Contacts of the helix formed by residues 160 - 167 (chain D) in PDB entry 3G33
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 PHE 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.3 19.7 - - + -
31D LEU* 4.0 27.4 - - + -
32D LEU* 3.9 18.4 - - + -
35D GLU* 3.8 17.3 - - + -
155D VAL* 3.8 13.0 - - + -
156D ILE 4.0 4.9 - - - -
157D ALA 2.9 15.5 + - - +
159D ASP* 1.3 83.8 - - - +
161D LEU* 1.3 69.2 + - - +
162D ALA 3.6 0.9 - - - -
163D PHE* 3.3 6.5 + + - +
164D ILE* 3.1 31.2 + - + +
200D PRO* 3.8 12.6 - - + -
201D SER* 3.5 43.3 - - - +
204D ALA* 3.5 12.8 - - + -
233D THR* 4.9 2.9 - - + -
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Residues in contact with LEU 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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157D ALA 4.1 0.4 + - - -
158D HIS* 3.2 36.7 + - + +
160D PHE* 1.3 80.7 - - - +
162D ALA* 1.3 67.9 + - - +
164D ILE* 3.3 5.7 - - + +
165D LEU* 2.9 31.3 + - + +
179D LYS* 4.2 22.9 - - + +
182D ALA* 4.6 7.0 - - + -
183D GLN* 4.0 13.2 - - + +
186D LEU* 3.8 33.9 - - + -
204D ALA* 5.1 6.3 - - + +
207D SER* 5.7 0.2 - - - +
208D ILE* 3.7 28.5 - - + -
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Residues in contact with ALA 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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158D HIS 4.9 0.2 + - - -
159D ASP 5.3 0.6 + - - -
160D PHE 3.6 0.4 - - - -
161D LEU* 1.3 78.8 - - - +
163D PHE* 1.3 70.0 + - + +
165D LEU* 3.4 8.9 + - - +
166D HIS* 2.8 46.2 + - + +
179D LYS* 6.1 2.9 - - - +
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Residues in contact with PHE 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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24D ASP* 4.0 36.8 - - + -
27D VAL* 3.5 37.5 - - + -
28D LEU* 4.2 26.8 - - + +
31D LEU* 3.8 12.8 - - + -
159D ASP 3.5 26.5 - - - -
160D PHE* 3.8 5.8 - - - +
161D LEU 3.0 1.2 + - - -
162D ALA* 1.3 85.6 - - + +
164D ILE* 1.3 61.8 + - - +
166D HIS* 3.4 9.0 + - - +
167D ARG* 3.4 25.3 + - - +
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Residues in contact with ILE 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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28D LEU* 4.9 2.0 - - + -
160D PHE* 3.1 31.1 + - + +
161D LEU* 3.0 9.8 + - - +
163D PHE* 1.3 76.0 - - + +
165D LEU* 1.3 59.8 + - - +
167D ARG 3.8 3.0 + - - -
168D LEU* 2.9 29.2 - - - +
204D ALA* 4.1 6.5 - - + +
205D THR* 4.0 18.8 - - - +
208D ILE* 3.3 43.1 - - + -
229D LEU* 4.9 3.8 - - + +
232D ILE* 3.9 34.1 - - + +
233D THR* 4.0 17.5 - - + -
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Residues in contact with LEU 165 (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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161D LEU* 2.9 28.0 + - + +
162D ALA* 3.7 7.4 - - - +
164D ILE* 1.3 75.0 - - - +
166D HIS* 1.3 65.7 + - - +
167D ARG 3.1 1.6 - - - -
168D LEU* 3.1 37.9 + - + +
170D LEU* 4.9 4.8 - - + +
175D GLN* 3.8 39.5 + - + +
178D VAL* 4.3 19.3 - - + -
179D LYS* 4.2 33.9 - - + -
208D ILE* 3.5 24.9 - - + -
212D VAL* 5.3 0.2 - - + -
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Residues in contact with HIS 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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24D ASP* 4.7 17.1 + - - +
162D ALA* 2.8 39.2 + - + +
163D PHE* 3.7 8.1 + - - +
165D LEU* 1.3 76.9 - - - +
167D ARG* 1.3 58.7 + - + +
168D LEU 3.1 10.3 + - - +
170D LEU 5.6 1.2 - - - +
172D ARG* 3.1 39.8 + - + -
175D GLN* 4.5 14.0 + - - +
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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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24D ASP* 6.1 2.2 - - - +
25D GLN* 3.3 40.8 - - - +
28D LEU* 3.8 23.4 - - + +
163D PHE 3.4 14.0 + - - +
164D ILE 3.8 0.4 + - - +
165D LEU 3.1 1.4 - - - -
166D HIS* 1.3 77.9 - - + +
168D LEU* 1.3 67.7 + - - +
228D LEU* 5.1 8.1 - - - +
231D GLY 4.7 2.6 + - - -
232D ILE* 3.5 63.1 + - + +
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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