Contacts of the helix formed by residues 160 - 170 (chain t) in PDB entry 5JPQ
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 GLU 160 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158t ALA 2.9 9.8 + - - +
159t LEU* 1.3 82.9 - - - +
161t LYS* 1.3 60.2 + - - +
162t ASN* 2.9 23.8 + - - +
163t ILE* 3.0 30.0 + - + +
164t GLU* 3.2 4.6 + - - +
192t GLU* 3.9 4.1 - - - +
193t GLY* 3.2 38.3 + - - -
196t LEU* 3.4 19.8 - - - +
197t GLU* 5.9 0.8 - - - +
22y LEU* 3.3 26.1 - - + +
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Residues in contact with LYS 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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160t GLU* 1.3 72.2 - - - +
162t ASN* 1.3 63.0 + - - +
164t GLU* 3.9 17.8 + - - +
165t GLU* 3.0 35.1 + - - +
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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
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160t GLU* 2.9 19.1 + - + +
161t LYS* 1.3 80.9 - - - +
163t ILE* 1.3 56.2 + - - +
164t GLU 3.2 1.6 - - - -
165t GLU* 3.7 14.8 + - - +
166t GLN* 2.8 39.2 + - + +
196t LEU* 3.7 24.6 - - + +
197t GLU* 5.1 12.0 - - - +
200t ILE* 4.8 14.8 - - + +
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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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75t TRP* 4.1 13.2 - - + +
77t SER* 4.9 0.2 - - - +
129t LEU* 6.4 0.4 - - + -
159t LEU* 4.0 33.9 - - + -
160t GLU* 3.0 38.2 + - + +
162t ASN* 1.3 78.1 - - - +
164t GLU* 1.3 67.0 + - - +
166t GLN* 3.3 15.7 - - + +
167t PHE* 3.3 34.8 - - + -
191t LEU 5.0 4.9 - - - +
192t GLU* 3.4 27.1 - - + +
196t LEU* 4.8 6.7 - - + -
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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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129t LEU* 5.4 7.3 - - + +
132t LYS* 4.5 20.2 + - - -
135t ARG* 3.6 26.0 + - - +
157t GLN 5.1 2.4 - - - +
158t ALA* 5.6 0.9 - - - -
159t LEU* 3.0 33.3 + - + +
160t GLU 3.2 3.8 + - - +
161t LYS* 3.9 18.4 - - - +
162t ASN 3.2 0.2 - - - -
163t ILE* 1.3 74.7 - - - +
165t GLU* 1.3 68.6 + - + +
166t GLN 3.1 0.9 + - - -
167t PHE* 3.1 17.5 + - - +
168t VAL* 3.5 15.7 + - - +
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Residues in contact with GLU 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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132t LYS* 6.5 0.4 - - - -
161t LYS* 3.0 23.6 + - - +
162t ASN* 3.7 18.2 - - - +
163t ILE 3.5 0.2 - - - -
164t GLU* 1.3 76.6 - - + +
166t GLN* 1.3 64.8 + - + +
168t VAL* 3.5 7.2 + - - +
169t SER* 3.1 27.5 + - - +
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Residues in contact with GLN 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* 2.8 26.1 + - + +
163t ILE* 3.3 12.1 - - - +
165t GLU* 1.3 80.6 - - - +
167t PHE* 1.3 67.3 + - + +
169t SER* 3.1 11.6 + - - -
170t GLN 3.3 1.9 + - - -
171t ARG* 2.7 25.9 - - - +
172t ILE* 3.3 9.7 - - + +
173t LEU* 2.6 61.7 + - - +
196t LEU* 5.3 8.3 - - + +
200t ILE* 5.7 4.4 - - - +
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Residues in contact with PHE 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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75t TRP* 3.2 43.7 - + - -
114t SER* 3.5 30.4 + - - -
117t PHE* 3.7 13.0 - - + -
118t ARG* 3.6 31.0 + - + -
129t LEU* 3.6 44.2 - - + +
159t LEU* 5.6 0.2 - - + -
163t ILE* 3.3 30.7 + - + -
164t GLU 3.1 8.0 + - - +
166t GLN* 1.3 79.9 - - + +
168t VAL* 1.3 55.9 + - - +
170t GLN* 2.7 31.2 + - - +
172t ILE* 4.4 10.8 - - + -
190t ILE* 6.2 0.4 - - + -
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Residues in contact with VAL 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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129t LEU* 3.1 23.7 + - + +
130t GLY* 4.4 5.2 - - - +
131t LEU* 4.0 39.7 - - + +
132t LYS* 5.2 8.3 - - + +
135t ARG* 5.4 4.0 - - - +
164t GLU* 3.6 15.7 - - + +
165t GLU* 3.9 7.2 - - - +
166t GLN 3.4 0.6 - - - -
167t PHE* 1.3 74.6 - - + +
169t SER* 1.3 59.0 + - - +
170t GLN* 3.0 16.0 + - - +
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Residues in contact with SER 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 GLU* 3.1 14.5 + - - +
166t GLN* 3.1 12.4 + - - -
168t VAL* 1.3 75.5 - - - +
170t GLN* 1.3 68.1 + - - +
171t ARG* 3.1 28.8 + - - +
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Residues in contact with GLN 170 (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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112t ILE 3.4 3.8 - - - +
113t ASP* 4.0 6.5 - - - +
114t SER* 3.4 34.8 + - - -
118t ARG* 4.1 26.5 + - - +
166t GLN 3.3 0.4 + - - -
167t PHE 2.7 18.3 + - - +
168t VAL* 3.0 9.1 - - - +
169t SER* 1.3 81.9 - - - +
171t ARG* 1.3 67.3 + - - +
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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