Contacts of the helix formed by residues 140 - 152 (chain B) in PDB entry 4PKO
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 ASP 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B PRO 5.7 0.2 - - - +
139B SER* 1.3 87.4 + - - +
141B SER* 1.3 61.1 + - - +
142B LYS* 2.9 45.4 + - + +
143B ALA* 3.0 28.7 + - - +
144B ILE* 3.2 10.4 + - - +
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Residues in contact with SER 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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139B SER 3.6 1.6 + - - -
140B ASP* 1.3 71.1 - - - +
142B LYS* 1.3 61.4 + - - +
144B ILE* 4.0 14.7 - - - +
145B ALA* 3.2 24.3 + - - +
160B LYS* 4.6 12.2 + - - -
163B ALA* 3.7 15.6 + - - +
167B ASP* 3.9 27.9 + - - +
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Residues in contact with LYS 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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140B ASP* 2.9 22.9 + - + +
141B SER* 1.3 79.2 - - - +
143B ALA* 1.3 65.0 + - - +
145B ALA* 3.4 6.6 + - - +
146B GLN* 2.9 52.4 + - + +
160B LYS* 5.6 2.7 - - - +
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Residues in contact with ALA 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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138B CYS* 4.1 17.0 - - - -
139B SER 4.9 1.8 - - - +
140B ASP* 3.0 25.5 + - - +
142B LYS* 1.3 79.0 - - - +
144B ILE* 1.3 65.7 + - - +
146B GLN* 3.0 26.6 + - - +
147B VAL* 3.1 20.1 + - - +
494B LEU* 4.6 10.9 - - + +
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Residues in contact with ILE 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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138B CYS* 3.7 21.8 - - - +
139B SER* 3.3 20.6 - - - +
140B ASP 3.2 13.8 + - - +
141B SER* 4.2 10.5 - - - +
143B ALA* 1.3 75.3 - - - +
145B ALA* 1.3 63.5 + - - +
147B VAL* 3.5 6.1 - - + +
148B GLY* 3.2 17.5 + - - -
159B GLY 4.8 0.3 - - - +
162B ILE* 5.6 0.2 - - - +
163B ALA* 4.5 14.4 - - + +
166B MET* 3.5 36.6 - - + -
171B LYS* 5.1 9.2 - - - +
403B THR* 3.7 14.3 - - + +
407B VAL* 4.3 17.0 - - + -
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Residues in contact with ALA 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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141B SER 3.2 18.7 + - - +
142B LYS* 3.6 6.3 - - - +
144B ILE* 1.3 78.8 - - - +
146B GLN* 1.3 53.8 + - + +
149B THR* 2.5 38.7 + - - +
159B GLY* 3.4 21.9 - - - +
160B LYS* 4.2 13.5 - - + +
163B ALA* 3.5 14.3 - - + +
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Residues in contact with GLN 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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142B LYS* 2.9 43.7 - - + +
143B ALA* 3.0 20.8 + - - +
145B ALA* 1.3 76.3 - - + +
147B VAL* 1.3 59.6 + - - +
149B THR* 3.2 5.9 + - - -
150B ILE* 3.0 34.7 + - - +
489B ILE 4.2 5.7 + - - +
490B ASP 5.0 4.0 + - - -
491B MET 5.0 0.2 - - - -
492B GLY* 3.5 34.8 - - - +
494B LEU* 3.6 17.8 - - + +
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Residues in contact with VAL 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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138B CYS* 4.5 2.7 - - - -
143B ALA 3.1 15.4 + - - +
144B ILE* 3.5 13.5 - - - +
146B GLN* 1.3 73.1 - - - +
148B GLY* 1.3 68.8 + - - +
150B ILE* 3.5 3.2 + - - +
151B SER* 3.1 24.4 + - - -
402B ALA* 4.5 3.2 - - - +
403B THR* 3.8 16.2 - - + +
406B ALA* 3.7 24.5 - - + -
411B VAL* 4.0 18.4 - - + -
494B LEU* 3.5 42.0 - - + +
496B PRO* 4.7 4.9 - - + +
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Residues in contact with GLY 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 ILE 3.2 7.3 + - - -
145B ALA 4.0 1.1 - - - -
147B VAL* 1.3 84.4 - - - +
149B THR* 1.3 61.1 + - - +
151B SER 3.5 0.7 + - - -
152B ALA* 3.1 19.1 + - - +
159B GLY* 4.1 10.3 - - - -
162B ILE* 4.9 1.1 - - - -
399B ALA* 3.2 21.7 - - - +
403B THR* 3.4 23.8 - - - -
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Residues in contact with THR 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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145B ALA* 2.5 24.5 + - - +
146B GLN* 3.2 7.8 + - - -
148B GLY* 1.3 77.2 - - - +
150B ILE* 1.3 62.8 + - + +
152B ALA* 3.3 5.0 + - - +
154B SER* 2.9 32.9 + - - -
155B ASP 3.1 36.8 + - - +
156B GLU* 3.6 19.6 + - + +
159B GLY* 3.3 12.7 + - - -
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Residues in contact with ILE 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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146B GLN 3.0 19.7 + - - +
147B VAL 3.8 4.5 - - - +
149B THR* 1.3 81.2 - - + +
151B SER* 1.3 62.5 - - - +
152B ALA 3.0 4.7 - - - -
153B ASN* 3.1 18.4 + - - -
154B SER* 4.1 5.6 + - - +
492B GLY 2.9 28.0 - - - +
493B ILE* 3.5 33.2 - - + -
494B LEU 3.6 20.6 - - - +
495B ASP* 4.4 9.2 - - - +
496B PRO* 6.0 1.3 - - + -
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Residues in contact with SER 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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51B LYS* 5.9 1.4 + - - -
87B ASP* 2.7 39.1 + - - +
147B VAL 3.1 9.8 + - - -
148B GLY 3.9 0.4 - - - -
150B ILE* 1.3 82.5 - - - +
152B ALA* 1.3 56.4 + - - +
153B ASN 3.2 3.4 + - - -
395B ARG* 4.0 4.5 - - - +
398B ASP* 3.1 26.0 + - - +
399B ALA* 3.6 10.1 - - - -
402B ALA* 3.5 21.5 - - - -
496B PRO* 6.2 0.7 - - - -
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Residues in contact with ALA 152 (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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148B GLY 3.1 18.1 + - - +
149B THR 3.5 6.5 - - - +
150B ILE 3.0 1.4 - - - -
151B SER* 1.3 77.7 - - - +
153B ASN* 1.3 63.2 + - - +
154B SER 3.5 0.2 - - - -
155B ASP* 3.7 10.2 - - + +
158B VAL* 3.9 28.5 - - + -
395B ARG* 2.8 43.6 + - + +
399B ALA* 3.9 6.3 - - + -
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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