Contacts of the helix formed by residues 127 - 146 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B SER 3.0 10.0 - - - +
124B MET* 2.7 32.7 + - + +
126B ASP* 1.3 80.7 - - - +
128B LEU* 1.3 63.8 + - - +
129B TRP 3.2 3.1 - - - -
130B SER* 2.9 25.0 + - - -
131B ILE* 3.1 14.6 + - + +
251B ASP* 3.4 13.8 - - - -
311B THR* 4.0 16.0 - - + +
333B LEU* 5.3 1.8 - - + -
1402B CA 2.2 31.0 - - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 4.7 1.8 - - + -
120B LEU* 4.3 13.5 - - + -
124B MET* 2.7 9.3 + - + +
125B LYS* 3.3 16.9 + - + +
127B ASP* 1.3 76.1 - - - +
129B TRP* 1.3 62.4 + - - +
131B ILE* 3.5 23.4 + - + -
132B GLN* 3.1 44.2 + - + +
210B GLN 3.3 27.8 - - - +
211B SER* 3.9 14.1 - - - -
212B VAL* 4.2 13.0 - - + +
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Residues in contact with TRP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS 4.9 0.6 + - - -
126B ASP 5.2 2.8 + - - +
127B ASP 3.2 1.0 - - - -
128B LEU* 1.3 76.7 - - - +
130B SER* 1.3 65.7 + - - +
132B GLN* 3.1 14.9 + - + +
133B ASN* 2.9 60.0 + - + -
208B LYS* 5.6 6.5 - - - +
335B MET* 3.9 49.4 - - + -
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 5.2 1.6 + - - -
127B ASP* 2.9 18.4 + - - -
129B TRP* 1.3 86.5 - - - +
131B ILE* 1.3 56.1 + - - -
133B ASN* 3.7 2.8 + - - +
134B LEU* 3.0 28.9 + - - +
333B LEU* 4.2 12.0 - - - +
334B SER* 3.5 23.9 - - - +
335B MET* 3.5 28.9 + - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 2.7 38.5 + - + +
118B MET* 3.6 32.5 - - + -
119B ASP 3.7 24.0 - - - +
120B LEU* 3.9 7.4 - - + -
124B MET* 3.5 25.6 - - + -
127B ASP* 3.1 10.4 + - + +
128B LEU* 3.5 18.6 - - + +
130B SER* 1.3 72.7 - - - +
132B GLN* 1.3 63.6 + - - +
134B LEU* 3.9 1.3 - - - -
135B GLY 3.0 12.5 + - - -
249B THR* 4.3 4.9 - - - +
333B LEU* 3.8 24.5 - - + -
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Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 4.4 2.7 - - + -
128B LEU* 3.1 34.2 + - + +
129B TRP* 3.1 13.0 + - + +
131B ILE* 1.3 76.9 - - - +
133B ASN* 1.3 64.9 + - - +
135B GLY* 3.4 1.4 + - - -
136B THR* 3.0 26.5 + - - -
207B VAL* 3.1 39.9 + - + +
208B LYS* 3.3 37.5 + - + +
210B GLN* 3.3 23.8 + - - +
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Residues in contact with ASN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TRP* 2.9 47.4 + - + +
130B SER 3.7 5.2 + - - +
132B GLN* 1.3 76.5 - - - +
134B LEU* 1.3 53.4 + - - +
136B THR* 3.0 9.5 + - - +
137B LYS* 2.7 60.7 + - - +
208B LYS* 4.6 6.4 - - - +
334B SER 4.8 1.2 + - - -
335B MET 3.4 22.8 + - - -
337B SER* 4.1 19.2 + - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.1 30.1 - - + +
130B SER 3.0 18.6 + - - +
132B GLN 3.3 0.2 - - - -
133B ASN* 1.3 78.3 - - - +
135B GLY* 1.3 56.7 + - - +
137B LYS* 3.1 3.9 + - - -
138B LEU* 2.7 44.5 + - + +
247B VAL* 4.9 1.3 - - + -
249B THR* 4.1 0.4 - - + -
309B ALA* 4.0 19.5 - - + -
333B LEU* 3.8 21.3 - - + -
334B SER 5.7 1.3 - - - +
337B SER* 4.2 7.6 - - - -
340B VAL* 4.1 22.0 - - + -
341B LEU* 3.8 27.1 - - + -
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.5 28.7 - - - -
131B ILE 3.0 13.2 + - - -
132B GLN 3.4 2.2 + - - -
133B ASN 3.3 0.2 - - - -
134B LEU* 1.3 76.6 - - - +
136B THR* 1.3 59.6 + - - +
138B LEU* 3.4 16.5 - - - +
139B ALA 3.7 1.9 + - - -
203B PHE* 3.0 27.2 - - - -
207B VAL* 4.9 4.5 - - - -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN 3.0 14.5 + - - -
133B ASN* 3.3 11.0 - - - +
