Contacts of the helix formed by residues 174 - 179 (chain D) in PDB entry 3LSU
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 TYR 174 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.8 9.9 - - - -
169D ALA* 3.8 15.8 + - - -
170D TRP 3.5 20.2 - - - -
171D GLU* 3.5 23.6 + - + +
172D HIS 3.2 1.2 + - - -
173D ALA* 1.3 80.2 - - - +
175D TYR* 1.3 70.9 + + - +
176D LEU 3.4 2.7 - - - -
177D GLN* 3.1 3.5 + - - -
178D TYR* 2.8 39.8 + - + +
179D GLN 3.3 25.1 - - - -
180D ASN* 5.1 0.7 - - - -
182D MLY 3.5 37.7 - - + +
185D TYR* 3.3 49.8 - + + -
186D PHE* 4.8 2.5 - + - -
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Residues in contact with TYR 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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25C LEU* 4.0 15.6 - - + +
30C HIS* 2.7 38.7 + + - -
172C HIS* 3.6 29.6 + - + +
175C TYR* 4.7 20.4 - - + -
176C LEU* 3.8 32.4 - - + +
171D GLU* 2.9 26.9 + - + +
172D HIS 4.5 1.8 + - - -
174D TYR* 1.3 88.3 - + - +
176D LEU* 1.3 60.3 + - - +
179D GLN* 2.9 68.6 + - + +
180D ASN* 4.0 2.9 + - - -
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Residues in contact with LEU 176 (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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175C TYR* 3.9 31.8 - - + +
176C LEU* 3.9 27.2 - - + +
179C GLN* 4.5 7.4 - - + +
19D SER* 5.5 0.7 - - - +
21D GLN* 4.9 11.7 - - + +
22D ILE* 4.0 24.3 - - + +
25D LEU* 3.6 31.0 - - + -
172D HIS 5.7 0.4 + - - +
174D TYR 3.4 1.0 - - - -
175D TYR* 1.3 76.7 - - - +
177D GLN* 1.3 57.0 + - - +
179D GLN* 3.0 12.0 + - - -
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Residues in contact with GLN 177 (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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16D PRO 2.9 28.1 + - - -
17D TYR 3.5 0.4 + - - -
18D ILE* 3.5 5.0 - - - -
19D SER* 2.9 37.6 + - - +
22D ILE* 3.7 15.8 - - + +
174D TYR 3.1 1.4 + - - -
175D TYR 3.1 0.4 - - - -
176D LEU* 1.3 80.0 - - - +
178D TYR* 1.3 92.4 + - + +
179D GLN* 3.6 8.9 + - - -
181D MLY 3.8 13.7 - - - -
209D GOL 4.9 2.5 + - - -
210D GOL 4.9 2.4 + - - -
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Residues in contact with TYR 178 (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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17D TYR 2.6 25.5 + - - -
18D ILE* 5.2 0.7 - - - -
22D ILE* 5.6 0.4 - - + -
174D TYR* 2.8 33.5 + - + +
177D GLN* 1.3 106.6 + - + +
179D GLN* 1.3 69.6 + - - +
181D MLY 2.9 39.5 + - - +
184D ASP* 3.7 8.5 - - + -
185D TYR* 3.6 46.2 - + + -
188D ALA* 3.3 17.6 - - + +
209D GOL 3.4 34.1 - - - -
210D GOL 3.8 8.0 + - - -
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Residues in contact with GLN 179 (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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21C GLN* 5.4 5.7 - - - +
25C LEU* 3.8 24.9 - - + -
176C LEU* 4.4 10.8 - - + +
174D TYR* 3.3 14.6 - - - -
175D TYR* 2.9 59.4 + - + +
176D LEU* 3.0 28.5 + - - +
177D GLN 3.6 6.3 + - - +
178D TYR* 1.3 76.0 - - - +
180D ASN* 1.3 72.1 + - - +
181D MLY 3.1 26.9 + - - -
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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