Contacts of the helix formed by residues 132 - 151 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 1.3 76.2 - - - +
133B PRO* 1.3 88.0 - - - +
134B GLU* 3.2 13.4 + - + +
135B GLN* 3.0 46.4 + - + +
136B GLN* 3.1 10.1 + - - +
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Residues in contact with PRO 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU 4.2 2.7 - - - +
132B THR* 1.3 91.5 - - - +
134B GLU* 1.3 62.4 + - - +
136B GLN* 3.2 14.9 + - + +
137B LYS* 2.9 24.8 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 3.2 15.6 + - + +
133B PRO* 1.3 78.0 - - - +
135B GLN* 1.3 57.7 + - + +
137B LYS* 3.4 9.3 - - - +
138B SER* 2.9 26.8 + - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 5.5 2.2 + - - +
141A GLU* 5.1 7.9 - - - +
142A ILE* 3.7 27.5 - - + +
145A ILE* 4.1 15.6 - - - +
130B ARG 4.2 1.4 - - - +
131B LEU* 3.6 24.2 - - + +
132B THR* 3.0 42.5 + - + +
134B GLU* 1.3 73.8 - - + +
136B GLN* 1.3 58.5 + - - +
138B SER* 3.5 7.7 - - - -
139B LEU* 2.7 35.7 + - - +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.3 33.6 + - - +
15A VAL* 3.4 18.8 - - + +
128B PHE* 3.1 49.0 + - + -
131B LEU* 3.2 24.2 + - + -
132B THR 3.1 10.9 + - - +
133B PRO* 3.6 13.8 - - + +
135B GLN* 1.3 74.1 - - - +
137B LYS* 1.3 67.1 + - - +
139B LEU* 3.7 6.3 - - - +
140B GLY 3.3 15.1 + - - -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 5.2 3.0 - - - +
133B PRO 2.9 13.5 + - - +
134B GLU* 3.4 12.8 - - - +
136B GLN* 1.3 78.9 - - - +
138B SER* 1.3 62.9 + - - +
140B GLY* 3.2 1.6 + - - -
141B GLU* 3.1 47.2 + - + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 5.5 2.6 + - - -
138A SER* 2.9 30.3 + - - -
142A ILE* 4.4 0.9 - - - -
134B GLU 2.9 18.0 + - - -
135B GLN* 3.2 9.4 + - - -
137B LYS* 1.3 76.9 - - - +
139B LEU* 1.3 60.5 + - - +
141B GLU* 3.4 14.2 + - - +
142B ILE* 3.0 34.6 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.8 19.7 - - + -
16A TRP* 6.4 1.3 - - + -
19A TYR* 4.6 11.9 - - + -
139A LEU* 5.4 2.2 - - + -
142A ILE* 4.1 26.8 - - + +
143A MET* 5.0 2.7 - - - -
127B VAL* 4.6 12.6 - - + -
128B PHE* 5.4 1.1 - - + -
131B LEU* 4.3 20.4 - - + -
135B GLN 2.7 20.5 + - - +
136B GLN* 3.7 5.8 - - - +
138B SER* 1.3 73.2 - - - +
140B GLY* 1.3 57.4 + - - +
142B ILE* 3.1 6.6 + - + +
143B MET* 2.9 72.9 + - + +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.0 19.9 - - - +
18A SER* 3.9 16.3 + - - -
136B GLN 3.3 4.0 + - - -
137B LYS 3.2 7.5 + - - -
139B LEU* 1.3 76.7 - - - +
141B GLU* 1.3 65.4 + - - +
143B MET* 4.9 0.2 - - - -
144B ARG* 3.1 29.9 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 5.0 12.8 + - - +
137B LYS* 3.1 41.2 + - + +
138B SER* 3.7 12.2 + - - +
140B GLY* 1.3 76.0 - - - +
142B ILE* 1.3 62.2 + - - +
144B ARG* 3.8 6.5 - - - +
145B ILE* 3.2 30.3 + - + +
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Residues in contact with ILE 142 (chain B).
