Contacts of the helix formed by residues 123 - 135 (chain A) in PDB entry 4ZCU
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 SER 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.8 5.5 - - - +
122A ILE* 1.3 80.6 - - - +
124A GLU* 1.3 64.6 + - - +
125A GLN* 3.6 15.8 + - - +
126A GLN* 2.7 37.1 + - - +
127A ALA 3.4 15.8 + - - -
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Residues in contact with GLU 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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108A ALA* 3.0 19.4 - - - +
109A SER* 3.3 17.9 + - - -
112A VAL* 4.1 8.8 - - - +
123A SER* 1.3 75.6 - - - +
125A GLN* 1.3 65.7 + - - +
127A ALA* 3.3 3.5 + - - +
128A GLU* 2.9 49.1 + - - +
1007A SO4 3.0 28.8 + - - -
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Residues in contact with GLN 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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123A SER* 3.3 15.8 + - - +
124A GLU* 1.3 81.4 - - + +
126A GLN* 1.3 60.6 + - + +
128A GLU* 3.6 19.2 - - - +
129A LEU* 2.9 27.0 + - - +
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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 ILE* 3.2 20.8 - - + +
123A SER* 2.7 42.7 + - - +
124A GLU 3.2 0.6 - - - -
125A GLN* 1.3 76.0 - - + +
127A ALA* 1.3 59.9 + - - +
129A LEU* 3.1 6.4 + - - +
130A ILE* 3.0 33.1 + - + +
172A ILE* 3.8 38.4 - - + +
1009A GOL 3.6 22.0 + - - -
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Residues in contact with ALA 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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108A ALA* 3.3 34.3 - - + +
111A ILE* 4.0 7.5 - - + +
112A VAL* 3.8 15.5 - - + -
122A ILE* 4.0 12.2 - - + +
123A SER 3.4 2.6 + - - +
124A GLU 3.3 7.5 + - - +
126A GLN* 1.3 75.3 - - - +
128A GLU* 1.3 60.5 + - - +
130A ILE* 3.2 11.6 + - - +
131A LEU* 2.9 32.2 + - - +
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Residues in contact with GLU 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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108A ALA* 3.8 16.6 - - + -
124A GLU* 2.9 39.3 + - - +
125A GLN* 3.6 19.9 - - - +
126A GLN 3.2 0.2 - - - -
127A ALA* 1.3 74.6 - - - +
129A LEU* 1.3 56.5 + - - +
131A LEU* 3.5 6.9 + - + +
132A GLN* 2.9 31.8 + - - +
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Residues in contact with LEU 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 GLN 2.9 15.7 + - - +
126A GLN* 3.1 10.8 - - - +
128A GLU* 1.3 77.2 - - - +
130A ILE* 1.3 57.6 + - - +
132A GLN* 3.4 18.3 + - - +
133A SER* 2.9 28.2 + - - -
170A THR* 4.6 17.5 - - - +
172A ILE* 3.6 28.7 - - + -
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Residues in contact with ILE 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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111A ILE* 4.0 19.5 - - + -
115A LEU* 4.8 0.7 - - + -
122A ILE* 4.5 7.4 - - + -
126A GLN* 3.0 16.0 + - + +
127A ALA* 3.4 14.1 - - - +
129A LEU* 1.3 75.6 - - + +
131A LEU* 1.3 59.2 + - - +
133A SER* 2.2 33.7 + - - -
134A ILE* 3.0 10.6 + - + +
166A TRP* 3.4 58.8 - - + +
170A THR* 4.3 18.2 - - + +
172A ILE* 5.2 4.0 - - + -
174A ILE* 4.2 17.3 - - + -
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Residues in contact with LEU 131 (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 ILE* 3.5 30.3 - - + +
107A GLU* 3.7 0.7 - - - -
108A ALA* 3.3 40.4 - - + +
111A ILE* 3.6 21.3 - - + -
127A ALA 2.9 15.2 + - - +
128A GLU* 3.8 5.6 - - + +
130A ILE* 1.3 76.2 - - - +
132A GLN* 1.3 52.3 + - - +
134A ILE* 3.0 10.2 + - + +
135A ASP* 2.6 38.8 + - - +
141A THR* 4.0 21.8 - - + +
142A VAL* 3.5 22.0 - - + +
147A TRP* 6.1 1.1 - - + -
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Residues in contact with GLN 132 (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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128A GLU 2.9 18.9 + - - +
129A LEU* 3.7 17.0 - - - +
131A LEU* 1.3 73.0 - - - +
133A SER* 1.3 64.9 + - - +
134A ILE 3.0 1.3 - - - -
135A ASP* 3.2 24.1 - - + +
138A GLY* 6.0 6.1 - - - -
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Residues in contact with SER 133 (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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129A LEU 2.9 12.6 + - - -
130A ILE* 2.2 34.6 + - - +
132A GLN* 1.3 76.8 - - - +
134A ILE* 1.3 63.8 + - - +
135A ASP 5.0 0.3 - - - +
150A TYR* 3.4 22.3 + - - -
166A TRP* 4.9 3.3 - - - -
169A SER* 4.7 10.1 + - - -
170A THR* 4.0 16.5 - - - +
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Residues in contact with ILE 134 (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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130A ILE* 3.3 17.0 - - + +
131A LEU* 3.0 11.9 + - + +
133A SER* 1.3 84.6 - - - +
135A ASP* 1.3 62.9 + - - +
136A VAL* 4.0 5.2 + - - +
142A VAL* 3.8 23.7 - - + +
146A GLU* 4.3 10.4 - - - +
147A TRP* 4.2 17.5 - - + -
150A TYR* 3.6 45.7 - - + +
151A PHE* 4.3 5.8 - - + -
166A TRP* 3.7 36.6 - - + +
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Residues in contact with ASP 135 (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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131A LEU 2.6 21.0 + - - +
132A GLN* 3.2 20.1 + - - +
133A SER 4.8 0.2 - - - -
134A ILE* 1.3 76.6 - - - +
136A VAL* 1.3 68.3 + - - +
137A ASP* 2.2 33.8 + - - +
138A GLY* 3.3 12.1 - - - +
139A THR* 2.7 15.6 + - - -
141A THR 2.6 26.9 + - - +
142A VAL* 3.6 12.8 - - + -
146A GLU* 2.7 12.4 - - - +
1004A CA 2.6 11.4 - - - -
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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
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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