Contacts of the helix formed by residues 134 - 150 (chain D) in PDB entry 3U8Z
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 PRO 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D TYR* 3.7 24.7 - - + +
133D CYS* 1.4 86.6 - - - +
135D PRO* 1.4 76.9 - - + +
136D GLU* 3.4 3.7 + - + +
137D ALA* 3.4 11.7 + - + +
138D SER* 2.9 20.5 + - - -
214D LEU* 3.5 22.4 - - + -
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Residues in contact with PRO 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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132D TYR* 4.6 5.4 - - - +
133D CYS 4.8 0.2 - - - +
134D PRO* 1.4 87.7 - - + +
136D GLU* 1.4 63.4 + - + +
138D SER* 3.3 9.0 - - - -
139D VAL* 3.2 27.5 + - + +
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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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134D PRO* 3.4 2.3 - - + +
135D PRO* 1.4 80.5 - - + +
137D ALA* 1.4 61.9 + - - +
139D VAL* 3.3 12.1 - - + +
140D LEU* 3.1 30.2 + - + +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D CYS* 3.6 19.5 - - - -
134D PRO* 3.4 20.0 + - + +
135D PRO 3.4 0.2 - - - -
136D GLU* 1.4 76.1 - - - +
138D SER* 1.3 54.2 + - - +
140D LEU* 3.6 7.7 - - - +
141D LEU* 2.8 39.6 + - + +
210D ILE* 4.1 19.5 - - + -
214D LEU* 4.4 6.5 - - + -
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Residues in contact with SER 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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126D ILE* 6.1 1.8 - - - -
133D CYS* 3.5 17.0 - - - -
134D PRO 2.9 14.6 + - - -
135D PRO* 3.3 15.3 - - - -
137D ALA* 1.3 76.2 - - - +
139D VAL* 1.4 60.0 + - - +
141D LEU* 3.9 3.1 - - - +
142D ALA* 3.1 28.2 + - - +
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Residues in contact with VAL 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 PRO* 3.2 14.7 + - + +
136D GLU* 3.3 16.2 - - + +
138D SER* 1.4 75.4 - - - +
140D LEU* 1.3 70.3 + - + +
142D ALA* 3.6 6.7 + - - +
143D SER* 3.2 24.4 + - - -
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Residues in contact with LEU 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* 3.1 21.7 + - + +
137D ALA* 3.6 8.1 - - - +
139D VAL* 1.3 77.3 - - + +
141D LEU* 1.4 64.0 + - - +
143D SER* 3.2 10.0 + - - -
144D TYR* 3.2 37.7 + - + +
210D ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 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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126D ILE* 4.0 30.1 - - + -
133D CYS* 3.7 28.7 - - - -
137D ALA 2.8 20.1 + - - +
138D SER* 3.9 4.0 - - - +
140D LEU* 1.4 72.1 - - - +
142D ALA* 1.3 56.9 + - - +
144D TYR* 3.2 4.4 + - - +
145D ALA 2.9 24.8 + - - -
207D TYR* 3.2 66.3 - - + +
210D ILE* 3.8 22.9 - - + +
211D ALA* 4.1 3.6 - - - +
214D LEU* 4.5 4.9 - - + -
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Residues in contact with ALA 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 SER 3.1 19.9 + - - +
139D VAL* 3.7 8.7 - - - +
140D LEU 3.3 0.2 - - - -
141D LEU* 1.3 73.9 - - - +
143D SER* 1.4 56.2 + - - +
145D ALA* 3.4 9.0 + - - +
146D VAL* 3.1 33.6 + - + +
207D TYR* 5.3 0.2 - - - -
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Residues in contact with SER 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 VAL 3.2 11.8 + - - -
140D LEU* 3.2 15.0 + - - -
142D ALA* 1.4 75.8 - - - +
144D TYR* 1.3 65.4 + - - +
146D VAL* 3.4 10.3 + - - +
147D GLN* 3.2 34.7 + - - +
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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 LEU* 3.2 33.7 + - + +
141D LEU* 3.2 6.7 + - - +
143D SER* 1.3 75.6 - - - +
145D ALA* 1.4 54.1 + - - +
147D GLN* 3.3 24.6 + - - +
148D ALA* 2.8 32.4 + - - +
203D ALA* 3.4 27.1 - - - +
206D GLU* 3.6 43.6 + - + -
207D TYR* 4.2 10.1 - - + -
210D ILE* 3.6 29.8 - - + -
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Residues in contact with ALA 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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119D PHE* 4.2 12.5 - - - -
123D LYS* 4.0 26.0 - - + -
141D LEU 2.9 13.2 + - - +
142D ALA* 3.5 12.8 - - - +
143D SER 3.4 0.2 - - - -
144D TYR* 1.4 73.6 - - - +
146D VAL* 1.4 64.3 + - + +
148D ALA* 3.3 2.6 + - - +
149D LYS* 3.0 24.8 + - - +
207D TYR* 4.0 6.4 - - + -
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Residues in contact with VAL 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 ALA 3.1 18.4 + - - +
143D SER* 3.6 10.5 - - - +
144D TYR 3.3 0.4 - - - -
145D ALA* 1.4 72.8 - - + +
147D GLN* 1.3 64.2 + - + +
149D LYS* 3.2 15.2 + - - +
150D TYR* 3.2 37.4 + - + +
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Residues in contact with GLN 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 SER* 3.2 21.3 + - - +
144D TYR* 3.3 38.7 + - - +
146D VAL* 1.3 75.4 - - + +
148D ALA* 1.4 63.2 + - - +
150D TYR* 3.2 22.6 - - - +
199D ALA 4.3 3.2 - - - +
200D ARG* 3.7 10.6 + - - +
203D ALA* 3.8 11.1 - - + +
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Residues in contact with ALA 148 (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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52B ARG* 4.8 9.0 + - - -
119D PHE* 3.7 26.5 - - + -
144D TYR 2.8 20.8 + - - +
145D ALA 3.3 5.8 + - - +
147D GLN* 1.4 72.7 - - - +
149D LYS* 1.3 58.6 + - - +
200D ARG* 3.4 41.8 - - - +
203D ALA* 3.5 6.9 - - + +
204D GLU* 3.9 9.9 - - + +
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Residues in contact with LYS 149 (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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38B GLU* 5.7 4.9 + - - -
41B TRP* 6.6 0.2 - - - -
52B ARG* 4.4 13.0 + - - +
145D ALA 3.0 13.0 + - - +
146D VAL* 3.2 12.7 + - - +
148D ALA* 1.3 77.2 - - - +
150D TYR* 1.3 96.3 + - + +
200D ARG* 3.8 14.0 + - - -
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Residues in contact with TYR 150 (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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146D VAL* 3.2 39.7 + - + +
147D GLN* 3.2 15.5 - - - +
148D ALA 3.5 0.8 - - - -
149D LYS* 1.3 119.3 + - + +
199D ALA* 6.0 0.7 - - - +
200D ARG* 3.4 27.7 - - - +
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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