Contacts of the helix formed by residues 158 - 164 (chain D) in PDB entry 4IL6
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 LEU 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602B CLA 3.8 26.7 - - + -
111D TRP* 5.5 0.2 - - + -
115D ALA* 4.7 15.5 - - + +
116D LEU* 4.5 17.0 - - + -
119D ALA* 4.4 21.3 - - + -
153D PHE* 4.6 5.8 - - + -
154D VAL* 3.1 27.5 + - + +
156D VAL 3.4 0.2 - - - -
157D PHE* 1.3 89.6 - - + +
159D ILE* 1.3 66.7 + - - +
160D TYR 3.4 1.1 - - - -
161D PRO* 3.3 3.8 - - - +
162D LEU* 3.1 32.5 + - + +
167D TRP* 4.2 18.6 - - + -
102H DGD 4.4 16.8 - - + -
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Residues in contact with ILE 159 (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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250B PHE* 4.0 22.2 - - + -
456B ALA* 5.0 2.5 - - + +
460B LEU* 4.3 9.0 - - + -
602B CLA 4.2 17.7 - - + -
154D VAL* 2.8 31.9 + - + +
155D SER* 3.6 16.4 - - - +
158D LEU* 1.3 71.5 - - - +
160D TYR* 1.3 67.3 + - - +
162D LEU* 3.1 8.1 + - - +
163D GLY* 3.0 16.8 + - - -
287D VAL* 4.1 27.4 - - + -
290D ALA* 3.6 8.8 - - + +
102H DGD 3.7 33.5 - - + +
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Residues in contact with TYR 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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362B PHE* 3.5 17.0 - - - -
155D SER 2.7 20.7 + - - +
156D VAL* 3.5 7.2 - - - +
159D ILE* 1.3 75.2 - - - +
161D PRO* 1.4 74.6 - - + +
163D GLY* 3.2 8.7 + - - -
164D GLN* 3.2 28.7 + - + +
169D PHE* 3.3 28.7 - - + -
181D PHE* 4.1 6.7 - + - -
184D PHE* 3.7 4.1 - + - -
185D PHE* 3.4 33.0 - + - -
189D HIS* 2.7 28.0 + - - -
286D VAL* 3.8 12.6 - - + -
289D LEU* 3.3 21.8 - - + -
290D ALA* 3.6 23.5 - - - +
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Residues in contact with PRO 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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87D HIS* 2.7 26.2 + - - -
156D VAL 3.3 13.7 - - - +
157D PHE 3.3 17.9 - - - +
158D LEU 3.3 16.6 - - - +
160D TYR* 1.4 101.3 - - + +
162D LEU* 1.3 51.7 + - - +
164D GLN* 3.1 17.1 + - + +
166D SER 3.5 16.8 - - - +
167D TRP* 3.6 17.5 - - + -
170D ALA* 3.6 25.1 - - + +
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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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257B TRP* 4.1 0.5 - - - -
258B TYR* 2.6 36.8 + - - +
273B TYR* 3.0 14.9 + - - -
602B CLA 4.0 20.9 - - + -
87D HIS* 3.5 19.7 + - + -
158D LEU* 3.1 31.4 + - + +
159D ILE 3.1 4.7 + - - +
161D PRO* 1.3 76.6 - - - +
163D GLY* 1.3 57.5 + - - +
167D TRP* 3.8 16.8 - - + -
102H DGD 3.5 64.4 - - + +
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Residues in contact with GLY 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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257B TRP* 2.8 29.8 + - - -
272B ARG* 3.4 9.5 + - - -
273B TYR* 3.2 3.5 + - - -
159D ILE 3.0 10.7 + - - -
160D TYR 3.7 1.1 - - - -
162D LEU* 1.3 73.5 - - - +
164D GLN* 1.3 62.6 + - - +
290D ALA 3.0 22.1 - - - +
102H DGD 3.7 15.2 - - - +
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Residues in contact with GLN 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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272B ARG* 3.2 22.8 + - - +
273B TYR* 2.8 22.1 + - - -
362B PHE* 3.1 32.8 - - + -
87D HIS* 3.0 12.0 + - - -
160D TYR* 3.4 35.1 - - + +
161D PRO* 3.1 12.4 + - + +
163D GLY* 1.3 78.3 - - - +
165D SER* 1.3 59.7 + - - +
166D SER 3.3 3.8 - - - +
169D PHE* 4.5 11.4 - - + -
189D HIS* 3.9 0.2 - - - -
289D LEU 3.0 21.4 + - - -
290D ALA 3.5 6.5 + - - -
292D ASN* 2.9 25.1 + - - +
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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