Contacts of the helix formed by residues 120 - 135 (chain A) in PDB entry 4P9U
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 ASN 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ALA 3.1 14.5 + - - +
119A LEU* 1.3 87.5 - - - +
121A LYS* 1.3 65.0 + - - +
122A GLU 3.5 1.8 - - - -
123A SER* 4.1 11.5 + - - +
124A ALA* 3.1 15.2 + - - +
195A HIS* 3.5 51.3 + - + +
197A GLY* 5.2 4.2 - - - +
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Residues in contact with LYS 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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116A ALA 3.7 1.7 + - - -
117A PHE 3.4 25.7 + - - +
118A LYS 4.5 6.7 - - - +
119A LEU 3.5 4.0 + - - -
120A ASN* 1.3 72.1 - - - +
122A GLU* 1.3 74.3 + - + +
124A ALA* 3.1 8.3 - - - +
125A GLU* 2.8 52.2 + - - +
240A CYS* 3.3 23.9 - - - +
241A GLN* 4.1 13.6 + - - +
243A GLY* 5.9 1.6 - - - +
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Residues in contact with GLU 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 ASN 3.5 0.2 - - - -
121A LYS* 1.3 93.0 + - + +
123A SER* 1.3 62.0 + - - +
124A ALA 3.1 0.7 - - - -
125A GLU* 3.5 18.3 - - + +
126A ARG* 2.9 27.0 + - - +
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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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120A ASN* 3.6 14.8 + - - +
121A LYS 3.6 0.4 - - - -
122A GLU* 1.3 76.5 - - - +
124A ALA* 1.3 58.6 + - - +
126A ARG* 3.4 22.4 + - - +
127A ILE* 3.0 35.8 + - - +
195A HIS* 3.7 29.3 - - - -
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Residues in contact with ALA 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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116A ALA* 4.0 11.9 - - + +
117A PHE* 4.1 4.9 - - + -
120A ASN* 3.1 14.1 + - + +
121A LYS 3.1 11.7 - - - +
123A SER* 1.3 76.2 - - - +
125A GLU* 1.3 62.7 + - - +
127A ILE* 3.1 11.2 - - - +
128A MET* 2.9 29.4 + - - +
192A LEU* 3.8 21.8 - - + -
195A HIS* 4.9 3.7 - - + -
240A CYS* 4.1 9.9 - - - -
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Residues in contact with GLU 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 LYS* 2.8 53.0 + - - +
122A GLU* 3.5 16.3 - - + +
123A SER 3.5 0.2 - - - -
124A ALA* 1.3 74.4 - - - +
126A ARG* 1.3 56.7 + - - +
128A MET* 3.8 2.2 - - - +
129A ILE* 2.8 41.7 + - + +
237A LEU* 4.0 15.9 - - + -
240A CYS* 3.6 12.3 - - + -
241A GLN* 3.1 33.5 + - - +
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Residues in contact with ARG 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 GLU 2.9 20.2 + - - +
123A SER* 3.4 16.5 + - - +
124A ALA 3.1 0.4 - - - -
125A GLU* 1.3 77.4 - - - +
127A ILE* 1.3 81.4 + - - +
129A ILE* 3.9 5.3 - - - +
130A ASN* 2.9 29.4 + - + +
191A ARG* 6.1 0.2 - - - +
195A HIS* 4.2 18.2 + - - -
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Residues in contact with ILE 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 3.0 15.9 + - - +
124A ALA* 3.1 15.7 - - - +
126A ARG* 1.3 101.0 - - + +
128A MET* 1.3 58.4 + - + +
130A ASN* 3.3 9.0 - - - +
131A VAL* 2.9 34.9 + - + +
187A MET* 6.2 0.9 - - + -
188A LEU* 5.0 4.0 - - + +
191A ARG* 3.6 53.2 - - + +
192A LEU* 3.9 26.5 - - + +
195A HIS* 4.6 10.8 - - + +
