Contacts of the helix formed by residues 127 - 144 (chain D) in PDB entry 1TYE
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 ASP 127 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER 2.9 8.8 - - - +
124D MET* 2.9 26.8 + - + +
126D ASP* 1.3 83.5 - - - +
128D LEU* 1.3 66.2 + - - +
129D TRP 3.3 2.9 - - - -
130D SER* 3.0 24.8 + - - -
131D ILE* 3.1 16.3 + - + +
251D ASP* 3.4 12.7 - - - +
311D THR* 4.0 16.6 - - + +
333D LEU* 5.4 1.1 - - + -
1409D CA 2.2 30.1 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D MET* 4.9 2.0 - - + -
120D LEU* 4.1 17.5 - - + -
124D MET* 2.7 10.7 + - + +
125D LYS* 3.7 15.3 - - + +
126D ASP 3.6 0.8 - - - -
127D ASP* 1.3 77.9 - - - +
129D TRP* 1.3 63.3 + - - +
131D ILE* 3.3 23.2 - - + +
132D GLN* 3.0 47.6 + - + +
210D GLN 3.4 25.8 - - - +
211D SER* 3.9 13.2 - - - -
212D VAL* 4.5 10.8 - - + +
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Residues in contact with TRP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS 5.1 0.2 + - - -
126D ASP 5.3 2.4 - - - +
127D ASP 3.3 0.8 - - - -
128D LEU* 1.3 76.7 - - - +
130D SER* 1.3 69.9 + - - +
132D GLN* 3.3 12.0 + - + +
133D ASN* 2.9 60.4 + - + +
335D MET* 3.4 58.8 - - + -
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP 5.1 2.1 + - - -
127D ASP* 3.0 18.8 + - - -
129D TRP* 1.3 90.2 - - - +
131D ILE* 1.3 58.1 + - - +
133D ASN* 3.5 2.8 + - - +
134D LEU* 3.0 27.5 + - - +
333D LEU* 4.2 14.1 - - - +
334D SER* 3.8 21.5 - - - +
335D MET* 3.8 23.9 + - - +
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Residues in contact with ILE 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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116D TYR* 2.7 34.0 + - + +
118D MET* 3.6 28.7 - - + -
119D ASP 4.1 9.4 - - - +
120D LEU* 4.2 2.9 - - + -
124D MET* 3.9 26.5 - - + -
127D ASP 3.1 7.7 + - - +
128D LEU* 3.3 29.8 - - + +
130D SER* 1.3 73.5 - - - +
132D GLN* 1.3 58.6 + - - +
133D ASN 3.2 0.7 - - - -
134D LEU* 4.3 1.1 - - - -
135D GLY 3.0 13.2 + - - -
249D THR* 3.7 17.9 - - + +
333D LEU* 3.7 29.6 - - + -
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Residues in contact with GLN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D MET* 4.4 6.1 - - + -
128D LEU* 3.0 45.5 + - + +
129D TRP* 3.7 10.7 - - + +
131D ILE* 1.3 75.4 - - - +
133D ASN* 1.3 65.4 + - - +
135D GLY* 3.4 1.2 + - - -
136D THR* 3.1 26.4 + - - -
207D VAL* 3.1 40.0 + - + +
208D LYS* 3.2 40.6 + - + +
210D GLN 3.9 11.3 + - - -
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Residues in contact with ASN 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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129D TRP* 2.9 46.0 + - + +
130D SER 3.5 6.3 + - - +
132D GLN* 1.3 75.2 - - - +
134D LEU* 1.3 60.8 + - - +
136D THR* 3.0 8.6 + - - -
137D LYS* 2.9 47.3 + - - +
208D LYS* 5.3 3.6 - - - +
334D SER 5.2 0.4 + - - -
335D MET 3.7 21.4 + - - -
337D SER* 4.1 15.8 + - - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TYR* 3.2 32.1 - - + +
130D SER 3.0 15.9 + - - +
131D ILE* 4.3 0.2 - - - -
133D ASN* 1.3 76.4 - - - +
135D GLY* 1.3 60.4 + - - +
137D LYS* 3.9 4.7 - - - -
138D LEU* 3.0 28.4 + - + +
247D VAL* 4.5 2.7 - - + -
249D THR* 4.2 0.4 - - + -
309D ALA* 4.1 10.3 - - + -
333D LEU* 4.1 20.2 - - + -
334D SER 5.8 0.4 - - - +
337D SER* 3.6 28.9 - - - -
340D VAL* 3.6 36.8 - - + -
341D LEU* 4.0 10.1 - - + -
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Residues in contact with GLY 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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116D TYR* 3.6 27.6 + - - -
131D ILE 3.0 11.7 + - - -
132D GLN 3.4 3.1 + - - -
133D ASN 3.1 0.6 - - - -
134D LEU* 1.3 78.0 - - - +
136D THR* 1.3 60.2 + - - +
138D LEU* 3.5 14.5 - - - +
139D ALA 3.8 1.2 + - - -
203D PHE* 3.0 27.9 - - - -
204D ASN* 4.2 0.2 - - - -