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* 4.2 20.9 - - + +
135A GLN* 3.6 48.5 - - + +
138A SER* 4.3 1.1 - - - -
139A LEU* 4.1 33.0 - - + +
142A ILE* 5.0 1.6 - - + -
138B SER* 3.0 36.6 + - - +
139B LEU* 3.1 8.3 + - + +
141B GLU* 1.3 74.3 - - - +
143B MET* 1.3 74.0 + - + +
145B ILE* 3.3 10.8 + - - +
146B VAL* 3.2 23.6 + - + +
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.5 27.8 - - - +
19A TYR* 3.7 34.5 - - + +
22A ALA* 3.7 14.6 - - + +
139A LEU* 3.9 24.5 - - + -
143A MET* 4.3 3.6 - - - -
19B TYR* 4.1 16.2 - - + -
139B LEU* 2.9 50.1 + - + +
142B ILE* 1.3 79.5 - - + +
144B ARG* 1.3 52.6 + - - +
146B VAL* 3.1 11.0 + - - +
147B ALA* 2.8 35.0 + - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 4.3 15.6 - - - -
140B GLY 3.1 21.4 + - - +
141B GLU* 3.8 6.1 - - - +
143B MET* 1.3 77.3 - - - +
145B ILE* 1.3 56.2 + - + +
147B ALA* 3.8 5.9 - - - +
148B GLU* 2.8 34.2 + - + +
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Residues in contact with ILE 145 (chain B).
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* 3.7 38.1 - - + +
131A LEU* 4.0 13.0 - - + -
135A GLN* 4.0 24.9 - - - +
141B GLU* 3.2 23.8 + - + +
142B ILE* 3.3 5.8 + - - +
143B MET 3.2 0.4 - - - -
144B ARG* 1.3 73.3 - - + +
146B VAL* 1.3 58.3 + - - +
148B GLU* 3.4 6.5 + - - +
149B GLY* 2.8 32.9 + - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 4.1 14.4 - - + -
26A LEU* 4.2 18.6 - - + -
126A ALA 4.1 20.9 - - - +
127A VAL* 4.5 18.2 - - + -
130A ARG* 5.0 0.9 - - + +
131A LEU* 4.9 7.4 - - + -
139A LEU* 6.2 1.1 - - + -
142B ILE* 3.2 20.8 + - + +
143B MET* 3.1 16.0 + - - +
145B ILE* 1.3 78.7 - - + +
147B ALA* 1.3 62.2 + - - +
149B GLY* 3.3 2.4 + - - -
150B LEU* 3.2 41.0 + - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 4.8 2.0 - - - +
21A GLU* 4.6 11.0 - - + +
22A ALA* 4.1 16.6 - - + +
25A LEU* 4.0 21.0 - - + +
143B MET 2.8 19.7 + - - +
144B ARG* 3.8 6.1 - - - +
146B VAL* 1.3 70.8 - - - +
148B GLU* 1.3 67.8 + - - +
150B LEU* 2.8 14.3 + - - +
151B GLN* 3.1 25.3 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ARG* 2.8 24.2 + - + +
145B ILE* 3.7 6.3 - - + +
147B ALA* 1.3 73.4 - - - +
149B GLY* 1.3 61.6 + - - +
150B LEU 3.2 0.3 + - - -
151B GLN* 3.3 27.8 + - - +
152B PRO* 3.8 4.0 - - - +
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Residues in contact with GLY 149 (chain B).
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* 3.2 47.9 + - - -
145B ILE 2.8 19.3 + - - -
146B VAL 3.7 2.7 - - - -
147B ALA 3.1 0.4 - - - -
148B GLU* 1.3 73.0 - - - +
150B LEU* 1.3 59.4 + - - +
152B PRO* 3.7 13.2 - - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 4.5 0.4 - - - +
25A LEU* 4.0 21.9 - - + +
26A LEU* 3.8 41.7 - - + +
29A HIS* 3.4 47.3 - - + +
126A ALA* 4.2 12.8 - - + -
130A ARG* 5.7 0.4 - - - +
146B VAL* 3.2 24.4 + - + +
147B ALA 2.8 5.8 + - - +
149B GLY* 1.3 77.6 - - - +
151B GLN* 1.3 60.2 + - - +
152B PRO* 3.4 8.3 - - - +
159B LEU* 3.7 9.7 - - - +
160B PRO* 6.1 0.2 - - - +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 4.4 10.5 + - - -
25A LEU* 4.1 10.9 - - + +
69B LYS* 2.8 33.8 + - - +
147B ALA* 3.1 25.2 + - - +
148B GLU* 3.3 12.4 + - - +
150B LEU* 1.3 81.8 - - - +
152B PRO* 1.3 65.5 - - - +
153B SER 3.9 0.5 + - - -
159B LEU* 3.5 18.7 - - + +
161B TRP* 3.3 19.6 - - + -
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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