Contacts of the helix formed by residues 114 - 129 (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 LEU 114 (chain A).
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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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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 5.5 0.2 - - - -
110A LEU* 2.8 21.5 + - - +
111A ALA* 3.3 24.1 + - - +
114A LEU* 1.3 78.0 - - - +
116A GLY* 1.3 56.8 + - - +
118A PHE* 3.1 10.5 + - - +
119A PHE* 2.8 55.2 + - + -
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 3.1 29.8 - - - -
69A TRP* 3.5 15.5 + - - -
88A ASN* 4.8 0.4 - - - -
111A ALA 3.0 12.2 + - - -
112A VAL 3.5 12.6 + - - -
114A LEU 3.2 0.6 - - - -
115A ASP* 1.3 75.4 - - - +
117A VAL* 1.3 57.2 + - - +
119A PHE* 3.4 2.6 + - - -
120A GLY 3.0 23.0 + - - -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.7 23.3 + - + +
90A ALA 5.0 7.2 - - - +
112A VAL 4.3 4.3 - - - +
113A ASN* 3.2 26.7 - - - +
114A LEU 3.2 7.0 + - - +
116A GLY* 1.3 73.2 - - - +
118A PHE* 1.3 60.6 + - - +
121A THR* 2.8 36.5 + - - +
139A ASN* 3.7 33.9 - - + +
140A MET 5.6 4.0 - - - +
162A VAL* 3.9 23.1 - - + -
165A MET* 4.1 4.9 - - + -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 2.9 15.0 + - + +
115A ASP* 3.4 9.6 - - + +
117A VAL* 1.3 73.6 - - - +
119A PHE* 1.3 80.0 + + - +
121A THR* 3.7 1.3 - - - -
122A ARG* 2.8 82.8 + - + +
165A MET* 4.0 30.2 - - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 4.1 12.1 - - - -
64A SER 3.6 18.2 - - - -
66A GLU* 3.7 45.1 - - + -
69A TRP* 3.5 22.2 - - + +
115A ASP* 2.8 43.8 + - + +
116A GLY 3.7 0.2 - - - +
118A PHE* 1.3 92.6 - + - +
120A GLY* 1.3 58.2 + - - +
122A ARG* 3.6 25.9 + - - +
123A LEU* 3.0 31.9 + - - +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.5 36.1 - - - -
73A PHE* 4.7 0.3 - - - -
86A LEU* 3.1 18.0 - - - +
88A ASN* 4.0 1.6 - - - -
116A GLY 3.0 12.0 + - - -
117A VAL 3.9 1.1 - - - -
119A PHE* 1.3 79.0 - - - +
121A THR* 1.3 57.4 + - - +
123A LEU* 3.9 0.5 - - - +
124A GLY 2.8 23.9 + - - -
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Residues in contact with THR 121 (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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88A ASN* 3.4 7.8 + - - +
117A VAL* 2.8 24.9 + - - +
118A PHE* 3.8 3.4 - - - -
120A GLY* 1.3 73.8 - - - +
122A ARG* 1.3 64.6 + - - +
124A GLY* 3.4 0.3 + - - -
125A ILE* 3.0 45.5 + - + +
137A ILE* 3.8 17.3 - - + +
139A ASN* 3.1 27.8 + - - +
165A MET* 4.2 12.0 - - + +
166A SER* 5.9 0.2 - - - -
169A ALA* 4.1 17.5 - - + -
182A VAL* 4.8 1.6 - - + -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 2.9 31.5 + - - +
118A PHE* 2.8 61.5 + - + +
119A PHE* 3.6 22.9 + - - +
121A THR* 1.3 76.2 - - - +
123A LEU* 1.3 62.4 + - - +
125A ILE* 3.5 8.6 + - - +
126A GLN* 3.2 48.2 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.3 46.4 - - + +
70A THR* 3.7 8.5 - - - +
73A PHE* 3.4 22.0 - - + -
119A PHE 3.0 19.2 + - - +
120A GLY* 4.2 1.6 - - - +
122A ARG* 1.3 76.3 - - - +
124A GLY* 1.3 66.1 + - - +
126A GLN* 3.2 17.4 + - + +
127A ARG* 2.9 51.1 + - + +
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Residues in contact with GLY 124 (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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73A PHE* 3.7 20.4 - - - -
86A LEU* 4.6 1.3 - - - -
120A GLY 2.8 19.6 + - - -
121A THR 3.8 0.9 - - - -
123A LEU* 1.3 77.0 - - - +
125A ILE* 1.3 62.9 + - - +
128A MET* 2.9 43.5 + - - +
137A ILE* 4.1 3.6 - - - -
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Residues in contact with ILE 125 (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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121A THR* 3.0 29.8 + - + +
122A ARG* 3.8 7.9 - - - +
123A LEU 3.3 0.2 - - - -
124A GLY* 1.3 73.7 - - - +
126A GLN* 1.3 67.5 + - + +
129A LYS* 3.1 32.4 + - + +
137A ILE* 3.9 13.2 - - + +
169A ALA* 4.0 23.1 - - + -
172A ASP* 5.9 2.0 - - + +
173A CYS* 3.7 24.2 - - - -
178A TYR* 3.8 33.7 - - + -
180A VAL* 4.5 6.1 - - + -
182A VAL* 5.1 0.2 - - + -
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Residues in contact with GLN 126 (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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122A ARG* 3.2 39.6 + - - +
123A LEU* 3.2 25.9 + - + +
125A ILE* 1.3 80.4 - - + +
127A ARG* 1.3 62.0 + - + +
129A LYS* 3.8 27.9 - - - +
131A LYS* 5.1 1.6 + - - -
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Residues in contact with ARG 127 (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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70A THR* 3.6 23.8 + - - -
73A PHE* 3.9 42.0 - - + +
74A ASP* 2.8 28.5 + - - +
77A GLU* 4.8 12.3 + - - -
82A PRO* 5.9 0.9 - - - +
83A VAL* 4.8 3.0 + - + +
123A LEU* 2.9 39.5 + - + +
124A GLY 4.1 0.2 - - - +
126A GLN* 1.3 78.8 - - + +
128A MET* 1.3 60.7 + - + +
129A LYS 3.6 0.2 - - - -
131A LYS* 2.7 36.6 + - - +
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Residues in contact with MET 128 (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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73A PHE* 4.4 11.0 - - + -
83A VAL* 3.2 38.6 - - - +
84A SER 3.3 26.0 - - - +
85A THR* 3.5 5.2 - - - -
86A LEU* 4.5 4.5 - - + +
124A GLY* 2.9 25.2 + - - +
127A ARG* 1.3 79.8 - - - +
129A LYS* 1.3 67.8 + - - +
130A ASN 3.7 0.5 + - - -
131A LYS* 4.0 7.3 + - - -
133A LEU* 4.1 14.3 + - + +
135A ALA* 3.8 24.6 - - + +
136A SER 4.4 4.3 - - - +
137A ILE* 3.6 31.0 - - + -
178A TYR 4.4 0.9 - - - +
179A ASP* 4.6 1.6 - - - +
180A VAL* 4.0 5.9 - - + +
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Residues in contact with LYS 129 (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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125A ILE* 3.1 19.1 + - + +
126A GLN* 3.8 27.3 - - - +
127A ARG 3.6 0.4 - - - -
128A MET* 1.3 80.1 - - - +
130A ASN* 1.3 78.3 + - + +
131A LYS* 3.2 13.3 + - - +
178A TYR* 3.3 68.5 + - + +
180A VAL* 3.7 4.4 - - + +
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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
------------------------------------------------------------
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