Contacts of the strand formed by residues 159 - 165 (chain S) in PDB entry 1T9G
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 LYS 159 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198R GLU* 3.8 24.9 + - - -
156S GLU* 2.6 46.8 + - + +
158S ASP* 1.3 97.1 - - - +
160S LEU* 1.3 57.9 + - - +
174S ARG* 4.0 30.7 - - + +
175S LEU 3.4 14.1 - - - +
176S LYS* 4.7 21.8 - - + +
177S LEU* 3.4 6.9 - - - +
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Residues in contact with LEU 160 (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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119S LEU* 3.7 24.0 - - + -
153S VAL* 4.1 17.0 - - + -
154S THR 3.3 24.7 - - - +
155S LEU* 3.7 22.4 - - + +
156S GLU* 5.5 0.2 - - - -
159S LYS* 1.3 72.8 - - - +
161S LYS* 1.3 58.8 + - - +
162S VAL* 3.8 12.9 + - + -
173S LEU 3.8 0.2 - - - +
174S ARG* 3.3 7.1 - - - +
175S LEU* 3.0 38.6 + - + +
177S LEU* 3.7 16.1 - - + +
179S ALA* 4.2 5.4 - - + -
181S VAL* 3.6 31.2 - - + -
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Residues in contact with LYS 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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200R LEU* 4.2 14.4 - - + -
152S GLN* 3.8 1.8 - - + +
153S VAL* 3.5 3.8 - - - -
154S THR* 2.8 48.4 + - - +
156S GLU* 3.9 28.3 + - - +
159S LYS 4.1 0.2 + - - -
160S LEU* 1.3 73.2 - - - +
162S VAL* 1.3 60.7 + - - +
163S GLU* 4.0 1.0 + - + +
172S THR* 3.9 22.4 - - + +
173S LEU 3.4 13.0 - - - +
174S ARG* 4.0 15.3 - - + +
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Residues in contact with VAL 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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147S GLY* 4.0 17.3 - - - -
150S ALA* 3.9 20.0 - - + -
152S GLN 3.5 2.2 - - - +
153S VAL* 4.2 5.6 - - + -
160S LEU* 3.8 10.0 + - + -
161S LYS* 1.3 75.7 - - - +
163S GLU* 1.3 75.3 + - - +
164S ARG* 3.8 8.1 + - + +
171S GLU 4.0 0.2 - - - +
172S THR* 3.5 3.6 - - - -
173S LEU* 2.7 44.9 + - + +
175S LEU* 4.0 17.9 - - + -
181S VAL* 3.9 25.1 - - + -
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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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150S ALA* 3.3 5.2 - - - -
151S SER* 2.7 42.0 + - - +
152S GLN* 2.9 43.7 + - + +
161S LYS* 4.0 1.6 + - + +
162S VAL* 1.3 73.1 - - - +
164S ARG* 1.3 60.7 + - - +
170S LEU* 3.6 34.9 - - + +
171S GLU 3.5 11.4 - - - +
172S THR* 4.3 16.5 + - + +
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Residues in contact with ARG 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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114R ALA* 5.1 3.8 + - - +
115R PHE* 6.1 1.2 - - - +
118R ASN* 3.5 21.9 + - - +
146S GLN 5.7 0.2 + - - -
147S GLY* 5.4 0.2 - - - -
148S THR* 2.5 54.4 + - - +
149S PHE* 3.2 33.0 - - - +
151S SER* 4.1 1.6 - - - +
162S VAL* 4.2 16.4 - - + +
163S GLU* 1.3 76.3 - - - +
165S GLU* 1.3 59.9 + - - +
166S ILE* 3.4 19.1 - - - +
170S LEU* 3.4 10.2 - - - +
171S GLU* 3.0 63.0 + - - +
173S LEU* 4.2 17.1 - - + +
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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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114R ALA* 4.3 2.9 - - - +
149S PHE* 3.0 43.2 + - + +
151S SER* 3.5 18.8 - - - -
164S ARG* 1.3 72.0 - - - +
166S ILE* 1.3 62.8 + - - +
169S GLY 4.0 5.2 - - - +
170S LEU* 3.8 13.5 - - - +
184S ASP* 3.0 29.4 - - - +
186S ARG* 3.3 32.2 + - - +
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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