Contacts of the helix formed by residues 137 - 147 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PRO* 1.3 75.0 - - - +
138A SER* 1.3 66.9 + - - +
139A GLY* 3.3 5.5 + - - -
140A THR* 2.8 44.6 + - - -
141A LEU* 2.8 27.7 + - - +
362B HIS* 3.3 17.4 + - - -
363B CYS 3.2 17.5 + - - +
364B LEU 4.9 2.1 - - - +
365B GLY* 4.3 18.4 - - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 1.3 77.5 - - - +
139A GLY* 1.3 66.0 + - - -
141A LEU* 3.1 9.6 + - - +
142A ALA* 3.1 24.0 + - - +
366B LYS* 3.5 29.2 + - - -
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.3 5.2 + - - -
138A SER* 1.3 80.0 + - - +
140A THR* 1.3 61.9 + - - +
142A ALA* 3.7 5.3 + - - +
143A LEU* 3.1 23.2 + - - +
344B ASN* 4.7 4.5 + - - -
347B LYS* 6.4 2.0 - - - -
363B CYS* 5.1 8.7 - - - -
364B LEU 5.9 1.8 - - - -
366B LYS* 4.3 13.8 - - - +
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 4.2 15.3 - - + -
137A ASN* 2.8 40.8 + - - -
139A GLY* 1.3 68.0 - - - -
141A LEU* 1.3 70.8 + - - +
143A LEU* 3.2 21.3 + - - +
144A LEU* 3.5 10.3 + - + +
360B ARG* 5.6 1.3 - - + -
361B PRO* 3.1 36.3 - - + +
362B HIS* 3.5 5.4 + - + +
363B CYS* 3.1 26.8 + - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.4 36.8 - - + +
137A ASN 2.8 35.6 + - - +
138A SER* 3.4 8.3 - - - +
140A THR* 1.3 75.5 - - - +
142A ALA* 1.3 64.8 + - - +
144A LEU* 3.0 17.1 + - - +
145A LEU* 3.3 9.5 + - - +
360B ARG* 5.1 6.5 - - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER* 3.1 13.9 + - - +
139A GLY* 3.9 6.3 - - - +
141A LEU* 1.3 79.0 - - - +
143A LEU* 1.3 54.4 + - - +
145A LEU* 2.7 29.9 + - - +
146A ASP* 3.0 27.2 + - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLY 3.1 13.4 + - - +
140A THR* 3.2 13.2 - - - +
141A LEU 3.1 0.2 + - - -
142A ALA* 1.3 74.9 - - - +
144A LEU* 1.3 59.4 + - + +
146A ASP* 3.2 5.5 + - + +
147A GLU* 2.9 60.9 + - + +
148A GLY 3.7 0.2 + - - -
207A LEU* 5.0 4.9 - - + -
342B TYR* 4.1 25.4 - - + -
344B ASN* 3.2 31.6 - - - +
346B THR* 5.9 1.6 - - - +
351B CYS* 5.0 0.9 - - + -
361B PRO* 4.4 20.2 - - + -
363B CYS* 3.8 15.9 - - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 4.4 10.1 - - + +
141A LEU* 3.0 10.6 + - - +
143A LEU* 1.3 79.1 - - + +
145A LEU* 1.3 58.9 + - - +
146A ASP 3.2 0.2 - - - -
148A GLY* 3.1 36.3 + - - +
179A ARG* 5.5 0.9 - - - +
205A ARG* 3.4 33.9 - - + +
207A LEU* 3.8 20.0 - - + +
210A GLN* 5.8 0.2 - - - +
360B ARG* 3.7 28.5 - - + -
361B PRO* 3.5 43.3 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU 3.3 6.5 + - - +
142A ALA* 2.7 22.6 + - - +
144A LEU* 1.3 74.5 - - - +
146A ASP* 1.3 65.0 + - - +
148A GLY 4.9 2.6 - - - +
205A ARG* 4.7 10.4 + - - +
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 3.0 28.6 + - - +
143A LEU* 4.0 4.1 - - - +
145A LEU* 1.3 86.8 - - - +
147A GLU* 1.3 68.2 + - + +
148A GLY 3.6 2.2 - - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 2.9 34.1 + - + +
146A ASP* 1.3 82.8 - - + +
148A GLY* 1.3 63.1 + - - +
149A SER* 3.9 4.4 + - - -
206A THR 4.1 5.4 - - - +
207A LEU* 4.2 10.8 - - + +
208A ASP* 5.0 11.0 + - - +
342B TYR* 2.5 35.7 + - - +
343B PHE 5.1 2.0 - - - +
344B ASN* 5.0 0.9 - - - +
345B LYS* 4.8 19.1 + - - +
346B THR* 5.1 5.0 + - - -
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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
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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