207D VAL* 4.7 4.5 - - - -
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Residues in contact with THR 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 GLN 3.1 12.6 + - - -
133D ASN* 3.0 11.9 + - - -
135D GLY* 1.3 73.8 - - - +
137D LYS* 1.3 70.0 + - + +
138D LEU 3.1 2.6 + - - -
139D ALA* 3.2 13.9 + - - +
140D THR* 3.3 17.5 + - - +
204D ASN* 3.1 33.1 + - + +
207D VAL* 5.4 1.2 - - - +
208D LYS* 3.8 21.2 + - - +
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Residues in contact with LYS 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 ASN* 2.9 38.9 + - - +
134D LEU* 4.0 4.0 - - - +
136D THR* 1.3 82.3 - - + +
138D LEU* 1.3 56.2 + - - +
140D THR* 3.4 14.1 - - + +
141D GLN* 2.8 33.6 + - - +
337D SER* 3.7 19.8 + - - +
341D LEU* 3.8 23.4 - - + +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ILE* 4.2 21.3 - - + +
116D TYR* 4.1 26.0 - - + -
134D LEU* 3.0 33.4 + - + +
135D GLY* 3.5 9.0 - - - +
136D THR 3.1 0.2 - - - -
137D LYS* 1.3 77.6 - - - +
139D ALA* 1.3 61.1 + - - +
140D THR 3.1 0.2 - - - -
141D GLN* 3.5 2.5 + - + +
142D MET* 3.2 28.4 + - - +
151D ILE* 4.6 9.2 - - + -
203D PHE* 5.7 0.2 - - + -
247D VAL* 4.0 24.0 - - + -
340D VAL* 4.7 3.8 - - + -
341D LEU* 3.6 22.4 - - + -
344D ILE* 4.2 19.4 - - + +
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Residues in contact with ALA 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 GLY 3.8 4.1 + - - +
136D THR 3.2 8.9 + - - +
138D LEU* 1.3 78.1 - - - +
140D THR* 1.3 57.3 + - - +
143D ARG* 3.1 34.2 + - - +
149D LEU* 4.0 8.6 - - + +
151D ILE* 3.8 23.3 - - + +
200D VAL* 3.6 36.0 - - + +
203D PHE* 4.7 4.9 - - + -
204D ASN* 4.9 0.7 - - - +
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Residues in contact with THR 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 THR* 3.3 17.9 + - - +
137D LYS* 3.2 19.6 + - + +
138D LEU 3.1 0.4 - - - -
139D ALA* 1.3 75.7 - - - +
141D GLN* 1.3 69.1 + - - +
143D ARG* 2.8 19.6 + - - +
144D LYS* 3.2 36.6 + - + +
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Residues in contact with GLN 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 LYS 2.8 20.1 + - - +
138D LEU* 4.0 4.0 - - - +
140D THR* 1.3 75.2 - - - +
142D MET* 1.3 61.5 + - + +
144D LYS* 3.6 17.3 + - - +
145D LEU* 3.8 16.7 + - + +
341D LEU* 3.9 43.5 + - + +
342D GLN* 4.9 2.8 + - - +
344D ILE* 5.0 8.3 - - + -
345D VAL* 3.6 31.0 - - + +
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Residues in contact with MET 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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112D VAL* 3.4 36.8 - - + -
114D ILE* 3.5 26.0 - - + -
138D LEU 3.2 11.5 + - - +
140D THR 3.1 1.0 - - - -
141D GLN* 1.3 75.1 - - - +
143D ARG* 1.3 59.8 + - - +
144D LYS 3.0 2.0 - - - -
145D LEU* 2.9 36.6 + - - +
146D THR* 2.9 41.2 + - + +
149D LEU* 3.8 20.2 - - + -
245D LEU* 5.3 1.6 - - + -
344D ILE* 3.6 27.8 - - + +
348D TYR* 3.8 11.2 - - + -
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Residues in contact with ARG 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 ALA 3.1 24.9 + - - +
140D THR* 2.8 8.9 + - - +
142D MET* 1.3 75.4 - - - +
144D LYS* 1.3 58.9 + - + +
145D LEU 3.2 1.3 + - - -
146D THR 2.9 22.2 + - - +
147D SER* 3.4 43.2 + - - +
149D LEU* 4.0 24.8 + - - +
198D ASP* 5.0 12.2 + - - +
200D VAL* 4.2 21.2 - - - +
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Residues in contact with LYS 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 THR* 3.2 30.3 + - + +
141D GLN* 3.9 14.6 - - - +
142D MET 3.0 1.0 - - - -
143D ARG* 1.3 80.5 - - + +
145D LEU* 1.3 68.9 + - + +
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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
------------------------------------------------------------
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