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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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117A PHE* 3.9 28.0 - - - -
124A ALA 2.9 26.9 + - - +
125A GLU 3.8 3.8 - - - +
127A ILE* 1.3 75.2 - - + +
129A ILE* 1.3 59.3 + - - +
131A VAL* 3.1 7.6 + - - +
132A ILE* 2.9 35.3 + - + +
188A LEU* 4.7 12.5 - - + +
192A LEU* 4.0 21.1 - - + -
233A TYR 3.5 9.2 - - - +
236A LEU* 3.4 22.4 - - + +
237A LEU* 3.2 46.2 - - + +
240A CYS* 4.6 2.5 - - - -
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Residues in contact with ILE 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 GLU* 2.8 30.0 + - + +
126A ARG* 3.9 4.7 - - - +
128A MET* 1.3 72.0 - - - +
130A ASN* 1.3 63.6 + - - +
132A ILE* 3.2 8.2 + - + +
133A GLU* 2.9 52.0 + - + +
237A LEU* 3.6 29.6 - - + -
241A GLN* 4.6 8.1 - - - +
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Residues in contact with ASN 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 ARG* 2.9 20.6 + - + +
127A ILE* 3.3 11.3 - - - +
129A ILE* 1.3 78.2 - - - +
131A VAL* 1.3 58.9 + - - +
133A GLU* 3.6 5.3 + - - +
134A SER* 2.8 44.2 + - - -
184A TYR* 4.5 3.6 - - - -
187A MET* 4.2 19.8 - - - +
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Residues in contact with VAL 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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127A ILE* 2.9 20.5 + - + +
128A MET 3.4 7.2 - - - +
130A ASN* 1.3 76.7 - - - +
132A ILE* 1.3 58.8 + - - +
134A SER* 3.3 2.3 + - - -
135A CYS* 2.9 36.0 + - - +
184A TYR* 3.8 37.5 - - + +
187A MET* 4.7 11.9 - - + -
188A LEU* 3.8 38.6 - - + +
191A ARG* 6.2 0.4 - - - -
233A TYR* 4.1 19.3 - - + -
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Residues in contact with ILE 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 MET* 2.9 20.4 + - + +
129A ILE* 3.7 5.2 - - - +
131A VAL* 1.3 76.7 - - + +
133A GLU* 1.3 62.4 + - + +
135A CYS* 3.2 12.6 + - - +
136A GLU* 2.9 27.1 - - - +
230A MET* 4.7 4.2 - - + +
233A TYR* 3.6 46.7 - - + +
234A ARG* 3.9 33.4 - - + +
237A LEU* 4.0 22.7 - - + -
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Residues in contact with GLU 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 ILE* 2.9 43.2 + - + +
130A ASN* 4.2 4.7 - - - +
132A ILE* 1.3 73.8 - - + +
134A SER* 1.3 62.9 + - - +
135A CYS 3.1 4.7 - - - -
136A GLU* 3.2 25.9 + - - +
147A PHE* 4.6 13.7 - - + -
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Residues in contact with SER 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 ASN* 2.8 31.4 + - - -
131A VAL 3.6 1.8 - - - -
133A GLU* 1.3 73.1 - - - +
135A CYS* 1.3 57.4 + - - +
136A GLU 3.0 8.5 + - - -
137A ALA* 4.0 1.4 + - - +
144A TRP* 3.2 32.2 - - - -
147A PHE* 4.9 8.3 - - - -
148A ILE* 5.5 3.5 - - - +
184A TYR* 3.4 41.4 + - - -
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Residues in contact with CYS 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 VAL* 2.9 28.0 + - - +
132A ILE* 3.5 9.0 - - - +
133A GLU 3.1 1.2 - - - -
134A SER* 1.3 75.7 - - - +
136A GLU* 1.3 64.4 + - - +
137A ALA* 3.1 7.2 - - - +
138A LEU* 3.2 21.1 - - - +
181A PHE* 3.7 29.8 - - + -
184A TYR* 3.8 26.7 - - - -
230A MET* 3.3 18.0 - - + +
233A TYR* 4.3 5.6 - - - -
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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