Contacts of the helix formed by residues 123 - 141 (chain A) in PDB entry 1PN9
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TYR* 3.0 28.3 + - + +
115A GLN* 4.7 0.6 - - - +
121A PRO 3.5 3.7 + - - +
122A ALA* 1.3 72.8 - - - +
124A PRO* 1.3 71.7 - - - +
125A GLU* 3.2 20.9 + - - +
126A ASN* 2.8 57.1 - - + +
127A GLU 3.1 5.5 + - - -
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Residues in contact with PRO 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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111A TYR* 5.2 0.2 - - + -
122A ALA 3.6 9.2 - - - +
123A ASN* 1.3 88.3 - - - +
125A GLU* 1.3 68.5 - - + +
127A GLU* 3.1 15.9 + - + +
128A LYS* 3.1 41.3 + - - +
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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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123A ASN* 3.2 12.4 + - - +
124A PRO* 1.3 82.9 - - + +
126A ASN* 1.3 73.7 + - - +
128A LYS* 3.5 14.0 + - - +
129A LYS* 3.2 43.1 + - - +
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Residues in contact with ASN 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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107A ARG* 4.7 2.1 - - - +
110A ASP* 4.4 20.3 + - + +
111A TYR* 3.8 22.1 - - + +
123A ASN* 2.8 41.3 + - + +
125A GLU* 1.3 84.8 - - - +
127A GLU* 1.3 60.5 + - - +
129A LYS* 3.3 17.8 + - + +
130A MET* 2.9 28.6 + - - +
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Residues in contact with GLU 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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111A TYR* 3.2 45.5 + - + +
123A ASN 3.1 6.5 + - - +
124A PRO* 3.1 16.8 + - - +
126A ASN* 1.3 78.9 - - - +
128A LYS* 1.3 60.2 + - + +
130A MET* 3.3 10.9 + - + +
131A LYS* 3.0 53.4 + - - +
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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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124A PRO* 3.1 28.8 + - - +
125A GLU* 3.7 12.0 - - - +
127A GLU* 1.3 82.1 - - + +
129A LYS* 1.3 57.0 + - + +
131A LYS* 3.2 14.6 + - + +
132A ASP* 2.9 37.0 + - - +
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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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107A ARG* 3.1 46.1 + - + +
125A GLU* 3.2 37.4 + - + +
126A ASN* 3.5 21.0 + - - +
128A LYS* 1.3 75.7 - - + +
130A MET* 1.3 65.0 + - - +
132A ASP* 3.2 7.8 + - - +
133A ALA 3.0 18.2 + - - -
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Residues in contact with MET 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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107A ARG* 4.0 17.6 - - - +
108A PHE* 3.9 16.8 - - - -
111A TYR* 3.5 32.5 - - + -
112A HIS* 3.9 26.2 - - - +
126A ASN 2.9 13.8 + - - +
127A GLU* 3.3 15.5 + - + +
129A LYS* 1.3 74.9 - - - +
131A LYS* 1.3 64.1 + - - +
133A ALA* 3.1 17.9 + - - +
134A VAL* 3.2 9.9 + - - +
166A TYR* 3.5 31.0 - - + +
171A PHE* 4.1 21.5 - - + -
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Residues in contact with LYS 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 GLU* 3.0 45.6 + - + +
128A LYS* 3.2 15.0 + - + +
130A MET* 1.3 77.2 - - - +
132A ASP* 1.3 64.4 + - - +
134A VAL* 3.2 4.0 + - - +
135A GLY* 3.0 17.3 + - - -
171A PHE* 4.0 28.5 - - + -
176A TYR* 3.3 21.2 + - - +
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Residues in contact with ASP 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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107A ARG* 4.1 10.2 + - - +
128A LYS* 2.9 24.0 + - - +
129A LYS* 3.2 11.8 + - - +
131A LYS* 1.3 78.9 - - - +
133A ALA* 1.3 56.0 + - - +
135A GLY* 3.1 4.1 + - - +
136A PHE* 2.9 44.8 + - + -
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Residues in contact with ALA 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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99A PHE* 3.5 8.0 - - - -
103A THR* 4.0 16.2 - - + +
104A LEU* 4.0 17.9 - - + -
107A ARG* 3.9 17.2 - - - +
129A LYS 3.0 12.5 + - - +
130A MET* 3.1 12.1 + - - +
132A ASP* 1.3 76.3 - - - +
134A VAL* 1.3 61.6 + - - +
