Contacts of the helix formed by residues 140 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PRO 5.7 0.3 - - - +
139A SER* 1.3 88.6 + - - +
141A SER* 1.3 64.1 + - - +
142A LYS* 3.0 18.7 + - + +
143A ALA* 3.1 39.7 + - - +
144A ILE* 3.2 10.2 + - - +
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Residues in contact with SER 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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139A SER 3.6 1.0 + - - -
140A ASP* 1.3 72.2 - - - +
142A LYS* 1.3 60.5 + - - +
144A ILE* 3.9 14.9 - - - +
145A ALA* 3.2 18.0 + - - +
160A LYS* 4.1 12.6 + - - -
163A ALA* 3.2 23.9 + - - +
167A ASP* 2.9 38.3 + - - +
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Residues in contact with LYS 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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140A ASP* 3.0 14.4 - - + +
141A SER* 1.3 78.6 - - - +
143A ALA* 1.3 62.1 + - - +
145A ALA* 3.4 7.3 + - - +
146A GLN* 3.2 48.6 + - + +
160A LYS* 4.9 5.6 - - - +
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Residues in contact with ALA 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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138A CYS* 4.2 13.9 - - - -
139A SER 5.2 0.4 - - - +
140A ASP* 3.1 26.6 + - - +
142A LYS* 1.3 77.2 - - - +
144A ILE* 1.3 61.0 + - - +
146A GLN* 3.0 14.8 + - - +
147A VAL* 2.9 34.1 + - - +
494A LEU* 3.8 14.8 - - + +
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Residues in contact with ILE 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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138A CYS* 4.2 14.4 - - - -
139A SER* 3.4 21.1 - - - +
140A ASP 3.2 12.3 + - - +
141A SER* 4.0 15.9 - - - +
143A ALA* 1.3 76.5 - - - +
145A ALA* 1.3 57.4 + - - +
147A VAL* 3.3 8.0 - - + +
148A GLY* 2.8 27.4 + - - -
159A GLY 4.4 0.7 - - - +
162A ILE* 4.5 0.4 - - + -
163A ALA* 4.1 18.8 - - + +
166A MET* 4.2 21.8 - - + -
171A LYS* 4.8 7.6 - - - +
403A THR* 3.7 24.2 - - + +
407A VAL* 4.5 18.2 - - + -
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Residues in contact with ALA 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 SER 3.2 17.2 + - - +
142A LYS* 3.6 7.4 - - - +
143A ALA 3.2 0.2 - - - -
144A ILE* 1.3 79.0 - - - +
146A GLN* 1.3 54.2 + - + +
149A THR* 2.4 38.8 + - - +
159A GLY* 3.3 28.1 - - - +
160A LYS* 3.8 19.3 - - + +
163A ALA* 3.8 2.0 - - + +
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Residues in contact with GLN 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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142A LYS* 3.2 37.9 + - + +
143A ALA* 3.0 17.3 + - - +
145A ALA* 1.3 77.4 - - + +
147A VAL* 1.3 60.3 + - - +
149A THR* 3.3 4.4 + - - -
150A ILE* 2.9 35.2 + - - +
489A ILE* 4.3 5.6 + - - +
490A ASP 4.8 4.4 + - - -
491A MET 4.5 2.4 + - - -
492A GLY* 3.2 41.8 - - - +
494A LEU* 4.3 9.4 - - + +
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Residues in contact with VAL 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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138A CYS* 4.4 4.9 - - - -
143A ALA 2.9 15.0 + - - +
144A ILE* 3.3 14.4 - - + +
146A GLN* 1.3 72.8 - - - +
148A GLY* 1.3 65.1 + - - +
150A ILE* 3.8 2.6 - - - +
151A SER* 3.0 30.3 + - - -
402A ALA* 4.6 2.2 - - - +
403A THR* 3.6 27.4 - - + +
406A ALA* 4.1 11.4 - - + -
411A VAL* 4.3 13.2 - - + -
494A LEU* 3.1 47.0 - - + +
496A PRO* 5.0 4.6 - - + +
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Residues in contact with GLY 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 ILE 2.8 18.0 + - - -
145A ALA 3.9 1.1 - - - -
147A VAL* 1.3 80.0 - - - +
149A THR* 1.3 60.2 + - - +
152A ALA* 3.1 25.5 + - - +
159A GLY* 4.0 12.1 - - - -
162A ILE* 5.0 1.8 - - - -
399A ALA* 3.2 14.7 - - - +
403A THR* 3.7 16.8 - - - -
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Residues in contact with THR 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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145A ALA* 2.4 26.2 + - - +
146A GLN* 3.3 6.9 + - - -
148A GLY* 1.3 77.9 - - - +
150A ILE* 1.3 65.4 + - + +
152A ALA* 3.3 7.6 + - - +
153A ASN 3.4 0.2 + - - -
154A SER* 2.8 34.7 + - - -
155A ASP 3.4 33.4 - - - +
156A GLU* 3.5 24.3 + - + +
159A GLY* 3.4 10.7 - - - -
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Residues in contact with ILE 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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87A ASP* 5.8 0.7 - - - +
146A GLN* 2.9 27.8 + - - +
147A VAL* 3.8 3.8 - - - +
148A GLY 3.3 0.2 - - - -
149A THR* 1.3 80.8 - - + +
151A SER* 1.3 64.7 + - - +
152A ALA 3.0 4.7 - - - -
153A ASN* 3.1 14.7 + - - -
154A SER* 4.6 3.8 - - - +
492A GLY 3.1 19.3 - - - +
493A ILE* 3.8 33.2 - - + -
494A LEU 3.6 21.5 - - - +
495A ASP* 4.5 8.5 - - - +
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Residues in contact with SER 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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51A LYS* 5.8 1.2 + - - -
87A ASP* 2.9 43.2 + - - +
147A VAL 3.0 13.8 + - - -
150A ILE* 1.3 81.0 - - - +
152A ALA* 1.3 57.7 + - - +
153A ASN* 3.3 2.2 + - - +
395A ARG* 5.3 1.7 - - - +
398A ASP* 3.2 26.2 + - - +
399A ALA* 3.8 9.4 - - - -
402A ALA* 3.3 23.0 - - - +
496A PRO* 6.0 1.3 - - - -
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Residues in contact with ALA 152 (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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148A GLY 3.1 18.6 + - - +
149A THR* 3.7 6.5 - - - +
150A ILE 3.0 1.2 - - - -
151A SER* 1.3 78.1 - - - +
153A ASN* 1.3 69.7 + - - +
154A SER 3.5 0.2 - - - -
155A ASP* 4.2 6.4 + - - +
158A VAL* 3.9 25.1 - - + -
395A ARG* 3.3 35.0 + - + +
399A ALA* 3.7 11.9 - - + -
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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