Contacts of the helix formed by residues 168 - 177 (chain D) in PDB entry 5L08
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 ASN 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLU* 3.2 27.7 - - + +
51B LYS* 4.2 9.9 - - + +
111D GLU 5.4 1.8 + - - -
116D GLU* 2.9 27.8 + - - +
164D CYS 2.9 17.6 + - - +
165D ALA 4.8 0.9 - - - -
167D ILE* 1.3 79.5 - - - +
169D LYS* 1.3 63.6 + - - +
170D SER* 2.6 27.4 + - - -
171D LEU* 2.7 34.6 + - - +
172D LEU* 3.7 6.8 + - - +
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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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50B GLU 2.7 5.8 + - - +
51B LYS* 3.3 33.0 - - + +
52B ARG* 3.4 23.5 + - + +
165D ALA* 4.2 30.3 + - - +
168D ASN* 1.3 72.6 - - - +
170D SER* 1.3 60.3 + - - +
171D LEU 3.2 2.2 - - - -
172D LEU* 3.2 28.2 + - + +
173D LYS 2.8 23.7 + - - -
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Residues in contact with SER 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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49B GLN 4.2 11.9 - - - -
50B GLU* 3.0 17.6 + - - +
52B ARG* 3.8 5.3 - - - +
111D GLU* 5.1 9.8 + - - +
168D ASN* 2.6 25.0 + - - -
169D LYS* 1.3 78.2 - - - +
171D LEU* 1.3 62.5 + - - +
173D LYS* 3.3 13.4 - - - +
174D ILE* 3.2 26.0 + - - +
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Residues in contact with LEU 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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108D ILE* 4.0 14.9 - - + +
111D GLU* 3.4 34.3 - - + -
112D VAL* 3.6 30.3 - - + +
116D GLU* 4.7 1.3 - - - +
120D PHE* 3.8 11.4 - - + -
164D CYS* 3.7 16.4 - - - -
167D ILE* 3.5 23.1 - - + -
168D ASN* 2.7 38.3 + - - +
170D SER* 1.3 70.0 + - - +
172D LEU* 1.3 67.3 + - - +
173D LYS 3.2 0.2 - - - -
174D ILE* 3.1 16.6 + - + +
175D ILE* 3.1 16.1 + - - +
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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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52B ARG* 6.0 2.2 - - - +
161D LYS* 3.6 50.5 - - + +
164D CYS* 4.0 10.6 - - + +
165D ALA* 5.9 2.7 - - + -
168D ASN 3.7 3.8 + - - +
169D LYS* 3.2 44.3 + - + +
171D LEU* 1.3 79.3 - - - +
173D LYS* 1.3 56.1 + - - +
175D ILE* 3.2 6.7 + - - +
176D ASN* 2.8 47.9 + - - +
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Residues in contact with LYS 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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52B ARG* 3.7 35.5 - - + +
55B GLU* 5.9 0.2 + - - -
56B GLU* 4.4 15.2 + - - -
169D LYS 2.8 14.4 + - - +
170D SER* 3.3 14.8 - - - +
172D LEU* 1.3 76.4 - - - +
174D ILE* 1.3 67.3 + - + +
176D ASN* 2.8 19.9 + - + +
177D ASP* 2.8 35.7 + - - +
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Residues in contact with ILE 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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104D MET* 3.2 41.0 - - - +
107D GLN* 3.8 28.0 - - + +
108D ILE* 3.7 24.7 - - + -
111D GLU* 4.1 22.4 - - + +
170D SER 3.2 15.0 + - - +
171D LEU* 3.1 11.5 + - - +
173D LYS* 1.3 80.0 - - + +
175D ILE* 1.3 62.1 + - - +
177D ASP* 3.3 18.6 + - - +
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Residues in contact with ILE 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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104D MET* 5.4 2.7 - - - -
108D ILE* 4.0 20.0 - - + -
157D LEU* 4.5 22.9 - - + +
160D LEU* 3.7 30.5 - - + -
161D LYS* 3.5 35.7 - - + +
164D CYS* 3.4 32.8 - - + -
171D LEU 3.1 8.0 + - - +
172D LEU* 3.3 8.3 - - - +
174D ILE* 1.3 77.7 - - - +
176D ASN* 1.3 56.5 + - - +
178D TYR* 3.0 27.4 + - - +
179D GLU* 4.0 4.2 + - - +
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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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52B ARG* 5.0 6.5 - - - +
161D LYS* 3.7 24.4 + - - +
172D LEU* 2.8 41.5 + - - +
173D LYS* 2.8 13.0 + - + +
175D ILE* 1.3 67.6 - - - +
177D ASP* 1.3 58.3 + - - +
178D TYR 3.0 5.8 - - - -
179D GLU* 3.0 36.9 + - + +
180D GLU 4.4 0.7 + - - -
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Residues in contact with ASP 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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104D MET* 3.6 19.3 - - + +
173D LYS* 2.8 36.3 + - - +
174D ILE* 3.4 26.0 - - - +
175D ILE 3.1 0.4 - - - -
176D ASN* 1.3 79.4 - - - +
178D TYR* 1.3 57.0 + - - +
179D GLU 3.2 1.3 - - - -
180D GLU* 3.5 25.7 - - - +
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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