Contacts of the helix formed by residues 166 - 171 (chain A) in PDB entry 5TSQ
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A MET* 4.2 2.0 - - + -
153A GLY* 3.2 10.2 - - - -
154A GLY* 2.9 51.8 + - - +
155A SER* 4.3 1.6 - - - +
160A ASN* 3.3 5.4 - - - -
161A ALA* 4.3 0.2 - - - -
164A VAL 4.2 0.8 + - - -
165A ALA* 1.3 73.6 - - - +
167A PHE* 1.3 67.1 + - - +
168A ASN* 2.8 28.8 + - - -
169A ILE* 3.1 13.4 + - + +
170A PHE* 2.8 28.0 + - - +
191A LEU* 3.6 23.3 - - + -
272A GLY 4.5 2.4 + - - -
274A THR 6.1 0.2 - - - +
402A BDR 2.6 35.8 + - - +
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.1 4.9 - - - -
38A GLY* 3.6 22.4 - - - -
39A ASN* 3.5 25.1 - - - -
76A ARG* 4.0 7.6 - - + -
77A THR 4.5 5.2 - - - -
78A ALA* 4.0 24.2 - - + -
80A GLN* 6.0 0.7 - - - -
160A ASN* 2.9 14.9 + - - +
161A ALA* 3.8 20.6 - - + +
166A GLU* 1.3 74.8 - - - +
168A ASN* 1.3 77.0 + - - +
170A PHE* 3.1 1.2 + + - -
171A VAL* 2.9 56.9 + - + +
402A BDR 3.6 26.0 - + - +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.3 2.1 - - - +
126A THR 3.2 11.3 + - - -
127A GLY* 3.4 30.2 - - - +
128A GLY* 3.5 11.7 + - - +
129A LEU* 4.4 3.7 + - + +
152A MET* 2.9 28.2 + - - +
153A GLY* 4.4 1.6 - - - -
166A GLU* 2.8 23.6 + - - +
167A PHE* 1.3 89.5 - - - +
169A ILE* 1.3 64.6 + - + +
171A VAL* 3.4 18.0 - - - +
172A ASP 3.9 3.3 + - - +
402A BDR 3.1 25.3 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.0 17.0 - - + -
151A LEU* 4.8 1.6 - - + -
153A GLY* 4.5 7.4 - - - -
154A GLY* 3.4 34.5 - - - +
166A GLU* 3.1 6.1 + - - +
168A ASN* 1.3 76.2 - - + +
170A PHE* 1.3 67.1 + - - +
172A ASP 3.1 3.5 + - - -
173A PRO* 3.1 24.1 - - - +
176A ALA* 3.7 31.0 - - + -
180A PHE* 4.2 13.2 - - + -
263A ILE* 4.0 18.2 - - + -
272A GLY* 3.1 27.6 - - - +
274A THR* 3.8 5.6 - - + -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 5.1 2.9 - - - +
76A ARG* 3.7 47.7 + - - -
161A ALA* 3.7 33.0 - - + -
162A SER* 4.0 17.0 - - - -
165A ALA* 3.7 12.6 - - + -
166A GLU 2.8 18.3 + - - +
167A PHE* 3.5 4.5 - + - +
169A ILE* 1.3 78.6 - - - +
171A VAL* 1.3 64.7 + - + +
172A ASP 3.4 0.5 + - - -
173A PRO* 3.4 13.6 - - + +
271A ALA* 3.6 26.9 - - + -
272A GLY* 4.3 7.8 + - - -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL 5.1 1.6 - - - +
38A GLY* 4.9 8.5 - - - -
70A PRO* 3.4 23.3 - - + +
73A ARG* 4.8 3.5 - - - +
74A LYS 4.8 3.3 - - - +
76A ARG* 4.0 31.4 - - + +
128A GLY* 4.0 17.3 - - - +
167A PHE* 2.9 56.1 + - + +
168A ASN* 3.4 19.5 - - - +
170A PHE* 1.3 79.5 - - + +
172A ASP* 1.3 62.2 + - + +
173A PRO* 3.9 2.0 - - - +
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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