Contacts of the helix formed by residues 160 - 168 (chain S) in PDB entry 5IY8
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 ALA 160 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157S ALA 5.1 0.4 - - - -
158S GLU 3.5 2.1 - - - -
159S GLU* 1.3 98.0 + - - +
161S GLU* 1.3 56.2 + - - +
162S GLU* 3.4 2.9 - - - +
163S GLU* 3.2 18.1 + - + +
164S TRP* 2.7 35.6 + - + +
167S ARG* 5.7 3.1 - - - +
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Residues in contact with GLU 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 5.3 10.1 - - + +
155S LEU* 3.5 18.7 - - + +
156S THR 2.7 28.7 - - - +
157S ALA* 3.3 21.1 + - + -
159S GLU* 3.4 26.7 + - - +
160S ALA* 1.3 76.5 - - - +
162S GLU* 1.3 57.4 + - - +
163S GLU 3.2 0.2 - - - -
164S TRP* 3.8 13.9 - - + +
165S GLU* 2.7 34.1 + - - +
176S ILE* 4.2 29.4 - - + +
180S ARG* 5.7 4.2 - - - +
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Residues in contact with GLU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASN* 5.7 0.7 - - - +
320B PHE* 3.9 22.2 - - + -
323B SER* 4.3 11.5 + - - -
324B ARG* 2.5 41.6 + - - +
157S ALA* 3.9 17.9 + - + +
158S GLU* 5.7 1.0 - - - +
160S ALA 3.4 0.8 - - - -
161S GLU* 1.3 77.7 - - - +
163S GLU* 1.3 59.4 + - - +
165S GLU* 3.5 14.0 - - - +
166S ARG* 3.4 18.0 + - - +
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Residues in contact with GLU 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160S ALA* 3.2 20.5 + - + +
161S GLU 3.2 0.2 - - - -
162S GLU* 1.3 75.6 - - - +
164S TRP* 1.3 60.9 + - - +
165S GLU 3.2 1.1 - - - -
166S ARG* 3.0 34.9 + - + +
167S ARG* 2.8 46.0 + - - +
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Residues in contact with TRP 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 4.2 14.6 - - + -
160S ALA* 2.7 21.1 + - + +
161S GLU* 3.4 19.5 + - + +
163S GLU* 1.3 69.7 + - - +
165S GLU* 1.3 60.9 + - + +
167S ARG* 3.0 40.3 + - + +
168S ASN* 2.7 70.4 + - + +
171S LEU* 5.8 1.3 - - + +
172S ASN* 3.4 41.7 - - + +
173S HIS* 5.0 1.1 - - - -
176S ILE* 4.7 37.9 - - + +
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Residues in contact with GLU 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLU* 5.8 1.9 - - - +
310B VAL* 3.8 34.5 - - + -
320B PHE* 5.4 8.3 - - + -
324B ARG* 4.3 13.5 + - - -
161S GLU 2.7 22.9 + - - +
162S GLU* 3.5 13.4 - - - +
164S TRP* 1.3 76.5 - - - +
166S ARG* 1.3 71.0 + - - +
168S ASN* 2.8 34.1 + - + +
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Residues in contact with ARG 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN* 4.8 7.1 + - - -
324B ARG* 5.0 12.2 - - - +
162S GLU 3.4 7.4 + - - +
163S GLU* 3.0 24.2 + - + +
165S GLU* 1.3 86.3 + - - +
167S ARG* 1.3 60.2 + - + +
168S ASN 4.5 2.1 - - - +
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Residues in contact with ARG 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN* 4.9 4.5 + - - +
160S ALA* 5.1 4.4 + - - +
163S GLU* 2.8 36.0 + - - +
164S TRP* 3.0 40.7 + - + +
166S ARG* 1.3 77.1 - - + +
168S ASN* 1.3 64.3 + - - +
169S LYS* 3.4 6.8 + - - +
171S LEU* 5.0 7.8 - - - +
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Residues in contact with ASN 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN* 3.8 14.9 + - - +
248B LYS* 4.9 5.2 + - - -
310B VAL* 4.6 9.5 - - - +
164S TRP* 2.7 51.7 + - + +
165S GLU* 2.8 26.6 + - + +
166S ARG 4.5 1.0 - - - +
167S ARG* 1.3 78.4 - - - +
169S LYS* 1.3 58.9 + - - +
170S VAL* 3.5 18.8 + - - +
171S LEU* 3.2 22.9 + - - +
172S ASN 5.1 0.2 + - - -
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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