Contacts of the helix formed by residues 135 - 144 (chain B) in PDB entry 2PK2
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 ILE 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLN* 2.5 26.4 + - + +
132B ASP* 3.7 20.0 - - - +
134B VAL* 1.3 75.9 - - - +
136B LEU* 1.3 60.1 + - + +
137B GLU 3.2 0.9 - - - -
138B SER* 3.1 9.0 + - - -
139B ILE* 2.8 45.1 + - + +
93C LYS* 4.0 10.5 - - - +
134C VAL 5.9 1.6 - - - +
137C GLU* 3.6 30.5 - - + +
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Residues in contact with LEU 136 (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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69B PHE* 3.8 15.6 - - + -
78B PHE* 4.3 17.0 - - + -
79B PRO* 6.5 0.4 - - + -
82B SER* 5.0 11.4 - - - +
83B VAL* 4.7 21.3 - - + -
86B ALA* 4.8 9.1 - - + +
132B ASP* 2.5 34.8 + - + +
133B LEU* 4.8 6.3 - - + -
135B ILE* 1.3 71.9 - - + +
137B GLU* 1.3 54.6 + - - +
138B SER 3.0 5.4 - - - -
139B ILE* 3.4 36.2 - - + +
140B ILE* 2.9 31.1 + - - +
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Residues in contact with GLU 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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86B ALA* 4.8 8.4 - - - +
89B PHE* 2.9 42.7 - - - +
90B LEU* 2.8 25.1 - - + +
93B LYS* 4.7 4.7 + - - +
133B LEU 2.9 22.5 + - - +
134B VAL* 3.5 20.1 - - - +
136B LEU* 1.3 78.3 - - - +
138B SER* 1.3 56.9 + - - +
140B ILE* 3.0 13.3 - - - +
141B LEU* 2.9 40.6 + - + +
135C ILE* 4.1 9.7 - - - +
138C SER* 3.9 4.5 - - - +
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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
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134B VAL 4.4 0.4 - - - -
135B ILE* 3.1 12.6 + - - -
136B LEU 3.0 0.4 - - - -
137B GLU* 1.3 78.2 - - - +
139B ILE* 1.3 57.6 + - - +
140B ILE 3.0 2.0 - - - -
141B LEU* 2.8 23.9 + - - +
142B GLN* 2.8 15.4 + - - -
137C GLU 4.9 1.1 + - - -
138C SER* 3.1 38.2 + - - -
141C LEU* 4.8 1.2 - - - +
142C GLN* 4.7 2.3 - - - +
146C PHE* 2.8 36.5 - - - -
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Residues in contact with ILE 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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69B PHE* 3.4 7.0 - - + -
73B GLN* 3.3 23.3 - - - +
78B PHE* 5.0 5.6 - - + -
135B ILE* 2.8 34.3 - - + +
136B LEU* 3.0 35.4 + - + +
138B SER* 1.3 76.7 - - - +
140B ILE* 1.3 50.6 + - - +
142B GLN* 5.0 1.3 - - - +
143B THR* 2.4 34.7 + - - +
146C PHE* 3.3 32.8 - - + -
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Residues in contact with ILE 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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65B TYR* 3.7 22.0 - - + +
69B PHE* 3.5 31.9 - - + -
83B VAL* 5.6 1.8 - - + -
86B ALA* 4.7 9.4 - - + +
87B ALA* 3.5 37.7 - - + +
90B LEU* 4.0 8.7 - - + -
136B LEU 2.9 14.7 + - - +
137B GLU* 3.0 26.7 - - - +
139B ILE* 1.3 75.7 - - - +
141B LEU* 1.3 64.5 + - - +
142B GLN 3.1 2.7 + - - -
143B THR* 3.3 9.7 + - - -
144B LEU* 3.5 28.9 - - + +
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Residues in contact with LEU 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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90B LEU* 3.5 27.8 - - + +
93B LYS* 5.8 5.4 - - - +
137B GLU* 2.9 42.1 + - + +
138B SER* 2.8 11.6 + - - +
140B ILE* 1.3 78.3 - - - +
142B GLN* 1.3 60.3 + - - +
144B LEU* 4.6 2.1 + - - +
146B PHE* 3.5 27.8 + - + -
148B LEU* 6.4 2.7 - - + -
135C ILE* 5.7 1.3 - - + -
138C SER* 3.6 19.7 - - - +
142C GLN* 3.3 31.0 - - - +
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Residues in contact with GLN 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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11B ARG* 5.6 2.9 + - - -
138B SER 2.8 11.6 + - - +
139B ILE 5.0 0.4 - - - +
141B LEU* 1.3 77.8 - - - +
143B THR* 1.3 63.4 + - - +
144B LEU 3.0 3.1 - - - -
145B GLY* 2.5 33.4 + - - -
146B PHE* 4.3 26.9 - - + -
142C GLN* 4.4 4.5 + - + -
145C GLY* 3.7 30.5 + - - -
146C PHE* 4.1 30.7 - - + -
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Residues in contact with THR 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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11B ARG* 3.4 8.3 + - - -
12B TRP* 2.9 20.9 - - + -
68B ARG 4.5 1.1 - - - +
69B PHE* 4.1 27.4 - - + +
72B ILE* 3.9 27.8 - - + +
73B GLN* 3.9 11.4 + - - +
139B ILE* 2.4 27.0 + - - +
140B ILE* 3.3 8.8 + - - -
142B GLN* 1.3 85.6 - - - +
144B LEU* 1.3 59.9 + - + +
145B GLY 3.3 1.7 + - - -
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Residues in contact with LEU 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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12B TRP* 3.3 19.5 + - + -
65B TYR* 3.4 53.2 - - + +
68B ARG* 3.3 46.9 - - + +
69B PHE 4.2 4.0 - - - +
90B LEU* 4.8 2.9 - - + -
140B ILE* 3.5 24.2 - - + +
141B LEU 5.0 2.0 - - - +
142B GLN 3.0 1.2 - - - -
143B THR* 1.3 77.0 - - + +
145B GLY* 1.3 53.6 + - - +
146B PHE* 3.1 2.2 - - - +
147B GLU* 2.7 46.8 + - - +
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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