Contacts of the helix formed by residues 121 - 130 (chain A) in PDB entry 2Z4U
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 GLN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 5.4 3.4 + - - +
119A ASN* 3.1 34.8 + - + +
120A SER* 1.3 79.9 + - - +
122A TYR* 1.3 66.1 + - - +
123A SER* 3.9 19.9 + - - +
124A THR* 3.0 5.2 + - - +
125A LEU* 3.0 19.2 + - - +
501A EDO 4.8 5.2 - - - -
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Residues in contact with TYR 122 (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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120A SER 3.5 1.8 + - - -
121A GLN* 1.3 71.8 - - - +
123A SER* 1.3 63.9 + - - +
125A LEU* 3.8 5.6 - - + +
126A GLN* 2.8 31.4 + - - +
134A ARG* 3.5 61.0 - - - +
167A LEU* 3.7 18.6 - - + -
170A ILE* 3.7 10.2 - - + +
171A GLN* 3.4 15.1 - - + +
175A GLU* 2.6 43.3 + - - +
204A GLU* 3.9 6.9 - - + -
205A GLU* 5.6 2.9 - - + -
501A EDO 3.7 35.2 + - - -
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Residues in contact with SER 123 (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 GLN* 3.9 19.3 + - - +
122A TYR* 1.3 77.6 - - - +
124A THR* 1.3 66.5 + - - +
126A GLN* 3.6 11.5 + - - +
127A ASN* 3.1 32.5 + - - +
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Residues in contact with THR 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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118A TYR* 3.8 25.6 - - + -
119A ASN* 2.7 49.3 + - - +
121A GLN* 3.0 9.2 + - - +
123A SER* 1.3 79.5 + - - +
125A LEU* 1.3 65.9 + - - +
127A ASN* 3.1 13.4 + - + +
128A LYS* 2.9 28.1 + - + +
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Residues in contact with LEU 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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89A PHE* 4.1 9.9 - - + -
118A TYR* 3.7 27.1 - - + -
119A ASN 4.0 8.7 - - - +
120A SER* 3.7 18.6 - - - +
121A GLN 3.0 16.1 + - - +
122A TYR* 3.8 6.3 - - + +
124A THR* 1.3 76.8 - - - +
126A GLN* 1.3 57.3 + - - +
128A LYS* 3.3 1.8 + - - -
129A ALA* 2.9 30.7 + - - +
163A ALA* 3.6 10.1 - - + +
166A LEU* 4.2 15.3 - - + -
167A LEU* 3.8 33.4 - - + -
170A ILE* 3.8 26.2 - - + -
501A EDO 4.0 2.5 - - - +
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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 TYR* 2.8 21.3 + - - +
123A SER* 3.7 11.5 - - - +
125A LEU* 1.3 73.9 - - - +
127A ASN* 1.3 66.9 + - - +
129A ALA 3.2 1.7 + - - -
130A GLY 3.0 4.3 + - - -
131A VAL* 3.0 47.2 + - + +
132A SER 3.9 12.4 - - - +
133A SER* 4.0 3.5 + - - +
134A ARG* 2.9 74.7 - - + +
167A LEU* 4.4 5.4 - - + -
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Residues in contact with ASN 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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123A SER* 3.1 23.7 + - - +
124A THR* 3.4 13.1 - - + +
126A GLN* 1.3 76.7 - - - +
128A LYS* 1.3 67.1 + - + +
130A GLY* 3.1 14.4 + - - -
131A VAL 4.5 4.8 - - - +
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Residues in contact with LYS 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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117A ASN 5.2 2.8 + - - -
118A TYR* 3.7 49.8 - - + +
124A THR* 2.9 24.7 + - - +
126A GLN 3.3 0.2 - - - -
127A ASN* 1.3 80.0 - - + +
129A ALA* 1.3 59.6 + - - +
130A GLY 3.4 0.9 + - - -
159A ASP* 4.3 21.9 + - + +
160A LYS* 3.3 22.2 + - - +
163A ALA* 3.6 20.4 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.5 + - - +
126A GLN 3.2 3.6 + - - +
128A LYS* 1.3 74.8 - - - +
130A GLY* 1.3 60.7 + - - +
131A VAL* 3.4 13.2 - - + +
137A VAL* 4.7 3.3 - - + +
160A LYS* 3.5 30.0 - - - +
163A ALA* 3.8 7.4 - - + +
164A GLU* 4.1 20.6 - - + +
167A LEU* 3.9 19.3 - - + -
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Residues in contact with GLY 130 (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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126A GLN 3.0 3.4 + - - -
127A ASN 3.1 11.8 + - - -
128A LYS 3.2 2.2 + - - -
129A ALA* 1.3 76.8 - - - +
131A VAL* 1.3 62.8 + - - +
160A LYS* 5.2 4.7 - - - -
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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