Contacts of the helix formed by residues 168 - 177 (chain D) in PDB entry 5XS0
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 ASP 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C GLU* 5.1 0.3 - - - +
69C HIS* 3.6 25.3 + - + +
70C ARG* 3.6 21.7 + - - -
186C VAL* 4.7 2.9 - - - +
46D ARG* 4.6 14.3 + - - +
165D CYS* 3.0 16.2 + - + +
167D LEU* 1.3 75.4 - - - +
169D LYS* 1.3 68.1 + - - +
170D ASP* 3.4 20.8 + - - +
171D TYR* 3.1 23.9 + - + +
172D LEU* 3.1 14.8 + - - +
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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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67C GLU* 4.4 21.7 + - - +
69C HIS* 5.3 0.2 + - - -
167D LEU 3.5 8.0 + - - +
168D ASP* 1.3 72.4 + - - +
170D ASP* 1.3 63.7 + - - +
172D LEU* 3.1 20.4 + - + +
173D ARG* 2.9 33.4 + - + +
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Residues in contact with ASP 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 3.9 12.9 + - - -
183C PRO* 3.6 12.4 - - - +
184C LEU* 3.4 31.8 + - - +
186C VAL* 3.8 13.4 + - + -
168D ASP* 3.2 15.3 + - - +
169D LYS* 1.3 76.2 - - - +
171D TYR* 1.3 61.1 + - - +
173D ARG* 3.0 26.1 + - - +
174D SER* 2.9 32.4 + - - -
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Residues in contact with TYR 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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186C VAL* 3.8 13.9 - - + +
188C LEU* 3.7 17.0 - - + -
46D ARG* 3.5 39.3 - - + +
47D LEU* 2.5 41.5 + - - +
52D ILE* 3.7 10.2 - - - +
165D CYS* 3.3 34.2 - - + +
166D ILE* 4.1 18.8 - - + -
168D ASP* 3.1 20.9 + - + +
170D ASP* 1.3 80.0 - - - +
172D LEU* 1.3 60.7 + - + +
174D SER* 3.4 2.9 + - - -
175D LEU* 2.9 50.6 + - + +
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Residues in contact with LEU 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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64D CYS* 4.1 32.1 - - + +
166D ILE* 4.1 21.8 - - + +
167D LEU 5.8 0.7 - - - -
168D ASP 3.1 15.6 + - - +
169D LYS* 3.1 23.3 + - + +
171D TYR* 1.3 83.8 - - + +
173D ARG* 1.3 65.5 + - + +
175D LEU* 3.0 11.4 + - + +
176D ASN* 2.9 34.0 + - - +
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Residues in contact with ARG 173 (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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183C PRO* 3.4 23.3 + - - +
184C LEU 3.0 20.8 + - - -
185C GLU* 4.5 12.3 - - - +
169D LYS* 2.9 16.7 + - + +
170D ASP* 3.0 34.8 + - - +
172D LEU* 1.3 75.8 - - + +
174D SER* 1.3 61.1 + - - +
175D LEU 3.2 0.9 + - - -
176D ASN* 3.3 16.8 + - - +
177D LYS* 3.4 45.1 + - - +
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Residues in contact with SER 174 (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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185C GLU* 3.8 9.7 - - - +
186C VAL* 2.6 53.1 + - - +
188C LEU* 3.3 18.5 - - - +
170D ASP 2.9 12.8 + - - -
171D TYR 3.8 4.3 - - - -
173D ARG* 1.3 76.0 - - - +
175D LEU* 1.3 60.1 + - - +
177D LYS* 4.1 9.6 + - - +
178D LEU* 3.5 16.5 + - - +
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Residues in contact with LEU 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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188C LEU* 3.6 17.9 - - + -
47D LEU 4.9 0.2 - - - +
48D GLY 4.8 1.6 - - - -
49D PRO* 3.9 26.9 - - + +
52D ILE* 3.7 29.4 - - + -
64D CYS* 5.6 2.5 - - - -
171D TYR* 2.9 41.6 + - + +
172D LEU* 3.0 18.1 + - + +
174D SER* 1.3 77.6 - - - +
176D ASN* 1.3 66.0 + - - +
178D LEU* 3.2 29.8 + - + +
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Residues in contact with ASN 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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62D LYS* 5.9 1.4 + - - -
172D LEU* 2.9 32.8 + - - +
173D ARG* 3.3 9.3 + - - +
175D LEU* 1.3 78.4 - - - +
177D LYS* 1.3 58.3 + - + +
178D LEU 3.1 13.4 + - - +
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Residues in contact with LYS 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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185C GLU* 3.1 28.1 + - - +
173D ARG* 3.4 39.5 + - - +
174D SER* 4.5 7.9 - - - +
175D LEU 3.3 0.8 - - - -
176D ASN* 1.3 76.8 - - + +
178D LEU* 1.3 61.5 + - - +
179D PRO* 4.0 2.6 - - - +
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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