Contacts of the helix formed by residues 129 - 142 (chain D) in PDB entry 1PY1
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 GLU 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D LYS* 4.3 7.7 + - - +
82D HIS* 3.2 29.8 - - + +
83D ASP* 3.0 27.4 - - - +
86D GLY* 3.9 14.4 - - - +
123D THR* 6.1 0.5 - - - -
126D LEU* 3.0 27.1 + - + +
127D PRO 3.8 4.8 - - - +
128D GLU* 1.3 79.5 - - + +
130D VAL* 1.3 64.8 + - - +
131D LYS* 3.2 3.4 - - - +
132D ILE* 3.0 43.5 + - + +
133D ALA* 3.5 4.0 + - - +
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO 3.8 9.2 + - - +
128D GLU* 3.1 11.2 + - - +
129D GLU* 1.3 71.3 - - - +
131D LYS* 1.3 90.0 + - + +
133D ALA* 3.0 10.9 + - - +
134D GLU* 2.8 26.0 + - - +
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLY* 3.1 28.3 - - - +
87D LYS* 4.4 4.3 - - + +
88D PHE* 3.4 41.2 - - + -
91D LEU* 3.6 10.0 - - + +
129D GLU* 3.2 2.8 - - - +
130D VAL* 1.3 93.0 - - + +
132D ILE* 1.3 60.7 + - - +
134D GLU* 3.3 5.3 + - - +
135D ALA* 3.0 20.8 + - - +
3H ASP* 2.9 31.9 + - - +
4H ILE 4.9 0.8 + - - -
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Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D MET* 4.6 11.2 - - + -
85D VAL 4.4 2.7 - - - +
86D GLY* 3.8 21.1 - - - +
91D LEU* 3.7 13.7 - - + +
119D LEU* 3.9 11.7 - - + +
122D TRP* 3.8 45.1 - - + -
123D THR* 3.7 19.3 - - + +
126D LEU* 5.0 3.4 - - + +
129D GLU* 3.0 36.9 + - + +
131D LYS* 1.3 76.2 - - - +
133D ALA* 1.3 58.2 + - - +
135D ALA* 3.5 2.3 + - - +
136D TYR* 3.0 27.0 + - - +
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D THR* 3.6 25.0 - - + +
127D PRO* 5.7 4.5 - - + +
129D GLU 3.5 3.8 + - - +
130D VAL* 3.0 13.1 + - - +
132D ILE* 1.3 78.1 - - - +
134D GLU* 1.3 55.2 + - - +
136D TYR* 3.2 2.3 + - - +
137D GLN* 2.7 38.3 + - - +
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Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PHE* 3.4 25.1 - - + -
130D VAL* 2.8 19.3 + - + +
131D LYS* 3.6 12.5 + - - +
133D ALA* 1.3 72.3 - - - +
135D ALA* 1.3 57.3 + - - +
137D GLN* 3.2 7.7 + - - +
138D MET* 2.9 29.0 + - - +
6H LEU* 3.8 21.0 - - + +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 4.4 6.5 - - + -
91D LEU* 4.3 17.5 - - + -
95D ILE* 4.0 23.6 - - + -
119D LEU* 5.4 5.4 - - + -
131D LYS 3.0 17.0 + - - +
132D ILE* 3.8 3.8 - - - +
134D GLU* 1.3 76.6 - - - +
136D TYR* 1.3 64.2 + - - +
138D MET* 3.2 8.8 + - - +
139D LEU* 3.0 28.9 + - + +
6H LEU* 4.6 8.1 - - + -
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.0 17.9 - - - -
119D LEU* 3.9 24.6 - - + +
120D TYR* 3.4 34.0 - + - +
123D THR* 3.8 21.1 - - + -
132D ILE 3.0 19.4 + - - +
133D ALA* 3.5 3.8 - - - +
135D ALA* 1.3 76.1 - - - +
137D GLN* 1.3 68.4 + - + +
139D LEU* 3.1 11.0 + - + +
140D LYS* 3.0 34.4 + - - +
145D VAL* 3.6 35.6 - - + +
148D ASP* 3.0 29.4 + - - -
149D PRO* 3.9 3.2 - - + +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ALA 2.7 21.5 + - - +
134D GLU* 3.5 7.9 - - - +
136D TYR* 1.3 77.7 - - - +
138D MET* 1.3 56.9 + - - +
140D LYS* 3.2 29.8 + - - +
141D LYS* 2.8 34.0 + - + +
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Residues in contact with MET 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 4.0 20.6 - - + -
99D SER* 6.2 0.2 - - - -
134D GLU 2.9 14.1 + - - +
135D ALA* 3.6 7.4 - - - +
137D GLN* 1.3 76.2 - - - +
139D LEU* 1.3 92.5 + - + +
141D LYS* 2.9 25.2 + - - +
142D GLN* 2.9 49.8 + - + +
6H LEU* 3.9 17.7 - - + -
7H LEU 3.5 26.0 - - - +
8H LYS* 4.0 11.2 - - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 4.2 21.1 - - + -
98D VAL* 4.1 10.8 - - + -
116D LEU* 4.0 15.0 - - + -
119D LEU* 3.6 30.3 - - + -
135D ALA* 3.0 20.0 + - + +
136D TYR* 3.1 11.4 + - + +
138D MET* 1.3 93.2 - - + +
140D LYS* 1.3 59.9 + - - +
142D GLN* 3.4 1.5 + - - +
143D GLY 3.2 2.8 + - - -
144D ILE* 2.9 57.8 + - + +
145D VAL* 3.2 15.3 + - + -
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D TYR* 3.0 21.4 + - + +
137D GLN* 3.4 32.8 - - - +
139D LEU* 1.3 75.8 - - - +
141D LYS* 1.3 65.3 + - - +
143D GLY* 3.0 13.7 + - - -
145D VAL* 3.8 37.4 - - + +
146D LYS 5.0 7.2 - - - +
147D SER* 5.3 2.4 - - - +
148D ASP* 2.9 33.1 + - - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN* 2.8 20.3 + - + +
138D MET* 2.9 17.1 + - - +
140D LYS* 1.3 77.0 - - - +
142D GLN* 1.3 72.9 + - - +
143D GLY 3.3 0.8 + - - -
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D SER* 4.6 3.8 + - - -
100D PRO* 6.1 0.2 - - - +
101D LYS* 3.8 26.5 + - - +
138D MET* 2.9 51.9 + - + +
139D LEU 3.4 4.7 + - - +
140D LYS 3.1 0.2 - - - -
141D LYS* 1.3 89.4 + - - +
143D GLY* 1.3 56.9 + - - +
144D ILE* 3.1 32.5 + - + +
8H LYS* 3.4 10.8 + - - +
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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