Contacts of the helix formed by residues 158 - 165 (chain D) in PDB entry 5TT2
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 LYS 158 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASP* 3.2 34.8 + - - +
156D CYS 3.0 3.2 - - - -
157D SER* 1.3 83.6 + - - +
159D ILE* 1.3 65.2 + - - +
160D LYS* 3.2 14.8 - - + +
161D LEU* 3.0 32.9 + - + +
162D LEU 3.5 3.3 + - - -
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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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156D CYS 3.5 19.1 - - - +
157D SER 4.3 8.3 - - - +
158D LYS* 1.3 71.8 - - - +
160D LYS* 1.3 62.8 - - - +
162D LEU* 3.3 7.6 + - + +
163D GLU* 3.2 20.7 + - - +
187D ASP* 4.0 29.8 - - + +
190D GLY* 4.2 11.2 - - - +
191D CYS* 4.1 14.1 - - - +
194D ILE* 3.9 31.0 - - + -
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Residues in contact with LYS 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 LYS* 4.4 14.1 - - + +
159D ILE* 1.3 77.4 - - - +
161D LEU* 1.3 78.8 + - + +
163D GLU* 3.1 13.1 + - - +
164D ALA* 2.8 31.1 + - - +
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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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154D VAL* 3.7 14.9 - - + +
155D ASP* 3.9 19.7 - - + +
158D LYS* 3.0 34.7 + - + +
160D LYS* 1.3 89.1 - - + +
162D LEU* 1.3 61.7 + - - +
164D ALA* 3.5 7.9 + - + +
165D ALA* 3.1 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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127D ILE* 4.2 20.0 - - + -
154D VAL* 3.8 7.0 - - - +
156D CYS* 4.1 26.0 - - + -
158D LYS 3.5 4.4 + - - +
159D ILE* 3.3 12.7 + - + +
160D LYS 3.2 0.2 - - - -
161D LEU* 1.3 78.9 - - - +
163D GLU* 1.3 62.7 + - - +
165D ALA* 3.0 14.2 + - - +
166D ILE* 3.2 22.9 + - + +
173D VAL* 4.3 18.4 - - + -
191D CYS* 3.7 40.8 - - + +
194D ILE* 3.9 20.9 - - + -
195D VAL* 4.4 5.6 - - + -
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Residues in contact with GLU 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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159D ILE 3.2 8.1 + - - +
160D LYS* 3.1 14.5 + - - +
162D LEU* 1.3 79.8 - - - +
164D ALA* 1.3 61.6 + - - +
165D ALA 3.3 0.5 + - - -
166D ILE* 3.5 18.4 + - + +
194D ILE* 4.0 33.2 - - + +
197D LYS* 4.8 13.2 - - - -
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Residues in contact with ALA 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 LYS 2.8 17.0 + - - +
161D LEU* 3.8 11.4 - - + +
163D GLU* 1.3 76.9 - - - +
165D ALA* 1.3 60.2 + - - +
166D ILE 3.4 4.2 + - - +
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Residues in contact with ALA 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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125D GLN* 4.4 3.6 + - - +
127D ILE* 3.4 17.5 - - + +
152D SER* 6.2 2.0 - - - -
154D VAL* 3.7 25.4 - - + -
161D LEU 3.1 15.5 + - - +
162D LEU* 3.0 7.6 + - - +
164D ALA* 1.3 77.5 - - - +
166D ILE* 1.3 61.4 + - - +
167D THR* 3.6 12.2 + - - +
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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