Contacts of the helix formed by residues 102 - 114 (chain A) in PDB entry 1ZK2
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS* 4.0 9.6 - - - +
100A GLU 4.4 1.6 - - - +
101A THR* 1.3 79.6 - - - +
103A THR* 1.3 63.8 + - - +
104A ALA* 3.6 8.1 + - - +
105A GLU* 2.9 43.6 + - - +
106A TRP* 2.9 19.3 + - - +
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR 3.9 1.0 + - - -
102A THR* 1.3 74.1 - - - +
104A ALA* 1.3 62.4 + - - +
106A TRP* 3.3 11.3 + - + +
107A ARG* 2.9 56.8 + - + +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR* 3.2 8.5 + - - +
103A THR* 1.3 79.4 - - - +
105A GLU* 1.3 62.1 + - + +
107A ARG* 3.4 4.9 + - - +
108A LYS* 3.0 26.7 + - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.9 31.9 - - + +
96A LYS* 2.9 44.6 + - - +
101A THR* 3.6 4.9 - - + -
102A THR* 2.9 38.4 + - - +
104A ALA* 1.3 75.3 - - + +
106A TRP* 1.3 63.4 + - - +
108A LYS* 3.4 7.8 + - + +
109A LEU* 3.0 27.5 + - - +
154A ALA* 5.5 0.2 - - - -
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Residues in contact with TRP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 6.2 5.4 - - + -
101A THR* 3.8 14.0 - - + +
102A THR 2.9 13.4 + - - +
103A THR* 3.3 16.1 + - + +
105A GLU* 1.3 76.3 - - - +
107A ARG* 1.3 81.8 + - + +
109A LEU* 3.5 1.7 + - - +
110A LEU* 3.0 56.0 + - + +
153A GLY 4.9 1.6 - - - -
154A ALA* 3.7 39.7 - - + -
157A ALA* 3.8 22.0 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR* 2.9 41.7 + - + +
104A ALA* 4.0 5.2 - - - +
106A TRP* 1.3 90.2 - - + +
108A LYS* 1.3 57.2 + - - +
110A LEU* 3.5 4.9 + - - +
111A ALA* 2.9 31.2 + - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.9 21.0 - - + +
94A VAL* 5.8 4.7 - - + -
104A ALA 3.0 19.0 + - - +
105A GLU* 3.8 7.6 - - + +
107A ARG* 1.3 77.0 - - - +
109A LEU* 1.3 62.8 + - - +
111A ALA* 3.3 15.0 + - - +
112A VAL* 3.4 16.1 + - + +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.7 29.4 - - + +
93A ALA* 4.0 2.2 - - - -
94A VAL* 3.7 32.5 - - + +
105A GLU 3.0 17.8 + - - +
106A TRP 4.0 1.6 - - - +
108A LYS* 1.3 77.0 - - - +
110A LEU* 1.3 62.4 + - + +
111A ALA 3.3 0.2 + - - -
112A VAL* 3.3 1.2 + - - -
113A ASN* 2.8 41.4 + - - +
154A ALA* 3.4 34.1 - - + +
155A TYR* 3.8 18.6 - - - +
158A SER* 3.7 21.8 - - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TRP* 3.0 59.3 + - + +
107A ARG* 4.0 4.0 - - - +
109A LEU* 1.3 82.4 - - + +
111A ALA* 1.3 59.8 + - - +
114A LEU* 2.9 34.0 + - + -
115A ASP* 2.8 32.9 + - - +
154A ALA 4.5 3.1 - - - +
157A ALA* 4.7 7.4 - - + -
158A SER* 4.1 25.8 - - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 3.3 25.6 - - - +
107A ARG 2.9 19.1 + - - +
108A LYS* 3.5 9.0 - - - +
109A LEU 3.2 0.4 - - - -
110A LEU* 1.3 76.3 - - - +
112A VAL* 1.3 56.7 + - + +
115A ASP* 3.3 20.6 + - + +
116A GLY 3.0 23.2 + - - -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 4.3 9.4 - - - +
63A SER* 3.6 18.8 + - - +
64A SER* 4.2 15.0 - - - +
90A ALA* 4.1 5.7 - - + +
91A GLY* 3.8 22.7 - - - +
92A ILE* 4.2 20.4 - - + +
108A LYS* 3.4 11.9 + - + +
109A LEU 3.3 4.2 + - - +
110A LEU 3.3 0.2 - - - -
111A ALA* 1.3 79.3 - - + +
113A ASN* 1.3 76.2 + - - +
114A LEU 3.4 0.6 + - - -
116A GLY* 3.5 18.0 + - - -
117A VAL* 3.9 5.5 + - - +
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA 4.9 2.9 - - - -
91A GLY* 3.3 8.8 - - - -
92A ILE* 2.9 45.8 + - - +
109A LEU* 2.8 25.9 + - - +
112A VAL* 1.3 77.1 - - - +
114A LEU* 1.3 58.5 + - - +
117A VAL* 3.2 20.2 - - - +
155A TYR* 3.7 15.2 - - - -
158A SER* 3.2 31.6 + - - +
159A LYS* 4.0 12.5 + - - +
162A VAL* 3.4 13.2 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 2.9 43.2 + - + +
112A VAL 3.4 0.2 - - - -
113A ASN* 1.3 80.9 - - - +
115A ASP* 1.3 72.5 + - - +
116A GLY 3.2 0.7 - - - -
117A VAL* 3.2 3.1 + - - +
118A PHE* 2.9 22.1 + - + +
157A ALA 5.4 0.4 - - - +
158A SER* 4.6 3.8 - - - -
161A ALA* 3.6 35.2 - - + -
162A VAL* 4.4 11.2 - - + +
165A MET* 4.8 14.1 - - + -
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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