Contacts of the helix formed by residues 158 - 169 (chain T) in PDB entry 5IYB
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 158 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B ASP* 2.8 14.2 - - - +
429B PHE 3.9 7.9 + - - +
430B ASN* 3.8 24.5 - - - +
433B LEU* 6.0 2.7 - - + -
181M CYS 5.9 1.0 + - - -
185M ARG* 6.4 2.2 - - - -
155T PRO* 4.7 4.5 - - - +
157T ALA* 1.3 74.2 - - - +
159T HIS* 1.3 86.5 + - - +
160T GLN* 3.2 8.5 - - - +
161T TYR* 2.7 33.8 + - + +
162T ASN* 2.8 34.0 + - - +
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Residues in contact with HIS 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 5.8 5.6 - - - -
143B GLN* 5.8 5.3 + - - -
429B PHE 4.4 7.0 - - - -
430B ASN* 5.2 6.0 + - - -
155T PRO* 5.2 5.4 - - + +
157T ALA 3.3 4.0 + - - -
158T ASN* 1.3 87.1 + - - +
160T GLN* 1.3 75.5 + - + +
162T ASN* 2.9 17.7 + - - +
163T ILE* 2.7 42.7 + - + +
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Residues in contact with GLN 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B PHE* 5.9 0.2 - - + -
427B LYS* 4.0 16.6 - - - +
428B ASP* 3.6 7.2 - - - +
429B PHE* 3.4 33.9 - - + +
158T ASN* 3.2 13.2 + - - +
159T HIS* 1.3 88.6 + - + +
161T TYR* 1.3 52.6 + - - +
163T ILE* 3.0 49.0 + - - +
164T GLU* 2.7 32.6 + - - +
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Residues in contact with TYR 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ARG* 5.1 11.4 - - - -
428B ASP* 3.1 36.7 + - - +
185M ARG* 4.8 14.8 - - - -
186M ILE* 6.2 0.2 - - - -
187M SER* 4.2 21.3 + - - -
190M GLU* 3.7 19.1 + - - -
157T ALA* 4.7 11.0 - - + -
158T ASN* 2.7 29.3 + - + +
160T GLN* 1.3 72.1 - - - +
162T ASN* 1.3 63.3 + - - +
164T GLU* 3.0 13.9 + - + +
165T TYR* 2.8 39.3 + + + -
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Residues in contact with ASN 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157T ALA* 5.3 6.1 - - + +
158T ASN 2.8 15.9 + - - +
159T HIS* 3.0 17.7 + - - +
161T TYR* 1.3 77.2 - - + +
163T ILE* 1.3 52.1 + - - +
165T TYR* 3.0 15.1 + - - +
166T GLU* 2.7 37.2 + - - +
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Residues in contact with ILE 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B LYS* 5.7 5.4 - - + -
159T HIS* 2.7 21.7 + - + +
160T GLN* 3.0 53.6 + - - +
162T ASN* 1.3 73.2 - - - +
164T GLU* 1.3 63.9 + - - +
166T GLU* 3.1 10.9 + - + +
167T ARG* 2.9 26.9 + - + +
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Residues in contact with GLU 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ARG* 5.5 11.2 - - - +
426B GLY 4.0 6.6 - - - +
427B LYS* 3.3 37.5 + - - +
428B ASP* 4.8 4.3 - - + +
160T GLN 2.7 11.2 + - - +
161T TYR* 3.1 20.4 - - + +
163T ILE* 1.3 72.8 - - - +
165T TYR* 1.3 56.8 + - - +
167T ARG* 3.5 34.0 + - - +
168T LYS* 3.0 42.4 + - + +
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Residues in contact with TYR 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M LYS* 4.5 17.2 + - - -
161T TYR* 2.8 27.2 + + + +
162T ASN* 3.0 18.4 + - - +
164T GLU* 1.3 77.0 - - - +
166T GLU* 1.3 64.4 + - - +
168T LYS* 3.7 13.8 - - + +
169T LYS* 3.0 70.5 + - + +
76Y C 4.2 20.1 + - - -
77Y T 5.4 0.5 + - - -
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Residues in contact with GLU 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T ASN* 2.7 20.4 + - - +
163T ILE* 3.1 15.2 + - + +
165T TYR* 1.3 75.7 - - - +
167T ARG* 1.3 62.7 + - - +
169T LYS* 3.8 11.8 + - - +
170T LYS* 3.8 17.3 + - - +
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Residues in contact with ARG 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B LYS* 3.4 38.6 - - + +
163T ILE* 2.9 21.9 + - + +
164T GLU* 3.5 33.1 + - - +
166T GLU* 1.3 71.1 - - - +
168T LYS* 1.3 74.6 + - - +
170T LYS* 2.7 47.8 + - - +
171T GLU 4.2 3.5 + - - +
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Residues in contact with LYS 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164T GLU* 3.0 28.7 + - + +
165T TYR* 3.2 16.8 + - + +
167T ARG* 1.3 88.3 - - - +
169T LYS* 1.3 58.9 + - + +
170T LYS 2.9 13.7 + - - -
171T GLU 3.1 18.1 - - - +
172T ASP* 4.8 16.4 - - - +
20X G 5.6 8.2 + - - -
21X G 5.0 9.5 + - - -
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Residues in contact with LYS 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165T TYR* 3.0 68.7 + - + +
166T GLU* 3.9 9.8 - - - +
167T ARG 3.3 0.2 - - - -
168T LYS* 1.3 76.7 - - + +
170T LYS* 1.3 60.7 + - - +
76Y C 3.7 9.3 + - - -
77Y T 3.1 36.6 + - - -
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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