Contacts of the helix formed by residues 132 - 151 (chain A) in PDB entry 3ZPL
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG 4.4 0.2 + - - -
131A LEU* 1.3 74.6 - - - +
133A PRO* 1.4 75.6 - - - +
134A GLU* 3.5 15.4 + - - +
135A GLN* 2.9 40.8 + - + +
136A GLN* 3.0 11.6 + - - +
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Residues in contact with PRO 133 (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 LEU 4.3 2.5 - - - +
132A THR* 1.4 84.0 - - - +
134A GLU* 1.3 64.0 + - - +
135A GLN 3.2 0.2 + - - -
136A GLN* 3.2 15.5 + - + +
137A LYS* 2.9 24.3 + - - +
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Residues in contact with GLU 134 (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 THR* 3.2 10.5 + - - +
133A PRO* 1.3 78.6 - - - +
135A GLN* 1.3 58.7 + - + +
137A LYS* 3.4 8.0 - - - +
138A SER* 2.9 27.0 + - - -
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Residues in contact with GLN 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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130A ARG 4.2 1.6 - - - +
131A LEU* 3.5 25.0 - - + +
132A THR* 2.9 42.8 + - - +
134A GLU* 1.3 72.8 - - + +
136A GLN* 1.3 57.1 + - - +
137A LYS 3.2 0.2 - - - -
138A SER* 3.5 7.6 - - - -
139A LEU* 2.7 35.9 + - - +
138B SER* 5.5 2.3 + - - +
141B GLU* 5.0 12.7 + - - +
142B ILE* 3.6 27.1 - - + +
145B ILE* 4.0 16.2 - - - +
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Residues in contact with GLN 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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128A PHE* 3.1 58.1 + - + +
131A LEU* 3.2 25.8 + - + +
132A THR 3.0 13.1 + - - +
133A PRO* 3.6 14.5 - - + +
135A GLN* 1.3 74.6 - - - +
137A LYS* 1.3 66.5 + - - +
139A LEU* 3.5 6.7 + - + +
140A GLY 3.3 15.1 + - - -
12B GLU* 4.2 17.2 + - - +
15B VAL* 3.4 19.1 - - + +
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Residues in contact with LYS 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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133A PRO 2.9 12.1 + - - +
134A GLU* 3.4 12.6 - - - +
136A GLN* 1.3 77.0 - - - +
138A SER* 1.3 64.8 + - - +
140A GLY* 3.2 1.4 + - - -
141A GLU* 3.2 21.6 + - - +
144A ARG* 5.5 0.3 + - - -
15B VAL* 5.1 3.1 - - - +
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Residues in contact with SER 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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134A GLU 2.9 18.3 + - - -
135A GLN* 3.2 8.7 + - - -
137A LYS* 1.3 77.0 - - - +
139A LEU* 1.3 62.4 + - - +
141A GLU* 3.4 7.2 + - - +
142A ILE* 3.0 35.1 + - - +
135B GLN* 5.5 2.4 + - - -
138B SER* 2.9 30.5 + - - -
142B ILE* 4.3 1.3 - - - -
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Residues in contact with LEU 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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127A VAL* 4.6 12.1 - - + -
128A PHE* 5.6 1.1 - - + -
131A LEU* 4.3 21.3 - - + -
135A GLN 2.7 19.7 + - - +
136A GLN* 3.7 6.1 - - - +
138A SER* 1.3 72.5 - - - +
140A GLY* 1.3 57.8 + - - +
142A ILE* 3.2 6.8 + - + +
143A MET* 2.9 52.7 + - + +
15B VAL* 3.9 19.1 - - + +
16B TRP* 6.2 2.2 - - + -
19B TYR* 4.5 11.9 - - + -
139B LEU* 5.4 2.7 - - + -
142B ILE* 4.1 19.4 - - + +
143B MET* 3.9 24.0 - - + -
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Residues in contact with GLY 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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136A GLN 3.3 3.6 + - - -
137A LYS 3.2 7.2 + - - -
139A LEU* 1.3 75.0 - - - +
141A GLU* 1.3 65.9 + - - +
144A ARG* 3.1 43.2 + - - +
15B VAL* 4.0 18.8 - - - +
18B SER* 3.6 15.0 + - - -
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Residues in contact with GLU 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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137A LYS 3.2 12.8 + - - +
138A SER* 3.7 10.5 - - - +
140A GLY* 1.3 75.8 - - - +
142A ILE* 1.3 63.4 + - + +
144A ARG* 3.8 11.5 - - - +
145A ILE* 3.2 30.3 + - + +
135B GLN* 5.1 8.1 - - - +
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Residues in contact with ILE 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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138A SER* 3.0 37.8 + - - +
