Contacts of the helix formed by residues 102 - 113 (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 GLU 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C LYS* 3.3 3.4 - - + +
101C LEU* 1.3 80.8 - - - +
103C HIS* 1.3 56.3 + - + +
104C VAL 3.0 2.9 - - - -
105C ILE* 2.5 30.5 + - + +
106C LYS* 2.6 48.3 + - + +
119C PRO* 5.6 2.3 - - - +
120C ASP* 5.0 8.3 + - - -
121C THR* 3.7 9.4 + - - -
126C TYR* 2.8 47.1 + - + +
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Residues in contact with HIS 103 (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* 3.6 21.7 - - + +
99C LYS* 3.2 49.5 + - + +
100C LYS* 4.2 21.6 - - + +
102C GLU* 1.3 78.4 - - + +
104C VAL* 1.3 60.8 + - - +
105C ILE 3.7 0.3 + - - -
106C LYS* 4.4 2.6 - - - +
107C VAL* 4.2 14.6 + - - +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET* 3.8 30.1 - - - +
49C GLY* 5.8 0.4 - - - -
52C LEU* 3.7 28.7 - - + -
85C PRO* 4.3 16.7 - - + +
88C LEU* 4.7 30.3 - - + +
89C PHE* 4.3 16.4 - - + -
92C ALA* 5.4 2.2 - - + -
99C LYS* 4.4 12.6 - - + -
100C LYS 3.6 21.3 - - - +
101C LEU 5.4 1.3 - - - +
102C GLU 3.0 0.2 - - - -
103C HIS* 1.3 74.5 - - - +
105C ILE* 1.3 64.1 + - + +
106C LYS 3.8 0.2 - - - -
107C VAL* 5.7 0.9 - - - -
108C ALA* 4.0 5.2 - - - +
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Residues in contact with ILE 105 (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* 4.1 14.4 - - + -
89C PHE* 5.6 8.5 - - + -
101C LEU* 3.4 25.4 - - + +
102C GLU* 2.5 26.0 + - + +
104C VAL* 1.3 75.8 - - + +
106C LYS* 1.3 64.4 + - + +
107C VAL 3.6 0.4 - - - -
108C ALA* 3.5 18.7 - - + +
109C HIS* 3.9 6.2 + - - +
126C TYR* 4.4 15.7 - - + -
129C GLN* 4.7 11.4 - - + +
130C VAL* 5.5 2.7 - - + -
133C LEU* 3.2 44.4 - - + -
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Residues in contact with LYS 106 (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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102C GLU* 2.6 48.0 + - + +
103C HIS* 5.1 2.5 - - - +
105C ILE* 1.3 72.3 - - + +
107C VAL* 1.3 66.1 + - - +
108C ALA 3.0 1.3 - - - -
109C HIS* 3.0 22.5 + - - +
110C THR* 3.4 5.0 + - - -
118C LEU* 4.1 22.0 - - - +
119C PRO* 3.6 33.8 - - + +
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Residues in contact with VAL 107 (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* 3.3 19.7 - - + +
51C ARG* 3.0 45.1 - - + +
52C LEU* 5.2 4.0 - - + -
103C HIS 4.2 15.3 + - - +
104C VAL 5.9 0.2 - - - -
106C LYS* 1.3 77.0 - - - +
108C ALA* 1.3 56.8 + - - +
110C THR* 2.7 31.4 + - + +
111C CYS* 2.8 24.0 + - - -
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Residues in contact with ALA 108 (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* 3.9 26.5 - - - +
82C SER* 5.8 3.4 - - - +
85C PRO* 6.0 4.7 - - + -
104C VAL 4.0 1.9 + - - +
105C ILE* 3.5 26.8 - - + +
106C LYS 3.0 0.2 - - - -
107C VAL* 1.3 79.3 - - - +
109C HIS* 1.3 53.9 + - - +
110C THR 3.0 0.3 + - - -
112C LEU* 2.5 51.3 + - + +
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Residues in contact with HIS 109 (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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105C ILE 3.9 5.3 + - - +
106C LYS 3.0 15.3 + - - +
108C ALA* 1.3 77.9 - - - +
110C THR* 1.3 48.9 + - - +
113C HIS* 2.5 73.2 + + + +
116C GLU* 3.8 16.5 - - + +
117C SER 2.7 28.8 + - - -
118C LEU* 4.6 2.2 - - + -
119C PRO* 3.6 36.5 - - + +
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Residues in contact with THR 110 (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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51C ARG* 3.2 24.2 + - - +
106C LYS 3.4 2.8 + - - -
107C VAL* 2.7 37.9 + - + +
109C HIS* 1.3 76.0 - - - +
111C CYS* 1.3 60.6 + - - -
113C HIS 4.3 1.6 - - - -
114C PRO* 3.4 24.6 - - + +
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Residues in contact with CYS 111 (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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44C LEU* 5.3 12.9 - - + +
47C ASP* 4.9 2.9 - - + -
48C MET* 3.3 28.5 - - + +
51C ARG* 3.2 31.8 - - - +
107C VAL* 2.8 32.9 + - - +
108C ALA 4.0 1.6 - - - +
110C THR* 1.3 73.8 - - - +
112C LEU* 1.3 69.6 + - + +
114C PRO* 4.4 6.4 - - - +
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Residues in contact with LEU 112 (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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44C LEU* 4.7 18.2 - - + -
48C MET* 5.4 4.5 - - + -
81C ASN* 3.9 39.3 - - + +
82C SER* 4.6 10.1 - - - +
108C ALA* 2.5 36.8 + - + +
111C CYS* 1.3 85.3 - - + +
113C HIS* 1.3 75.0 + - + +
114C PRO* 2.8 14.5 - - - +
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Residues in contact with HIS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C HIS* 2.5 57.5 + + + +
110C THR* 3.5 1.6 - - - +
112C LEU* 1.3 94.2 - - + +
114C PRO* 1.3 59.5 - - - +
115C GLN 3.0 9.7 + - - +
116C GLU* 3.4 45.0 + - + +
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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