Contacts of the helix formed by residues 76 - 89 (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 SER 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ASN 4.2 1.4 + - - -
75B ILE* 1.3 78.9 - - - +
77B ILE* 1.3 66.4 + - - +
78B PHE* 4.1 5.2 + - - +
79B ASN* 3.3 28.5 + - - +
80B TYR* 3.2 17.0 + - - +
120B HIS* 4.9 0.2 - - - -
238B SER* 5.1 4.0 + - - -
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Residues in contact with ILE 77 (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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40B SER* 3.9 17.7 - - - +
43B LEU* 3.9 25.1 - - + -
44B VAL* 3.2 35.7 - - + -
47B ILE* 5.4 3.1 - - + -
75B ILE 3.7 0.8 + - - -
76B SER* 1.3 73.0 - - - +
78B PHE* 1.3 55.0 + - + +
80B TYR* 3.2 4.9 + - - +
81B PHE* 2.7 35.7 + - + +
119B ALA* 3.8 22.2 - - + -
120B HIS* 3.7 28.7 - - + +
123B LEU* 3.7 27.8 - - + -
235B PRO* 5.9 1.8 - - + -
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Residues in contact with PHE 78 (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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33B THR* 4.6 1.8 - - + -
36B VAL* 3.4 24.0 - - + -
37B VAL* 3.5 32.3 - - + -
40B SER* 3.3 20.2 - - - +
76B SER* 3.3 3.9 + - - +
77B ILE* 1.3 81.8 - - + +
79B ASN* 1.3 72.9 + - - +
81B PHE* 2.7 19.4 + - - +
82B ILE* 2.8 46.9 + - + +
235B PRO* 6.1 0.9 - - + -
238B SER* 3.6 29.6 - - - +
239B ARG* 3.3 42.2 - - - -
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Residues in contact with ASN 79 (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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75B ILE* 3.9 18.6 - - + +
76B SER* 3.3 23.6 + - - +
78B PHE* 1.3 94.4 - - - +
80B TYR* 1.3 59.4 + - - +
82B ILE* 3.8 15.9 - - - +
83B ARG* 3.5 20.3 + - - +
239B ARG* 5.6 2.2 - - - +
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Residues in contact with TYR 80 (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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75B ILE* 3.8 13.4 - - + +
76B SER 3.2 12.5 + - - +
77B ILE* 3.2 9.6 + - - +
78B PHE 3.0 0.4 - - - -
79B ASN* 1.3 77.2 - - - +
81B PHE* 1.3 63.1 + - - +
83B ARG* 3.5 20.9 - - - +
84B LEU* 3.2 44.2 + - + +
120B HIS* 4.0 37.0 - + + -
123B LEU* 4.0 17.5 - - + -
124B LEU* 3.4 21.5 - - - +
148B GLY* 3.0 32.7 + - - -
294B MES 3.5 34.5 - - - -
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Residues in contact with PHE 81 (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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36B VAL* 3.7 20.0 - - + -
39B ILE* 3.7 42.6 - - + -
40B SER* 3.6 19.5 - - - +
43B LEU* 5.5 2.5 - - + -
77B ILE* 2.7 20.4 + - + +
78B PHE 2.7 5.2 + - - +
80B TYR* 1.3 71.3 - - - +
82B ILE* 1.3 58.0 + - - +
84B LEU* 3.2 8.1 + - + +
85B THR* 2.6 30.7 + - - -
90B LEU* 4.6 7.9 - - + -
95B LEU* 4.6 13.9 - - + -
98B SER* 4.6 10.5 - - - -
123B LEU* 3.6 41.7 - - + -
127B THR* 4.0 15.5 - - - -
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Residues in contact with ILE 82 (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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33B THR* 5.2 10.1 - - + +
36B VAL* 3.4 23.6 - - + -
78B PHE* 2.8 45.0 + - + +
79B ASN* 3.8 24.2 - - - +
81B PHE* 1.3 71.2 - - - +
83B ARG* 1.3 58.1 + - + +
85B THR* 2.9 10.2 + - - -
86B LYS* 2.8 54.5 + - + +
239B ARG* 5.5 2.7 - - - +