134B LEU 3.0 0.2 - - - -
135B GLY* 1.3 75.3 - - - +
137B LYS* 1.3 75.7 + - + +
138B LEU 3.1 2.1 + - - -
139B ALA* 3.4 13.3 + - - +
140B THR* 3.4 13.0 + - - +
204B ASN* 2.9 35.5 + - - +
207B VAL* 5.3 1.4 - - - +
208B LYS* 3.9 23.1 - - - +
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 2.7 41.8 + - - +
134B LEU* 3.7 6.7 - - - +
136B THR* 1.3 81.5 - - + +
138B LEU* 1.3 63.5 + - - +
140B THR* 3.4 15.6 + - + +
141B GLN* 3.1 25.6 + - - +
337B SER* 3.6 25.5 + - - +
341B LEU* 3.9 11.6 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 4.3 22.8 - - + +
116B TYR* 3.8 36.6 - - + -
134B LEU* 2.7 30.6 + - + +
135B GLY* 3.4 9.6 - - - +
137B LYS* 1.3 75.0 - - - +
139B ALA* 1.3 65.5 + - - +
140B THR 3.1 1.2 + - - -
141B GLN* 3.3 1.7 + - - +
142B MET* 3.2 24.7 + - - +
151B ILE* 4.4 7.2 - - + -
247B VAL* 4.2 17.0 - - + -
340B VAL* 5.2 4.0 - - + -
341B LEU* 3.9 21.3 - - + +
344B ILE* 4.1 18.0 - - + +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLY 3.7 4.8 + - - +
136B THR 3.4 9.1 + - - +
138B LEU* 1.3 79.3 - - - +
140B THR* 1.3 57.0 + - - +
143B ARG* 3.1 28.6 + - - +
149B LEU* 3.9 9.2 - - + +
151B ILE* 3.8 26.4 - - + +
200B VAL* 3.7 30.3 - - + +
203B PHE* 4.3 9.2 - - + -
204B ASN* 4.6 2.0 - - - +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 3.4 11.6 + - - +
137B LYS* 3.4 19.9 + - + +
138B LEU 3.1 0.8 - - - -
139B ALA* 1.3 77.8 - - - +
141B GLN* 1.3 70.4 + - - +
143B ARG* 3.2 6.6 + - - +
144B LYS* 3.1 47.3 + - + +
200B VAL* 6.1 0.2 - - - -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS 3.1 5.3 + - - +
138B LEU 3.8 2.0 - - - +
140B THR* 1.3 83.5 - - + +
142B MET* 1.3 64.1 + - - +
144B LYS* 3.2 20.4 + - - +
145B LEU* 3.2 22.6 + - + +
341B LEU* 3.4 50.5 - - + +
344B ILE* 4.8 7.9 - - + -
345B VAL* 3.8 28.4 - - + +
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Residues in contact with MET 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 3.6 22.2 - - - -
114B ILE* 3.3 28.9 - - + -
138B LEU 3.2 10.7 + - - +
141B GLN* 1.3 73.7 - - + +
143B ARG* 1.3 53.5 + - - +
144B LYS 3.0 4.7 - - - -
145B LEU* 2.7 40.8 + - + -
146B THR* 2.7 60.4 + - - +
149B LEU* 3.7 23.1 - - + -
245B LEU* 5.4 0.7 - - + -
344B ILE* 3.7 27.8 - - + +
348B TYR* 4.0 9.9 - - + -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ALA 3.1 19.6 + - - +
140B THR* 3.2 7.2 + - - +
142B MET* 1.3 77.2 - - - +
144B LYS* 1.3 60.3 + - + +
145B LEU 3.4 0.2 - - - -
146B THR 3.7 14.2 - - - +
147B SER* 3.2 44.4 + - - +
149B LEU* 4.1 14.4 - - + +
198B ASP 5.9 0.2 + - - -
200B VAL* 4.6 21.5 - - + +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 3.1 32.7 + - + +
141B GLN* 3.5 15.0 - - - +
142B MET 3.0 1.2 - - - -
143B ARG* 1.3 78.7 - - + +
145B LEU* 1.3 67.8 + - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.8 8.1 - - - +
141B GLN* 3.2 16.8 + - + +
142B MET* 2.7 36.2 + - + +
144B LYS* 1.3 86.4 - - + +
146B THR* 1.3 60.1 + - - +
345B VAL* 3.9 37.5 - - + -
348B TYR* 3.3 40.3 + - + -
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.4 14.0 - - - +
110B TYR 2.8 22.5 + - - -
112B VAL* 3.6 14.4 - - + -
142B MET* 2.7 48.5 + - + +
143B ARG* 3.7 15.6 + - - +
144B LYS 3.5 0.6 - - - -
145B LEU* 1.3 78.5 - - - +
147B SER* 1.3 59.2 + - - +
148B ASN* 2.9 27.5 + - - +
149B LEU* 4.3 2.6 - - + +
348B TYR* 3.9 7.0 - - + -
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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