Contacts of the strand formed by residues 166 - 174 (chain G) in PDB entry 3S4S
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 166 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3G VAL* 3.8 42.0 + - + +
5G LEU* 3.3 23.3 - - + +
161G VAL 3.7 0.3 - - - +
162G LEU* 3.1 8.3 - - - +
163G GLN 2.7 38.5 + - - +
164G ASN* 2.9 33.1 + - - +
165G GLN* 1.3 75.7 - - - +
167G LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 167 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G LEU* 4.5 9.5 - - - +
129G GLN* 5.7 4.3 - - - +
160G THR* 3.4 30.6 - - + +
161G VAL 3.5 5.2 - - - +
162G LEU* 3.3 37.0 - - + -
165G GLN 5.2 1.3 - - - +
166G LYS* 1.3 79.8 - - - +
168G VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU* 4.2 16.6 - - + +
6G GLY* 4.6 11.0 - - - +
7G LYS* 3.4 35.0 - - + -
98G PHE* 4.4 12.6 - - + -
159G CYS 4.1 0.2 - - - +
160G THR* 3.8 2.9 - - - -
161G VAL* 3.0 50.3 + - + +
163G GLN* 6.5 0.2 - - + -
167G LYS* 1.3 78.4 - - - +
169G GLU* 1.3 61.1 + - - +
170G PHE* 4.2 11.3 + - + -
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Residues in contact with GLU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LYS* 2.7 40.8 + - - +
158G THR* 3.1 23.3 - - + +
159G CYS 3.7 6.7 - - - +
160G THR* 4.7 8.9 + - + +
168G VAL* 1.3 75.6 - - - +
170G PHE* 1.3 70.7 + - - +
171G LYS* 3.4 26.3 + - + -
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Residues in contact with PHE 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LYS* 3.7 37.2 - - + +
8G LYS* 5.0 2.5 - - + -
98G PHE* 3.3 39.3 - - + -
99G GLY* 4.2 2.9 - - - -
100G LEU* 3.4 52.7 - - + -
118G LEU* 4.8 0.2 - - + -
157G TRP 3.7 0.3 - - - +
158G THR* 3.5 4.3 - - - -
159G CYS* 2.8 35.4 + - - +
161G VAL* 4.2 16.2 - - + -
168G VAL* 4.2 17.0 - - + -
169G GLU* 1.3 76.7 - - - +
171G LYS* 1.3 64.7 + - - +
172G ILE* 4.2 1.6 - - + -
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Residues in contact with LYS 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LYS* 5.1 2.8 - - - +
156G THR* 4.1 17.4 - - + +
157G TRP 3.3 7.2 - - - +
158G THR* 3.2 32.4 + - + +
169G GLU* 3.4 23.3 + - + -
170G PHE* 1.3 80.2 - - - +
172G ILE* 1.3 61.9 + - - +
173G ASP* 5.5 0.2 - - - -
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Residues in contact with ILE 172 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G LEU* 4.8 13.2 - - + +
101G THR* 4.3 9.4 - - - -
102G ALA* 3.7 37.7 - - + +
116G LEU* 4.6 15.3 - - + -
156G THR* 3.4 0.9 - - - +
157G TRP* 2.8 46.8 + - + +
159G CYS* 4.8 6.3 - - - -
170G PHE* 5.4 0.7 - - + +
171G LYS* 1.3 76.7 - - - +
173G ASP* 1.3 72.0 + - - +
174G ILE* 3.1 23.7 - - + +
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Residues in contact with ASP 173 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155G GLY 3.2 6.1 - - - +
156G THR* 2.8 35.3 + - - +
172G ILE* 1.3 77.4 - - - +
174G ILE* 1.3 66.9 + - - +
175G VAL 4.3 0.5 + - - -
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Residues in contact with ILE 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G ALA* 5.4 4.0 - - + -
108G LEU* 5.2 5.6 - - + -
114G LEU* 5.0 24.5 - - + -
116G LEU* 5.5 2.2 - - + -
149G LEU* 5.1 5.4 - - + -
153G ASP 4.5 4.0 - - - +
154G SER* 3.7 2.8 + - - -
155G GLY* 2.9 22.8 + - - +
157G TRP* 3.1 34.8 - - + +
172G ILE* 3.1 39.9 - - + +
173G ASP* 1.3 79.2 - - - +
175G VAL* 1.3 63.4 + - - +
176G VAL* 3.5 29.2 + - + +
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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