Contacts of the helix formed by residues 129 - 147 (chain D) in PDB entry 5ON2
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 THR 129 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TYR* 3.6 22.2 - - + +
126D ALA* 2.6 37.9 + - + +
128D CYS* 1.3 76.8 - - - +
130D PRO* 1.4 70.9 - - + +
131D GLU* 4.0 18.9 + - - +
132D TYR* 3.0 19.6 + - - +
133D TYR* 3.1 12.9 + - - -
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Residues in contact with PRO 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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128D CYS 3.8 6.3 - - - +
129D THR* 1.4 84.5 - - + +
131D GLU* 1.3 70.1 + - - +
132D TYR 3.4 0.5 + - - -
133D TYR* 3.5 27.3 - - + +
134D ARG* 3.4 29.5 + - - +
451D PRO* 4.6 6.8 - - + +
453D ILE* 4.0 30.3 - - + -
454D LEU 5.6 0.9 - - - +
456D GLU* 4.8 11.2 - - - +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D THR* 3.1 19.4 + - - +
130D PRO* 1.3 86.5 - - - +
132D TYR* 1.3 57.0 + - - +
134D ARG* 3.8 7.0 - - - +
135D TRP* 3.3 25.1 + - - -
502D ARG* 4.0 8.3 + - - +
506D PRO 6.0 1.3 - - - +
509D LYS* 4.4 22.2 - - + +
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Residues in contact with TYR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU* 4.2 23.3 - - + -
126D ALA 3.9 13.2 - - - +
127D THR* 3.6 41.5 - - + -
129D THR* 3.0 11.9 + - - +
131D GLU* 1.3 76.2 - - - +
133D TYR* 1.3 63.6 + - + +
134D ARG 3.2 9.1 + - - -
135D TRP* 3.4 14.1 + - - -
136D GLU* 4.2 0.7 - - - -
495D GLU* 2.6 36.7 + - + -
498D TRP* 3.5 39.8 - + - -
499D TYR* 3.2 20.7 + - + +
502D ARG* 3.8 35.4 - - + +
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 4.0 10.1 - + - -
127D THR 3.8 17.9 - - - +
128D CYS 3.4 20.9 - - - -
129D THR 3.1 18.8 + - - -
130D PRO* 3.5 26.5 - - + +
132D TYR* 1.3 77.8 - - + +
134D ARG* 1.3 62.8 + - - +
135D TRP 3.3 0.9 - - - -
136D GLU* 3.3 29.3 - - - +
137D GLN* 3.3 23.0 - - - +
430D ALA* 3.9 23.1 - - + -
431D PRO* 3.8 11.0 - - + -
451D PRO* 5.1 2.7 - - + -
452D VAL 3.6 19.7 - - - -
453D ILE* 3.5 6.0 - - - +
454D LEU* 2.8 33.4 + - + +
495D GLU* 5.1 0.9 - - + -
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PRO 3.4 22.1 + - - +
131D GLU* 3.8 8.7 - - - +
133D TYR* 1.3 79.1 - - - +
135D TRP* 1.3 118.0 + - + +
137D GLN* 3.5 14.7 + - - +
138D LYS* 3.2 33.3 + - - +
450D LEU* 4.9 10.0 + - + +
451D PRO* 3.5 37.6 - - + +
509D LYS 4.4 5.5 + - - -
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Residues in contact with TRP 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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131D GLU 3.3 25.7 + - - -
132D TYR 3.4 10.2 + - - -
133D TYR 3.3 0.8 - - - -
134D ARG* 1.3 120.5 - - + +
136D GLU* 1.3 60.5 + - - +
138D LYS* 3.6 22.4 + - + +
139D PHE* 3.0 27.4 + - - +
498D TRP* 3.8 8.7 - + + -
502D ARG* 3.3 28.9 - - - +
508D TYR 4.0 1.6 - - - -
509D LYS* 3.4 24.0 - - - -
510D GLU* 4.2 1.8 - - - -
511D GLY* 3.2 44.4 - - - -
512D MET* 3.5 31.0 - - + +
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Residues in contact with GLU 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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132D TYR* 4.2 0.7 - - - -
133D TYR* 3.3 21.5 - - - +
135D TRP* 1.3 74.8 - - - +
137D GLN* 1.3 63.3 + - - +
139D PHE* 3.6 8.7 - - - +
140D PHE* 2.9 28.6 + - - +
430D ALA* 3.6 13.7 - - - +
490D PHE* 3.7 14.6 - - + -
494D MET* 3.5 19.8 - - + +
495D GLU* 3.0 43.0 - - - +
498D TRP* 3.0 40.3 + - + +
512D MET* 4.9 1.1 - - - -
544D PHE* 5.3 2.7 - - + -
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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 TYR* 3.3 24.4 + - + +
134D ARG* 3.5 7.0 - - - +
135D TRP 3.3 0.4 - - - -
136D GLU* 1.3 77.1 - - - +
138D LYS* 1.3 61.2 + - - +
140D PHE* 3.2 2.1 + - - -
141D THR* 3.2 20.8 + - - +
431D PRO* 2.8 37.3 + - - +
433D PRO* 3.3 30.1 - - + +
450D LEU* 4.3 7.9 - - + -
451D PRO* 3.4 28.6 - - - +
452D VAL* 3.3 33.1 + - - +
490D PHE* 4.1 9.9 - - + -
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Residues in contact with LYS 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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134D ARG* 3.2 20.0 + - - +
135D TRP* 4.0 24.7 - - + +
136D GLU 3.5 0.2 - - - -
137D GLN* 1.3 78.4 - - - +
139D PHE* 1.3 57.0 + - - +
141D THR* 2.6 24.2 + - - +
142D GLU* 3.1 33.0 + - + +
447D ASP* 3.6 30.6 + - - +
450D LEU* 4.0 19.9 - - + +
