + - - -
126B ALA* 2.9 23.3 + - - +
127B GLY* 3.0 47.1 - - - +
128B VAL* 3.8 18.6 - - + +
132B VAL* 4.1 2.9 - - + +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.2 25.2 + - - +
97A GLY* 6.0 1.1 - - - -
98A GLU* 6.0 1.3 - - - -
146A ALA 3.6 7.6 - - - +
147A LYS* 3.0 6.5 + - - +
148A HIS* 1.3 84.9 - - - +
150A GLU* 1.3 67.5 + - - -
151A PRO* 3.7 1.7 - - - +
278A SER* 6.4 1.8 - - - -
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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