Contacts of the helix formed by residues 159 - 170 (chain D) in PDB entry 3A68
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 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LYS 3.3 12.2 - - - +
41D TYR* 3.4 14.6 - - - -
42D VAL* 4.8 1.0 + - + +
45D SER* 4.3 14.0 + - - +
105D ARG* 2.9 43.3 + - - -
154D ALA* 2.8 15.3 + - - +
155D THR* 6.1 0.2 - - - -
157D ASN* 3.0 5.0 + - + +
158D GLY* 1.3 73.1 - - - +
160D VAL* 1.3 64.2 + - - +
161D GLN* 3.4 2.6 + - - +
162D LEU* 3.0 20.0 + - + +
163D ALA* 3.1 23.2 + - - +
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Residues in contact with VAL 160 (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 GLY 3.2 12.2 + - - +
159D ASP* 1.3 73.6 + - - +
161D GLN* 1.3 58.8 + - - +
163D ALA* 3.4 5.4 + - - +
164D ASP* 3.0 24.9 + - - +
148I LEU* 4.1 21.2 - - + +
151I HIS* 3.5 44.6 - - + +
152I SER* 6.0 1.3 - - - +
167I GLU* 4.0 8.8 - - + +
171I LEU* 3.5 20.9 - - + -
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Residues in contact with GLN 161 (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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101D TYR* 2.4 35.9 + - - -
105D ARG* 3.8 9.7 + - - +
159D ASP* 3.4 2.2 + - - +
160D VAL* 1.3 77.1 - - - +
162D LEU* 1.3 59.9 + - - +
164D ASP* 3.7 9.5 + - + +
165D PHE* 2.8 40.2 + - - +
148I LEU* 5.2 4.4 - - + +
171I LEU* 3.7 38.8 - - + +
172I GLY* 3.7 16.5 - - - +
175I VAL* 3.7 23.6 - - + +
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Residues in contact with LEU 162 (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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41D TYR* 4.5 3.6 - - + -
45D SER* 3.9 29.4 - - - +
49D VAL* 4.0 21.5 - - + -
101D TYR* 3.3 34.9 + - + +
105D ARG* 4.0 1.3 - - - +
150D LEU* 4.5 11.0 - - + -
153D VAL* 5.9 0.2 - - + -
154D ALA* 3.6 22.9 - - + +
159D ASP* 3.0 24.4 + - + +
161D GLN* 1.3 73.1 - - - +
163D ALA* 1.3 66.3 + - - +
165D PHE* 3.2 4.3 + - + +
166D VAL* 3.0 35.9 + - + +
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Residues in contact with ALA 163 (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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151D HIS* 3.5 24.0 - - - +
154D ALA* 3.7 16.1 - - + +
155D THR* 4.5 9.0 - - - +
159D ASP 3.1 15.5 + - - +
160D VAL* 3.7 5.4 - - - +
162D LEU* 1.3 80.1 - - - +
164D ASP* 1.3 59.2 + - - +
166D VAL* 3.4 1.6 + - - -
167D GLU* 3.0 35.8 + - - +
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Residues in contact with ASP 164 (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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160D VAL 3.0 17.4 + - - +
161D GLN* 3.7 13.0 + - + +
162D LEU 3.2 0.2 - - - -
163D ALA* 1.3 75.0 - - - +
165D PHE* 1.3 59.6 + - - +
167D GLU* 3.4 7.2 + - - -
168D THR* 2.8 47.8 + - - -
331D CA 2.5 27.4 - - - -
167I GLU* 2.9 41.5 - - + +
168I THR* 4.6 4.6 + - - -
171I LEU* 5.7 0.6 - - + +
172I GLY* 5.6 1.6 + - - -
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D LYS* 4.1 18.2 - - + -
98D LEU* 3.9 13.9 - - + -
101D TYR* 3.6 61.5 - + + -
104D LYS* 6.1 3.1 - - - -
161D GLN* 2.8 25.4 + - - +
162D LEU* 3.2 5.8 + - + +
164D ASP* 1.3 77.0 + - - +
166D VAL* 1.3 66.9 + - + +
168D THR* 4.8 2.9 - - - -
169D GLU* 2.9 61.3 + - + +
170D TYR* 3.6 27.4 - + - -
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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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147D LEU* 3.8 27.6 - - + +
150D LEU* 3.6 32.1 - - + -
151D HIS* 4.3 13.0 - - + +
162D LEU* 3.0 25.9 + - + +
163D ALA* 3.8 5.4 - - - +
165D PHE* 1.3 83.4 - - + +
167D GLU* 1.3 62.3 + - - +
170D TYR* 3.0 33.3 + - + +
171D LEU* 3.1 23.9 + - + -
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Residues in contact with GLU 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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151D HIS* 3.0 29.8 + - + +
163D ALA* 3.0 21.4 + - - +
164D ASP* 3.4 12.7 - - - +
166D VAL* 1.3 77.9 - - - +
168D THR* 1.3 63.8 + - - +
171D LEU* 3.5 31.2 + - + +
172D GLY* 3.9 5.5 + - - -
331D CA 2.5 26.7 - - - -
167I GLU* 3.7 3.5 - - - +
332I CA 4.3 0.9 - - - -
160W VAL* 4.0 7.4 - - + +
164W ASP* 3.4 36.7 - - + +
167W GLU* 5.2 2.2 - - - +
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Residues in contact with THR 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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164D ASP* 2.8 34.9 + - - -
165D PHE* 4.2 2.2 - - - -
167D GLU* 1.3 78.0 - - - +
169D GLU* 1.3 77.4 + - - +
173D GLU* 3.6 2.1 - - - +
214D CA 2.6 26.7 - - - -
164W ASP* 4.9 4.9 + - - -
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Residues in contact with GLU 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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94D HIS* 6.2 0.2 - - - -
97D LYS* 2.7 41.8 + - - +
165D PHE* 2.9 41.5 + - + +
168D THR* 1.3 97.1 - - - +
170D TYR* 1.3 81.2 + - + +
173D GLU* 3.3 19.4 - - - +
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Residues in contact with TYR 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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56D GLU* 4.4 4.9 - - - -
94D HIS* 2.8 56.9 + + + -
97D LYS* 3.3 23.1 - - - +
98D LEU* 3.3 23.1 + - + +
147D LEU* 3.8 33.6 - - + +
150D LEU* 6.4 0.2 - - + -
165D PHE* 3.6 29.4 - + - -
166D VAL* 3.0 22.2 + - + +
168D THR 3.5 0.6 - - - -
169D GLU* 1.3 92.6 - - + +
171D LEU* 1.3 58.3 + - - +
172D GLY 3.5 2.0 - - - -
173D GLU* 3.4 6.3 + - - +
174D GLN* 2.8 32.6 + - - +
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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