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Residues in contact with ARG 83 (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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75B ILE* 4.3 12.8 - - - +
79B ASN 3.5 12.3 + - - +
80B TYR* 3.5 21.3 + - - +
81B PHE 3.2 0.2 - - - -
82B ILE* 1.3 84.0 - - + +
84B LEU* 1.3 64.4 + - - +
86B LYS* 4.8 1.1 - - - -
87B PHE* 3.1 50.1 + - + +
146B LYS 5.1 0.4 + - - -
147B VAL* 2.6 34.4 + - + +
148B GLY 3.7 9.3 + - - -
149B GLY* 4.0 0.8 - - - +
294B MES 2.7 40.9 + - - -
165C PHE* 4.5 4.1 - - + -
184C ARG* 3.9 40.9 - - - +
240C PRO* 5.2 4.2 - - - +
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Residues in contact with LEU 84 (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* 3.2 35.7 + - + +
81B PHE* 3.2 8.3 + - + +
83B ARG* 1.3 77.9 - - - +
85B THR* 1.3 57.4 + - - +
88B SER* 3.1 37.7 + - - +
90B LEU* 3.6 12.3 - - + +
123B LEU* 4.6 8.1 - - + -
124B LEU* 4.0 25.8 - - + +
127B THR* 3.9 28.7 - - + +
144B TYR 5.5 0.2 - - - +
147B VAL* 4.2 13.9 - - + +
148B GLY* 3.9 30.5 - - - +
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Residues in contact with THR 85 (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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32B ARG* 3.3 41.3 + - - +
36B VAL* 3.4 25.2 - - + +
81B PHE* 2.6 22.3 + - - -
82B ILE* 2.9 11.1 + - - -
84B LEU* 1.3 75.0 - - - +
86B LYS* 1.3 63.6 + - - +
89B SER* 3.0 25.8 + - - -
90B LEU* 3.3 32.0 + - + +
95B LEU* 4.4 4.5 - - + +
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Residues in contact with LYS 86 (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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32B ARG* 4.1 26.6 + - - +
33B THR* 4.3 17.6 + - - +
82B ILE* 2.8 39.1 + - + +
83B ARG* 4.9 0.2 - - - -
85B THR* 1.3 81.7 - - - +
87B PHE* 1.3 82.8 + - + +
89B SER* 4.6 0.2 - - - -
32D ARG* 4.2 25.6 + - - +
89D SER* 2.9 23.0 + - - -
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Residues in contact with PHE 87 (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* 3.1 34.1 + - + -
84B LEU 4.0 0.2 - - - -
86B LYS* 1.3 94.3 - - + +
88B SER* 1.3 60.2 + - - +
89B SER 3.7 0.4 - - - -
143B HIS* 2.8 26.3 + - - -
147B VAL* 3.7 22.7 - - + +
163C ASN* 3.0 49.6 - - + -
165C PHE* 3.7 20.0 - + + -
184C ARG* 4.4 7.0 - - - -
32D ARG* 6.1 3.4 - - - -
89D SER* 4.1 11.8 + - - -
91D GLU* 4.7 9.4 - - + -
137D SER* 3.9 9.2 + - - +
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Residues in contact with SER 88 (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* 3.1 19.1 + - - +
87B PHE* 1.3 79.9 + - - +
89B SER* 1.3 76.1 + - - +
90B LEU* 3.2 12.0 + - - +
127B THR* 6.0 0.7 - - - -
131B THR* 5.7 1.9 - - - +
139B SER* 5.4 3.0 + - - -
143B HIS* 3.7 12.7 + - - -
144B TYR* 3.5 40.2 + - - -
147B VAL* 3.8 12.1 - - - +
89D SER* 5.2 0.2 - - - -
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Residues in contact with SER 89 (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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32B ARG* 4.2 9.8 + - - +
85B THR 3.0 11.2 + - - -
86B LYS 4.6 0.2 - - - -
88B SER* 1.3 82.1 + - - +
90B LEU* 1.3 64.7 - - - +
91B GLU* 3.1 11.1 + - - +
131B THR* 5.9 2.6 - - - +
137B SER* 5.9 0.4 - - - -
86D LYS 3.2 19.3 + - - -
87D PHE* 3.8 20.6 + - - -
88D SER* 4.2 0.9 - - - -
89D SER* 2.4 37.4 + - - -
143D HIS* 5.1 2.1 + - - -
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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