Contacts of the helix formed by residues 137 - 148 (chain B) in PDB entry 1T8U
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 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A HIS* 3.4 16.0 - - - -
363A CYS* 2.9 27.7 + - - +
364A LEU 4.8 1.5 - - - +
365A GLY* 4.3 18.3 - - - +
366A LYS* 6.6 0.2 - - + -
136B PRO* 1.3 76.7 - - - +
138B SER* 1.3 63.8 + - - +
139B GLY* 3.4 5.5 + - - +
140B THR* 2.7 39.5 + - - -
141B LEU* 2.9 26.0 + - - +
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Residues in contact with SER 138 (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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366A LYS* 3.6 34.7 + - - +
137B ASN* 1.3 75.4 - - - +
139B GLY* 1.3 60.0 + - - +
141B LEU* 3.8 2.8 - - - +
142B ALA* 2.8 37.1 + - - +
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Residues in contact with GLY 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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344A ASN* 4.2 7.0 + - - -
347A LYS* 6.0 4.7 - - - -
363A CYS* 4.7 11.2 - - - -
364A LEU 6.0 0.7 - - - -
366A LYS* 5.4 2.8 - - - +
137B ASN* 3.4 5.0 + - - -
138B SER* 1.3 79.8 + - - +
140B THR* 1.3 61.1 - - - +
142B ALA* 3.9 5.8 - - - +
143B LEU* 3.0 24.3 + - - +
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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
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360A ARG* 5.3 3.8 - - + -
361A PRO* 3.0 34.6 - - + +
362A HIS* 3.6 3.7 + - - +
363A CYS* 3.0 26.9 + - - +
136B PRO* 3.8 18.4 - - + -
137B ASN* 2.7 41.1 + - - -
139B GLY* 1.3 69.8 - - - +
141B LEU* 1.3 69.8 + - - +
143B LEU* 2.9 24.0 + - - +
144B LEU* 3.4 8.2 + - + +
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Residues in contact with LEU 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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360A ARG* 5.5 8.5 - - - +
136B PRO* 5.1 7.0 - - + -
137B ASN 2.9 20.2 + - - +
138B SER* 3.9 2.7 - - - +
140B THR* 1.3 75.3 - - - +
142B ALA* 1.3 66.1 + - - +
143B LEU 2.9 1.0 + - - -
144B LEU* 3.0 17.8 + - - +
145B LEU* 3.1 14.7 + - - +
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Residues in contact with ALA 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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138B SER* 2.8 27.0 + - - +
139B GLY* 3.9 6.3 - - - +
141B LEU* 1.3 72.9 - - - +
143B LEU* 1.3 60.9 + - - +
145B LEU* 3.9 6.3 - - - +
146B ASP* 3.1 27.7 + - - +
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Residues in contact with LEU 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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342A TYR* 4.0 24.9 - - + -
344A ASN* 3.1 29.4 - - - +
346A THR* 5.8 0.4 - - - +
351A CYS* 4.6 2.5 - - + -
361A PRO* 4.6 19.1 - - + -
363A CYS* 3.8 16.4 - - - -
139B GLY 3.0 13.4 + - - +
140B THR* 2.9 16.1 + - - +
142B ALA* 1.3 77.6 - - - +
144B LEU* 1.3 52.6 + - + +
146B ASP* 3.1 1.5 + - - -
147B GLU* 2.6 75.9 + - + +
207B LEU* 4.5 6.3 - - + -
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Residues in contact with LEU 144 (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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360A ARG* 4.3 26.0 - - + +
361A PRO* 3.6 30.3 - - + -
140B THR* 3.4 6.8 + - + +
141B LEU* 3.0 9.4 + - - +
143B LEU* 1.3 78.2 - - - +
145B LEU* 1.3 60.3 + - - +
148B GLY* 2.8 36.6 + - - +
179B ARG* 5.9 1.1 - - - +
205B ARG* 4.0 50.0 + - + +
206B THR 4.4 0.4 - - - -
207B LEU* 3.6 30.1 - - + +
210B GLN* 5.3 0.4 - - - +
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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
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141B LEU 3.1 15.6 + - - +
142B ALA* 4.1 7.0 - - - +
144B LEU* 1.3 76.6 - - - +
146B ASP* 1.3 58.2 + - - +
148B GLY 4.6 4.1 - - - +
205B ARG* 5.2 13.4 - - - +
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Residues in contact with ASP 146 (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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346A THR* 4.6 8.1 + - - -
142B ALA 3.1 20.6 + - - +
143B LEU* 3.8 1.1 - - - +
145B LEU* 1.3 81.2 - - - +
147B GLU* 1.3 80.8 + - + +
148B GLY 3.5 2.6 - - - +
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Residues in contact with GLU 147 (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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342A TYR* 2.6 40.0 + - - +
343A PHE 4.5 4.7 - - - +
344A ASN* 4.5 3.5 - - - +
345A LYS* 4.6 10.9 + - - +
346A THR* 4.2 11.6 + - - -
143B LEU* 2.6 38.5 + - + +
146B ASP* 1.3 91.7 - - - +
148B GLY* 1.3 58.1 + - - +
206B THR 4.5 0.7 - - - +
207B LEU* 4.3 10.7 - - + +
208B ASP* 4.3 14.6 + - - +
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Residues in contact with GLY 148 (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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143B LEU 3.7 0.2 + - - -
144B LEU* 2.8 28.7 + - - +
145B LEU 4.6 3.6 - - - +
146B ASP 4.6 4.0 - - - +
147B GLU* 1.3 81.7 + - - +
149B SER* 1.3 65.2 + - - -
205B ARG* 5.0 3.4 + - - -
206B THR 3.1 16.6 - - - -
207B LEU* 4.2 5.2 - - - -
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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