Contacts of the helix formed by residues 164 - 172 (chain D) in PDB entry 3L3T
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 THR 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ALA* 3.7 23.1 - - + -
162D VAL 4.0 0.2 + - - -
163D LEU* 1.3 78.9 - - - +
165D GLN* 1.3 63.6 + - - +
166D ALA* 3.5 7.9 + - - +
167D GLU* 3.2 37.0 + - - +
168D CYS* 3.1 20.8 + - - +
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Residues in contact with GLN 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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236C ASP* 5.2 4.8 + - - +
164D THR* 1.3 75.8 - - - +
166D ALA* 1.3 58.9 + - - +
168D CYS* 3.3 7.2 + - + +
169D LYS* 2.9 59.1 + - + +
176D ILE* 5.9 3.4 - - + -
178D ASN* 5.6 1.4 - - - +
230D LYS* 6.4 0.4 - - - +
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Residues in contact with ALA 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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164D THR* 3.3 8.1 + - - +
165D GLN* 1.3 78.6 - - - +
167D GLU* 1.3 60.1 + - + +
168D CYS 3.1 1.3 - - - -
169D LYS* 4.2 4.8 - - - +
170D ALA* 3.0 33.1 + - - +
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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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163D LEU* 3.6 25.2 - - + +
164D THR* 3.2 38.2 + - - +
166D ALA* 1.3 77.9 - - + +
168D CYS* 1.3 58.7 + - - +
170D ALA* 4.2 4.2 - - - +
171D SER* 2.9 28.2 + - - -
185D LEU* 3.6 33.0 - - + +
225D PRO* 5.2 0.5 - - - +
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Residues in contact with CYS 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 THR 3.1 14.1 + - - +
165D GLN* 3.5 11.7 - - + +
166D ALA 3.1 0.6 - - - -
167D GLU* 1.3 76.3 - - - +
169D LYS* 1.3 65.4 + - - +
171D SER* 3.1 13.1 + - - -
172D TYR* 3.2 11.1 + - - -
176D ILE* 3.8 26.4 - - + +
181D PHE* 3.9 6.7 - - - -
182D CYS* 2.0 66.0 - - + +
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Residues in contact with LYS 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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236A ASP* 5.6 5.5 + - - +
240A ASP* 3.6 35.4 + - - +
236C ASP* 3.7 24.5 + - - +
165D GLN* 2.9 51.5 + - + +
166D ALA* 4.2 4.5 - - - +
168D CYS* 1.3 75.8 - - - +
170D ALA* 1.3 61.5 + - - +
172D TYR 4.7 0.2 - - - -
173D PRO* 3.2 29.1 - - - +
176D ILE* 4.0 39.9 + - + -
178D ASN* 6.1 1.6 - - - -
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Residues in contact with ALA 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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240A ASP 4.3 4.0 - - - +
243A ALA* 4.7 6.1 - - + +
244A ALA* 3.5 43.4 - - + +
166D ALA 3.0 19.7 + - - +
167D GLU* 4.3 4.9 - - - +
169D LYS* 1.3 76.1 - - - +
171D SER* 1.3 62.9 + - - +
173D PRO* 3.6 6.9 - - - +
224D ARG* 5.6 0.2 + - - -
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Residues in contact with SER 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 GLU 2.9 20.3 + - - -
168D CYS 3.1 7.2 + - - -
170D ALA* 1.3 81.2 - - - +
172D TYR* 1.3 67.2 + - - +
173D PRO* 3.5 3.1 - - - +
185D LEU* 3.6 18.0 - - - +
223D ASN* 3.4 24.8 + - - +
224D ARG* 3.2 28.9 + - - +
225D PRO* 3.8 13.5 - - - -
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Residues in contact with TYR 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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240A ASP* 4.5 0.5 - - - +
168D CYS 3.2 11.0 + - - -
169D LYS 3.3 5.2 - - - +
171D SER* 1.3 86.5 - - - +
173D PRO* 1.3 67.4 - - - +
174D GLY 3.2 0.7 + - - -
175D LYS* 3.0 33.0 + - + +
176D ILE* 3.9 14.3 + - + +
182D CYS* 4.4 2.0 - - - -
215D TRP* 3.5 28.0 - + + -
216D GLY* 3.5 2.1 - - - -
217D HIS* 3.1 37.9 + - + -
224D ARG* 3.2 29.0 + - - +
225D PRO* 2.8 42.5 + - + -
227D VAL* 3.6 20.6 - - + -
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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