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Residues in contact with PHE 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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135D TRP 3.0 19.1 + - - +
136D GLU* 3.6 7.2 - - - +
137D GLN 3.2 0.2 - - - -
138D LYS* 1.3 76.1 - - - +
140D PHE* 1.3 58.7 + - - +
142D GLU* 3.2 22.6 + - + +
143D LEU* 2.9 60.6 + - + +
512D MET* 3.9 19.1 - - - -
544D PHE* 3.4 35.4 - + - -
547D LEU* 3.8 28.9 - - + -
548D MET* 4.1 12.6 - - + -
551D ALA* 4.9 3.6 - - + -
553D MET* 3.6 25.4 - - + -
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Residues in contact with PHE 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 GLU 2.9 18.3 + - - +
137D GLN 3.2 5.8 + - - +
139D PHE* 1.3 77.5 - - - +
141D THR* 1.3 56.9 + - - +
143D LEU* 3.6 9.1 + - + +
144D TYR* 3.2 22.5 + - - +
149D VAL* 3.6 24.9 - - + +
191D TRP* 4.3 17.0 - + + -
193D ILE* 3.9 35.0 - - + -
422D VAL* 4.0 6.1 - - + -
432D ILE* 3.9 15.9 - - + -
433D PRO* 3.9 18.2 - - + -
434D MET* 3.6 26.7 - - + -
490D PHE* 3.6 30.1 - + + -
494D MET* 5.0 2.2 - - + -
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Residues in contact with THR 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 3.2 12.2 + - - +
138D LYS* 2.6 31.2 + - - +
140D PHE* 1.3 74.2 - - - +
142D GLU* 1.3 63.5 + - - +
144D TYR* 3.3 9.8 + - - +
145D LYS* 3.2 37.2 + - - +
433D PRO* 3.9 21.5 - - + +
434D MET* 5.3 0.2 - - - -
444D PRO* 3.5 28.8 - - + +
445D THR 4.2 11.7 - - - +
447D ASP* 5.1 3.9 + - - -
450D LEU* 4.6 6.3 - - + +
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Residues in contact with GLU 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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138D LYS* 3.1 39.7 + - + +
139D PHE* 3.2 26.6 + - + +
141D THR* 1.3 81.5 + - - +
143D LEU* 1.3 61.1 + - - +
145D LYS* 3.5 19.9 + - - +
146D LYS* 3.3 28.9 + - + +
551D ALA* 5.6 3.1 - - - +
553D MET* 5.3 3.3 - - - +
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Residues in contact with LEU 143 (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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139D PHE* 2.9 52.2 + - + +
140D PHE* 3.8 7.6 - - + +
142D GLU* 1.3 75.0 - - - +
144D TYR* 1.3 62.2 + - - +
146D LYS* 3.5 9.4 + - + +
147D GLY 3.2 4.5 + - - -
148D LEU* 3.1 55.8 + - + -
149D VAL* 3.7 14.8 + - + -
193D ILE* 4.3 26.2 - - + -
544D PHE* 5.3 1.8 - - + -
547D LEU* 4.0 26.2 - - + -
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Residues in contact with TYR 144 (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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140D PHE 3.2 14.7 + - - +
141D THR* 3.5 10.3 - - - +
142D GLU 3.3 0.4 - - - -
143D LEU* 1.3 76.8 - - - +
145D LYS* 1.3 66.2 + - + +
147D GLY* 3.3 12.4 + - - +
149D VAL* 3.8 31.2 - - + +
150D TYR* 5.8 0.9 - - - -
191D TRP* 4.2 16.5 - + - -
434D MET* 3.5 29.4 - - + -
442D VAL* 4.0 17.8 + - - +
443D MET* 4.9 1.8 - - + -
444D PRO* 3.7 30.1 - - + -
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Residues in contact with LYS 145 (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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141D THR* 3.2 37.0 + - - +
142D GLU* 3.5 18.3 + - - +
143D LEU 3.4 0.2 - - - -
144D TYR* 1.3 83.8 - - + +
146D LYS* 1.3 61.6 + - + +
147D GLY* 3.5 0.7 + - - -
444D PRO* 5.2 9.2 - - + -
447D ASP* 5.0 11.9 + - - -
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Residues in contact with LYS 146 (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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142D GLU* 3.3 20.6 + - - +
143D LEU* 3.8 10.3 - - + +
144D TYR 3.4 0.4 - - - -
145D LYS* 1.3 76.6 - - + +
147D GLY* 1.3 58.8 + - - +
148D LEU* 3.6 24.8 - - + +
547D LEU 5.2 1.6 + - - -
550D ASP* 4.3 11.3 + - - +
551D ALA* 4.2 30.1 - - - +
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Residues in contact with GLY 147 (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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143D LEU 3.2 3.4 + - - -
144D TYR 3.3 9.3 + - - -
145D LYS 3.3 4.0 - - - -
146D LYS* 1.3 77.9 - - - +
148D LEU* 1.3 64.6 + - - +
149D VAL 3.4 10.3 + - - +
150D TYR* 5.9 0.9 - - - +
194D LYS* 4.4 13.3 + - - +
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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
------------------------------------------------------------
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