Contacts of the helix formed by residues 165 - 175 (chain D) in PDB entry 5E6J
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 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D TYR* 4.5 0.9 - - - -
158D LYS* 5.0 2.0 - - - +
164D GLY* 1.3 72.3 - - - -
166D VAL* 1.3 73.4 + - - +
167D ARG* 3.0 30.5 + - - +
168D GLU* 3.8 26.5 + - + +
169D THR* 2.9 27.3 + - - -
274D TYR* 3.2 11.3 + - - -
302D THR* 5.4 0.3 + - - -
303D ASP* 5.0 0.9 - - - +
71E LEU 4.7 1.6 - - - +
72E ARG* 4.0 6.7 - - + -
73E LEU* 3.3 43.5 + - - +
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Residues in contact with VAL 166 (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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113D TYR* 3.5 31.4 - - + +
116D SER* 4.0 0.9 - - - -
117D VAL* 3.8 21.1 - - + +
120D ALA* 6.0 0.2 - - + -
164D GLY 4.1 0.4 + - - -
165D ASP* 1.3 74.7 + - - +
167D ARG* 1.3 59.0 + - - +
169D THR* 3.7 1.6 - - - -
170D MET* 2.8 38.6 + - + +
244D MET* 4.4 4.7 - - + -
263D ASN* 3.4 24.9 - - - +
274D TYR* 3.3 29.0 + - + +
303D ASP* 3.6 14.1 - - - +
305D PHE* 5.2 2.0 - - + -
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Residues in contact with ARG 167 (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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165D ASP* 3.0 19.1 + - - +
166D VAL* 1.3 80.0 - - - +
168D GLU* 1.3 62.2 + - - +
170D MET* 3.3 3.1 + - - +
171D THR* 2.6 43.7 + - - +
207D MET* 4.5 14.6 - - + +
208D TYR 5.3 1.4 - - - -
209D MET* 3.7 41.0 - - - +
244D MET* 4.1 12.3 - - + -
246D SER* 3.5 35.7 - - - +
303D ASP* 4.2 7.9 + - - +
42E ARG* 4.6 14.8 - - - +
44E ILE* 4.7 2.6 - - - +
49E GLN* 3.2 43.8 + - - +
70E VAL* 5.9 1.0 - - - +
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Residues in contact with GLU 168 (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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158D LYS* 5.7 2.6 + - - +
165D ASP* 3.4 23.7 + - + +
167D ARG* 1.3 87.6 - - - +
169D THR* 1.3 58.4 + - - +
171D THR* 3.1 9.9 + - - -
172D HIS* 2.8 47.2 + - + -
42E ARG* 2.5 48.3 + - - +
49E GLN* 6.0 1.3 - - - +
72E ARG* 3.1 24.4 + - - +
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Residues in contact with THR 169 (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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113D TYR* 3.8 16.2 - - + -
114D LEU* 4.6 3.8 - - + -
117D VAL* 4.0 21.5 - - + -
152D ILE* 3.2 34.8 - - + -
156D SER* 3.8 15.1 + - - +
158D LYS* 4.5 7.6 - - - +
165D ASP 2.9 16.6 + - - -
166D VAL* 3.7 3.8 - - - -
168D GLU* 1.3 77.8 - - - +
170D MET* 1.3 57.4 + - - +
172D HIS* 3.2 3.8 + - - +
173D LEU* 2.8 33.2 + - + +
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Residues in contact with MET 170 (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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117D VAL* 4.0 26.9 - - + +
120D ALA* 5.2 1.6 - - + -
121D LEU* 4.0 27.6 - - + -
124D LEU* 4.2 9.4 - - + -
166D VAL* 2.8 41.0 + - + +
167D ARG 3.6 4.5 - - - +
169D THR* 1.3 69.1 - - - +
171D THR* 1.3 59.7 + - - +
173D LEU* 3.8 4.7 - - - +
174D LEU* 2.8 60.5 + - + +
207D MET* 4.7 1.1 - - - -
242D PHE* 5.2 0.9 - - + -
244D MET* 4.1 19.1 - - + -
305D PHE* 4.2 23.6 - - + -
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Residues in contact with THR 171 (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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167D ARG* 2.6 28.6 + - - +
168D GLU* 3.2 11.0 + - - -
170D MET* 1.3 75.2 - - - +
172D HIS* 1.3 69.7 + - + +
174D LEU* 3.0 3.5 + - - +
175D GLN* 2.9 41.5 + - - +
203D VAL* 4.3 6.7 - - + +
207D MET* 3.3 31.2 - - + +
49E GLN* 5.4 5.1 - - + +
51E GLU* 4.2 18.8 - - - +
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Residues in contact with HIS 172 (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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155D TYR* 4.0 16.1 - - - +
156D SER* 3.5 42.2 - - - +
157D ASN* 5.9 1.8 - - + -
168D GLU* 2.8 35.8 + - + +
169D THR 3.6 4.5 - - - +
171D THR* 1.3 78.4 - - + +
173D LEU* 1.3 63.0 + - + +
175D GLN* 3.4 22.3 - - + +
176D HIS* 3.9 12.6 - - - -
51E GLU* 5.8 3.3 + - - -
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Residues in contact with LEU 173 (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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117D VAL* 3.9 8.3 - - + -
121D LEU* 3.5 32.5 - - + -
128D PHE* 3.8 19.2 - - + -
133D LEU* 5.0 8.7 - - + -
148D PHE* 4.4 5.2 - - + -
152D ILE* 3.8 52.0 - - + +
155D TYR* 4.7 8.1 - - + -
156D SER* 4.3 5.2 - - - +
169D THR* 2.8 23.1 + - + +
170D MET* 3.8 7.4 - - - +
172D HIS* 1.3 73.0 - - - +
174D LEU* 1.3 62.8 + - + +
175D GLN 3.1 1.6 - - - -
176D HIS* 2.9 28.9 + - - +
177D ALA 3.7 1.9 + - - -
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Residues in contact with LEU 174 (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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121D LEU* 5.2 7.0 - - + -
124D LEU* 6.0 0.2 - - + -
126D VAL* 4.3 12.3 - - + -
128D PHE* 5.6 2.0 - - + -
170D MET* 2.8 50.2 + - + +
173D LEU* 1.3 71.1 - - + +
175D GLN* 1.3 66.3 + - - +
177D ALA* 3.0 35.0 + - + +
179D LEU* 4.1 9.0 - - + +
203D VAL* 3.3 26.0 - - + +
206D VAL* 4.2 14.8 - - + -
207D MET* 4.3 18.4 - - + -
242D PHE* 4.1 28.9 - - + -
244D MET* 5.6 0.4 - - - -
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Residues in contact with GLN 175 (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 ASN* 5.3 1.0 + - - -
171D THR* 2.9 33.7 + - + +
172D HIS* 3.4 22.0 - - + +
173D LEU 3.1 0.2 - - - -
174D LEU* 1.3 77.9 - - - +
176D HIS* 1.3 63.5 + - + +
177D ALA 3.6 3.8 + - - +
203D VAL* 3.7 21.5 - - - +
204D GLU* 4.5 10.5 + - - -
51E GLU* 5.5 6.3 + - - +
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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