136A PHE* 3.1 24.3 + - - +
137A LEU* 3.2 9.7 + - - +
166A TYR* 4.2 2.7 - - - +
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Residues in contact with VAL 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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104A LEU* 4.3 7.9 - - + -
130A MET 3.5 7.9 - - - +
131A LYS 3.2 6.6 + - - +
133A ALA* 1.3 75.7 - - - +
135A GLY* 1.3 57.5 + - - +
137A LEU* 3.2 5.8 + - + +
138A ASN* 2.9 25.8 + - - +
163A ILE* 5.2 2.9 - - + -
166A TYR* 3.5 35.4 - - + -
171A PHE* 3.5 23.3 - - + -
173A PHE* 4.1 15.7 - - + -
176A TYR* 3.8 25.8 - - + -
179A VAL* 3.8 10.3 - - + +
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Residues in contact with GLY 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 LYS 3.0 12.1 + - - -
132A ASP* 3.1 5.5 + - - -
134A VAL* 1.3 74.0 - - - +
136A PHE* 1.3 65.3 + - - +
138A ASN* 3.2 3.7 + - - +
139A THR* 3.1 26.2 + - - -
176A TYR* 3.4 22.8 - - - -
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Residues in contact with PHE 136 (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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99A PHE* 3.9 17.3 - + + -
103A THR* 4.4 2.2 - - + -
107A ARG* 4.1 21.1 - - - -
132A ASP* 2.9 33.7 + - + -
133A ALA* 3.1 13.4 + - - +
135A GLY* 1.3 76.3 - - - +
137A LEU* 1.3 62.9 + - - +
139A THR* 3.2 7.8 + - - -
140A PHE* 3.0 36.3 + + + -
48B PRO* 3.4 30.1 - - + -
49B GLN* 3.7 29.8 - - + -
50B HIS* 3.8 26.5 - + - -
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Residues in contact with LEU 137 (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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96A ARG* 6.1 0.7 - - + -
99A PHE* 4.1 7.9 - - + -
104A LEU* 4.4 11.0 - - + -
133A ALA 3.2 7.6 + - - +
134A VAL* 3.2 11.1 + - - +
136A PHE* 1.3 77.7 - - - +
138A ASN* 1.3 66.1 + - - +
140A PHE* 3.2 19.6 + - + +
141A LEU* 3.1 43.5 + - + +
147A ALA* 5.0 3.4 - - + -
159A LEU* 4.1 26.9 - - + -
163A ILE* 4.1 26.9 - - + -
179A VAL* 4.1 11.2 - - + -
182A TRP* 4.2 20.6 - - + -
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Residues in contact with ASN 138 (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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134A VAL 2.9 13.1 + - - +
135A GLY* 3.2 10.3 + - - +
137A LEU* 1.3 76.1 - - - +
139A THR* 1.3 63.3 + - - +
141A LEU 3.5 6.2 + - - -
142A GLU 3.5 0.3 + - - -
175A PRO 4.9 1.2 - - - +
176A TYR* 3.1 35.0 - - + +
177A PRO* 3.5 5.1 - - - +
178A ASN* 3.0 69.8 + - - +
179A VAL* 3.3 13.4 - - + +
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Residues in contact with THR 139 (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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135A GLY 3.1 13.0 + - - -
136A PHE* 3.5 11.5 - - - -
137A LEU 3.1 0.2 - - - -
138A ASN* 1.3 78.5 + - - +
140A PHE* 1.3 65.6 + - - +
142A GLU* 3.1 23.0 + - + +
178A ASN* 5.1 0.4 - - - +
48B PRO* 4.0 31.1 - - + +
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Residues in contact with PHE 140 (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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95A GLN* 4.4 4.0 - - - -
96A ARG* 3.2 42.0 + - - +
99A PHE* 3.6 34.5 - + - -
136A PHE* 3.0 29.9 + - + -
137A LEU* 3.2 23.3 + - + +
139A THR* 1.3 77.7 - - - +
141A LEU* 1.3 60.0 + - + +
142A GLU 3.4 2.3 + - - +
144A GLN* 3.1 23.1 - - - +
147A ALA 4.7 1.8 - - - +
48B PRO* 4.2 17.5 - - + -
49B GLN* 3.8 23.1 - - + -
63B TRP* 3.7 24.7 - + - -
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Residues in contact with LEU 141 (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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137A LEU* 3.1 37.0 + - + +
138A ASN 3.7 5.4 - - - +
139A THR 3.1 1.2 - - - -
140A PHE* 1.3 75.6 - - - +
142A GLU* 1.3 64.4 + - - +
143A GLY 3.0 1.2 + - - -
144A GLN* 2.9 27.3 + - - +
145A GLU 4.4 3.1 - - - +
146A TYR* 3.7 7.0 - - - +
147A ALA* 3.7 23.6 - - + +
178A ASN* 3.7 33.6 - - + +
179A VAL* 3.8 13.9 - - + +
182A TRP* 3.6 40.4 - - + +
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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