Contacts of the helix formed by residues 83 - 95 (chain C) 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 VAL 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C TYR 5.3 0.2 - - - +
66C MET* 5.1 6.7 - - + -
69C PHE* 4.5 18.2 - - + -
70C TYR* 3.1 39.5 - - + +
78C PHE* 4.5 6.5 - - + -
79C PRO 2.5 26.4 + - - +
80C GLY 2.5 13.5 + - - +
82C SER* 1.3 69.7 - - - +
84C ALA* 1.3 55.3 + - - +
85C PRO* 3.2 2.5 - - - -
86C ALA* 2.5 42.7 + - + +
87C ALA* 3.0 9.9 + - + +
136C LEU* 4.1 19.3 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 4.8 5.2 - - + +
44C LEU* 5.8 1.6 - - + -
45C LEU* 4.5 14.6 - - + +
48C MET* 4.0 12.6 - - + -
66C MET* 6.0 2.0 - - - +
80C GLY 3.3 4.1 + - - +
81C ASN* 3.9 11.4 - - - +
83C VAL* 1.3 79.6 - - - +
85C PRO* 1.3 58.7 - - + +
87C ALA* 3.1 5.3 + - - +
88C LEU* 2.5 61.7 + - + +
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Residues in contact with PRO 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C MET* 5.0 9.6 - - + -
81C ASN 4.0 2.0 - - - +
82C SER* 2.8 36.3 - - - +
83C VAL 3.3 0.2 - - - -
84C ALA* 1.3 92.7 - - + +
86C ALA* 1.3 52.2 + - - +
88C LEU* 3.4 5.5 - - + -
89C PHE* 2.6 39.4 + - + +
104C VAL* 4.3 16.6 - - + +
105C ILE* 4.1 25.1 - - + -
108C ALA* 6.0 4.0 - - + -
133C LEU* 3.6 17.3 - - + -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 6.2 2.5 - - + -
83C VAL* 2.5 29.9 + - + +
85C PRO* 1.3 71.9 - - + +
87C ALA* 1.3 63.0 + - - +
88C LEU 3.1 1.3 - - - -
89C PHE* 3.0 15.2 + - - +
90C LEU* 3.3 11.1 + - - +
133C LEU* 5.0 5.8 - - - +
136C LEU* 3.8 36.3 - - + -
137C GLU* 4.7 4.1 - - - +
140C ILE* 4.2 18.4 - - + +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 3.9 12.1 - - + +
65C TYR* 2.8 51.9 - - + +
66C MET* 4.0 6.7 - - + +
83C VAL* 3.0 8.4 + - + +
84C ALA* 3.8 9.0 - - - +
86C ALA* 1.3 79.2 - - - +
88C LEU* 1.3 50.8 + - + +
89C PHE 3.3 0.4 - - - -
91C ALA* 2.8 34.9 + - - +
140C ILE* 4.0 5.7 - - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 3.3 31.2 - - + +
48C MET* 4.4 9.2 - - + -
49C GLY* 4.0 27.6 - - - +
54C VAL* 5.4 5.6 - - + -
58C THR* 4.8 9.4 - - + +
59C ILE* 5.8 2.0 - - - -
62C ALA* 3.4 15.0 - - + -
84C ALA* 2.5 49.3 + - + +
85C PRO* 3.4 5.6 - - + +
87C ALA* 1.3 71.3 - - + +
89C PHE* 1.3 59.4 + - - +
90C LEU 3.6 0.4 - - - -
91C ALA* 3.9 5.4 - - - -
92C ALA* 3.0 30.5 - - + +
104C VAL* 4.7 19.0 - - + +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PRO* 2.6 21.0 + - + +
86C ALA* 3.0 8.0 + - - +
88C LEU* 1.3 76.6 - - - +
90C LEU* 1.3 61.1 + - - +
92C ALA* 6.0 0.9 - - + -
93C LYS* 2.8 43.4 + - + +
99C LYS* 4.5 10.8 - - + -
100C LYS 2.8 34.5 - - - -
101C LEU* 3.3 36.3 - - + -
104C VAL* 4.3 13.7 - - + -
105C ILE* 5.6 7.9 - - + -
133C LEU* 4.9 13.5 - - + -
134C VAL* 5.0 5.8 - - + -
137C GLU* 2.8 26.9 - - + +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TYR* 3.8 17.3 - - + -
86C ALA 3.3 8.8 + - - +
89C PHE* 1.3 78.2 - - - +
91C ALA* 1.3 52.5 + - - +
93C LYS* 3.3 29.4 - - + +
94C VAL* 2.5 60.2 + - + +
137C GLU* 4.0 24.0 + - + +
140C ILE* 5.0 8.1 - - + -
141C LEU* 3.3 44.9 - - + -
148C LEU* 5.6 2.2 - - + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C THR* 4.3 5.8 - - - +
61C THR* 3.9 12.4 - - - -
62C ALA* 3.5 32.8 - - + +
65C TYR* 3.6 11.8 - - + -
87C ALA 2.8 24.8 + - - +
88C LEU* 3.9 1.3 - - - -
90C LEU* 1.3 77.2 - - - +
92C ALA* 1.3 61.9 + - - +
94C VAL* 3.6 2.3 - - - +
95C GLU* 3.0 27.7 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 5.2 10.8 - - + -
54C VAL* 5.0 4.9 - - + -
58C THR* 3.4 25.7 - - + +
88C LEU* 3.0 25.1 + - + +
89C PHE* 4.6 1.1 - - + +
91C ALA* 1.3 77.7 - - - +
93C LYS* 1.3 58.7 + - - +
95C GLU* 3.3 3.8 - - - +
97C GLN 2.3 35.2 - - - +
98C PRO* 3.7 4.0 - - + -
99C LYS* 5.1 7.2 - - + +
104C VAL* 5.4 3.6 - - + -
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 4.0 14.3 - - - +
89C PHE* 2.8 37.7 + - + +
90C LEU* 3.2 24.9 - - + +
92C ALA* 1.3 77.8 - - - +
94C VAL* 1.3 64.8 + - - +
95C GLU 2.7 15.9 - - - +
98C PRO* 3.3 27.7 - - + +
99C LYS 4.9 2.9 - - - +
137C GLU* 2.5 41.5 + - - -
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 4.9 11.7 - - + -
65C TYR* 4.2 16.4 - - - +
90C LEU* 2.5 49.4 + - + +
91C ALA* 3.6 5.2 - - - +
93C LYS* 1.3 74.1 - - - +
95C GLU* 1.3 71.1 + - - +
96C GLU* 3.5 1.4 + - - -
147C GLU 5.9 0.2 - - - +
148C LEU* 3.9 34.5 - - + +
150C ILE* 6.0 1.8 - - + -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C SER* 4.9 1.1 - - - +
57C LEU* 3.3 47.7 - - + +
58C THR* 4.0 17.5 - - - +
61C THR* 3.5 24.9 + - - +
91C ALA 3.0 11.7 + - - +
92C ALA 3.3 6.1 - - - +
93C LYS 2.7 17.7 - - - +
94C VAL* 1.3 83.8 - - - +
96C GLU* 1.3 61.9 + - + +
97C GLN* 2.8 17.9 + - + +
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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