139A LEU* 3.2 8.0 + - + +
141A GLU* 1.3 75.3 - - - +
143A MET* 1.3 73.4 + - - +
145A ILE* 3.3 11.6 + - - +
146A VAL* 3.3 23.5 + - + +
131B LEU* 4.3 20.0 - - + +
135B GLN* 3.7 47.1 - - + +
138B SER* 4.4 0.7 - - - +
139B LEU* 4.1 33.2 - - + +
142B ILE* 5.0 1.6 - - + -
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Residues in contact with MET 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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19A TYR* 3.9 22.2 - - + +
139A LEU* 2.9 36.5 + - + +
142A ILE* 1.3 82.2 - - - +
144A ARG* 1.3 53.8 + - - +
146A VAL* 3.1 12.0 + - + +
147A ALA* 2.8 35.3 + - - +
18B SER* 3.4 26.7 - - - +
19B TYR* 3.3 42.2 - - + +
22B ALA* 3.4 28.1 - - + +
23B ALA 4.1 0.2 - - - +
26B LEU* 5.8 0.4 - - + -
139B LEU* 5.0 2.2 - - - -
143B MET* 4.3 13.9 - - - -
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Residues in contact with ARG 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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137A LYS 5.5 0.4 + - - -
140A GLY* 3.1 40.6 + - - +
141A GLU* 3.8 9.2 - - - +
143A MET* 1.3 76.0 - - - +
145A ILE* 1.3 56.4 + - + +
147A ALA* 3.8 4.4 - - - +
148A GLU* 2.8 33.9 + - + +
14B LEU* 3.3 36.4 + - - +
15B VAL* 5.4 3.2 - - - +
18B SER* 3.2 34.4 + - - -
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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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141A GLU* 3.2 22.7 - - + +
142A ILE* 3.3 5.6 + - - +
143A MET 3.2 0.6 - - - -
144A ARG* 1.3 76.0 - - + +
146A VAL* 1.3 57.2 + - - +
148A GLU* 3.4 5.8 + - - +
149A GLY* 2.8 31.9 + - - -
130B ARG* 3.9 37.8 + - + +
131B LEU* 4.0 20.6 - - + -
135B GLN* 4.1 15.9 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ILE* 3.3 21.5 + - + +
143A MET* 3.1 15.0 + - + +
145A ILE* 1.3 80.1 - - + +
147A ALA* 1.3 63.0 + - - +
149A GLY* 3.4 1.6 + - - -
150A LEU* 3.2 40.4 + - + +
22B ALA* 3.9 15.3 - - + -
26B LEU* 4.1 20.2 - - + -
126B ALA 4.1 21.4 - - - +
127B VAL* 4.5 16.4 - - + -
130B ARG* 5.3 0.9 - - + +
131B LEU* 5.0 7.0 - - + -
139B LEU* 6.3 0.9 - - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A MET 2.8 18.8 + - - +
144A ARG* 3.8 6.5 - - - +
146A VAL* 1.3 70.5 - - - +
148A GLU* 1.3 66.5 + - - +
150A LEU* 2.8 14.3 + - - +
151A GLN* 3.2 24.6 + - - +
18B SER* 4.6 2.9 - - - +
21B GLU* 4.3 8.5 - - + -
22B ALA* 4.0 23.5 - - + +
25B LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 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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144A ARG* 2.8 24.6 + - + +
145A ILE* 3.7 7.2 - - - +
147A ALA* 1.3 72.1 - - - +
149A GLY* 1.3 62.5 + - - +
150A LEU 3.3 0.5 + - - -
151A GLN* 3.3 26.3 + - - +
152A PRO* 3.7 4.2 - - - +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ILE 2.8 17.4 + - - -
146A VAL 3.7 2.7 - - - -
147A ALA 3.0 0.4 - - - -
148A GLU* 1.3 77.1 - - - +
150A LEU* 1.3 58.8 + - - +
152A PRO* 3.7 13.2 - - - +
130B ARG* 3.6 41.6 + - - -
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Residues in contact with LEU 150 (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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146A VAL* 3.2 25.0 + - + +
147A ALA 2.8 6.0 + - - +
149A GLY* 1.3 78.1 - - - +
151A GLN* 1.3 59.6 + - - +
152A PRO* 3.4 8.1 - - - +
159A LEU* 3.7 10.6 - - - +
22B ALA 4.4 0.4 - - - +
25B LEU* 4.0 21.6 - - + +
26B LEU* 3.8 41.3 - - + +
29B HIS* 3.5 46.2 - - + +
126B ALA* 4.5 12.1 - - + -
130B ARG* 6.0 0.7 - - - +
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Residues in contact with GLN 151 (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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69A LYS* 2.9 35.6 + - - +
147A ALA* 3.2 24.5 + - - +
148A GLU* 3.3 11.5 + - - +
150A LEU* 1.3 80.5 - - - +
152A PRO* 1.3 65.6 - - - +
153A SER 3.8 0.7 + - - -
159A LEU* 3.6 17.9 - - + -
161A TRP* 3.3 19.3 - - + -
21B GLU* 5.6 1.6 - - - +
25B LEU* 4.0 14.6 - - + +
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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
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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