Contacts of the helix formed by residues 140 - 149 (chain D) in PDB entry 2PK9
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 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B PHE 5.7 0.3 + - - -
139B SER* 6.0 1.6 - - - -
140B THR* 4.3 27.7 - - + +
139D SER* 1.3 77.8 - - - +
141D ASN* 1.3 67.3 + - - +
142D ALA* 4.1 11.9 - - - +
143D HIS* 3.3 16.8 + - - +
144D TYR* 3.1 20.1 + - - -
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Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY 3.5 13.5 + - - +
128D THR* 5.4 0.4 + - - -
132D LYS* 3.0 38.6 - - - +
140D THR* 1.3 70.6 - - - +
142D ALA* 1.3 58.8 + - - +
144D TYR* 2.8 8.3 + - - +
145D ALA* 2.7 33.1 + - - +
152D CYS* 4.2 6.1 - - - -
155D LEU* 3.8 18.6 - - + +
156D ASN* 2.9 33.7 + - - +
159D GLU* 3.3 19.3 - - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D THR* 4.1 10.5 - - - +
141D ASN* 1.3 76.3 - - - +
143D HIS* 1.3 56.1 + - - +
145D ALA* 3.8 1.0 - - - +
146D LYS* 3.0 30.0 + - - +
152D CYS* 3.6 24.6 - - + +
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 5.1 2.2 + - - -
137B SER* 3.2 28.3 + - - -
138B PHE* 3.2 32.6 + - - +
139B SER* 4.8 5.0 + - - -
87D PHE 2.8 20.9 + - - -
88D SER* 3.8 13.5 + - - -
139D SER* 3.1 31.6 + - - -
140D THR* 3.3 21.7 + - - +
141D ASN 2.9 1.6 + - - -
142D ALA* 1.3 76.2 - - - +
144D TYR* 1.3 66.2 + - - +
146D LYS* 3.3 6.5 + - - +
147D VAL* 3.1 31.9 + - + +
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Residues in contact with TYR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 5.4 0.5 - - - +
88D SER* 3.6 38.2 + - - -
90D LEU* 4.5 10.1 - - + -
124D LEU* 3.7 9.8 - - + +
127D THR* 5.3 1.3 - - + -
128D THR* 3.6 37.0 - - + -
131D THR* 3.2 29.6 - - + +
132D LYS* 4.0 17.7 - - + -
138D PHE* 3.8 1.6 - - - +
139D SER* 3.1 47.0 + - - -
140D THR 3.1 16.8 + - - -
141D ASN* 2.8 12.8 + - - +
143D HIS* 1.3 75.6 - - - +
145D ALA* 1.3 56.8 + - - +
147D VAL* 3.3 2.3 + - - +
148D GLY 2.9 25.1 + - - -
155D LEU* 3.8 5.6 - - + -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 5.2 0.2 - - - +
124D LEU* 4.9 1.8 - - - -
141D ASN 2.7 19.6 + - - +
142D ALA 3.8 4.0 - - - +
144D TYR* 1.3 72.3 - - - +
146D LYS* 1.3 57.1 + - - +
148D GLY 3.2 1.2 + - - -
149D GLY 2.8 26.5 + - - -
150D VAL* 3.1 32.5 + - + +
152D CYS* 3.8 31.0 - - + +
155D LEU* 3.9 11.3 - - + +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.7 25.9 - - + +
166A SER 3.6 26.5 + - - +
167A SER* 3.6 21.3 + - - +
168A GLU 5.5 0.7 - - - +
136B ASP* 3.3 29.1 + - - +
137B SER* 4.8 4.5 - - - -
138B PHE* 4.4 15.6 - - - -
83D ARG* 5.1 0.3 + - - -
142D ALA 3.0 19.5 + - - +
143D HIS* 3.3 7.4 + - - +
145D ALA* 1.3 74.7 - - - +
147D VAL* 1.3 64.5 + - + +
149D GLY* 3.3 12.7 + - - -
150D VAL 4.4 2.9 + - - -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 4.1 13.0 - - + -
137B SER* 4.1 11.7 - - - +
83D ARG* 3.0 46.4 + - + +
84D LEU* 4.0 27.2 - - + +
87D PHE* 3.9 28.3 - - + +
88D SER* 3.6 25.4 - - - +
143D HIS* 3.1 19.5 + - + +
144D TYR 3.7 1.8 - - - +
146D LYS* 1.3 77.5 - - + +
148D GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D TYR* 2.6 41.7 + - - -
83D ARG* 3.9 0.9 - - - -
84D LEU* 3.9 6.5 - - - +
124D LEU* 3.8 12.1 - - - -
144D TYR 2.9 15.6 + - - -
145D ALA 3.6 2.7 - - - -
147D VAL* 1.3 76.3 - - - +
149D GLY* 1.3 59.6 + - - +
150D VAL* 3.5 4.7 - - - +
294D MES 3.5 9.5 + - - -
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LYS* 3.6 23.4 + - - -
83D ARG* 4.2 1.8 - - - -
145D ALA 2.8 5.5 + - - -
146D LYS* 3.3 8.0 + - - -
147D VAL 3.2 4.4 - - - -
148D GLY* 1.3 79.6 - - - +
150D VAL* 1.3 63.2 + - - +
294D MES 3.0 20.8 + - - -
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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