Contacts of the helix formed by residues 140 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU* 3.6 17.5 - - + +
44A GLU* 4.6 13.5 - - + +
139B SER* 1.3 78.8 - - - +
141B ASN* 1.3 66.1 + - - +
142B ALA* 3.6 4.3 + - - +
143B HIS* 3.0 25.5 + - - +
144B TYR* 3.0 24.5 + - - -
140D THR* 4.3 30.5 - - + +
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Residues in contact with ASN 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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43A GLU 3.4 7.5 + - - +
44A GLU* 3.0 19.7 + - - +
45A GLY* 3.4 1.2 - - - -
128B THR* 5.0 1.5 + - - -
132B LYS* 3.1 28.3 - - - +
140B THR* 1.3 71.7 - - - +
142B ALA* 1.3 53.7 + - - +
144B TYR* 2.9 6.2 + - - -
145B ALA* 2.6 37.6 + - - +
152B CYS* 4.3 2.9 - - - -
155B LEU* 3.3 20.4 - - + +
156B ASN* 3.3 28.3 + - - +
159B GLU* 3.0 30.9 - - - +
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Residues in contact with ALA 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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43A GLU* 3.0 33.4 + - + +
140B THR* 3.1 5.1 - - - +
141B ASN* 1.3 76.2 - - - +
143B HIS* 1.3 60.4 + - - +
145B ALA* 4.1 1.6 - - - +
146B LYS* 3.5 23.6 + - - +
152B CYS* 3.6 25.6 - - + +
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Residues in contact with HIS 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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87B PHE 2.8 23.5 + - - -
88B SER* 3.7 17.2 + - - -
139B SER* 3.4 29.5 + - - +
140B THR* 3.0 23.2 + - - +
142B ALA* 1.3 77.5 - - - +
144B TYR* 1.3 63.2 + + - +
146B LYS* 3.5 9.8 + - - +
147B VAL* 3.3 22.2 + - + +
89D SER* 6.2 1.8 - - - -
137D SER* 3.2 25.6 + - - -
138D PHE 2.9 31.6 + - - +
139D SER* 4.4 7.1 + - - -
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Residues in contact with TYR 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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84B LEU* 5.5 0.5 - - - +
88B SER* 3.5 39.2 + - - -
90B LEU* 4.8 8.1 - - + -
124B LEU* 3.6 10.2 - - + +
127B THR* 5.3 1.8 - - + -
128B THR* 3.7 37.5 - - + -
131B THR* 3.4 26.7 - - - +
132B LYS* 4.4 11.7 - - + -
138B PHE* 3.9 0.9 - - - +
139B SER* 3.0 45.9 + - - -
140B THR 3.0 21.3 + - - -
141B ASN* 2.9 10.9 + - - +
143B HIS* 1.3 75.4 - + - +
145B ALA* 1.3 61.8 + - - +
147B VAL* 3.6 2.3 + - - +
148B GLY 3.0 22.5 + - - -
155B LEU* 3.6 13.0 - - + -
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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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124B LEU* 5.0 0.4 - - - -
141B ASN 2.6 20.1 + - - +
142B ALA 4.1 3.8 - - - +
144B TYR* 1.3 71.7 - - - +
146B LYS* 1.3 55.8 + - - +
148B GLY 3.4 0.4 + - - +
149B GLY 2.9 24.8 + - - -
150B VAL* 2.9 37.2 + - + +
151B ARG 3.7 4.0 - - - +
152B CYS* 3.6 26.5 - - + +
155B LEU* 3.6 10.9 - - + +
168C GLU* 5.3 0.7 - - - +
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Residues in contact with LYS 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 ALA 3.5 12.7 + - - +
143B HIS* 3.5 13.9 + - - +
144B TYR 3.3 0.6 - - - -
145B ALA* 1.3 75.5 - - - +
147B VAL* 1.3 67.2 + - + +
149B GLY* 3.3 12.0 + - - -
150B VAL 4.6 2.2 - - - -
165C PHE* 3.7 33.5 - - + +
166C SER 4.1 15.3 - - - +
167C SER* 3.7 25.3 + - - +
168C GLU 5.6 1.3 - - - +
136D ASP* 3.2 28.4 + - - +
137D SER* 4.7 7.0 - - - -
138D PHE* 4.3 16.4 - - - +
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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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83B ARG* 2.6 56.5 + - + +
84B LEU* 4.2 16.3 - - + +
87B PHE* 3.7 42.8 - - + +
88B SER* 3.8 11.0 - - - +
143B HIS* 3.3 21.6 + - - +
144B TYR 4.1 3.8 - - - +
146B LYS* 1.3 77.6 - - + +
148B GLY* 1.3 52.1 + - - +
165C PHE* 3.9 19.3 - - + -
137D SER* 4.4 8.5 - - - +
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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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80B TYR* 3.0 30.6 + - - -
83B ARG* 3.7 2.9 - - - -
84B LEU* 3.9 11.2 - - - +
124B LEU* 3.9 9.2 - - - -
144B TYR 3.0 17.9 + - - -
145B ALA 3.7 0.9 - - - -
147B VAL* 1.3 77.6 - - - +
149B GLY* 1.3 56.3 + - - +
150B VAL 3.4 2.7 - - - -
294B MES 3.2 19.2 - - - +
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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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83B ARG* 4.3 0.4 - - - -
145B ALA 2.9 5.3 + - - -
146B LYS* 3.3 7.4 + - - -
147B VAL 3.3 3.8 - - - -
148B GLY* 1.3 78.5 - - - +
150B VAL* 1.3 62.7 + - - +
294B MES 3.4 21.9 - - - -
241C LYS* 4.4 16.4 - - - -
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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