Contacts of the strand formed by residues 162 - 167 (chain G) in PDB entry 5UWC
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 ARG 162 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G TRP* 2.9 31.2 + - + -
126G VAL* 4.3 0.3 - - - +
135G GLN* 2.9 34.8 + - - +
136G TYR* 3.0 28.9 + - - +
137G ASP* 3.0 27.7 + - - -
154G TYR* 3.6 49.1 - - + +
155G LYS 3.4 6.7 - - - +
156G THR* 3.7 16.1 - - + +
161G THR* 1.3 74.7 - - - +
163G ILE* 1.3 60.6 + - - +
164G GLY 3.8 0.2 - - - -
187G ARG* 3.7 10.7 - - - +
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Residues in contact with ILE 163 (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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123G SER* 3.4 6.8 - - - -
124G TRP* 3.0 44.0 + - - +
126G VAL* 3.9 15.0 - - + +
155G LYS* 3.0 29.5 + - + +
156G THR 4.0 4.5 - - - +
157G ASP* 3.7 42.6 - - + +
161G THR 3.7 8.1 - - - +
162G ARG* 1.3 78.5 - - - +
164G GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G CYS 3.1 14.6 - - - -
123G SER* 4.1 0.9 - - - -
124G TRP* 3.6 11.4 - - - -
154G TYR* 3.4 8.7 - - - -
155G LYS* 2.9 42.5 + - - +
163G ILE* 1.3 80.7 - - - +
165G CYS* 1.3 62.2 + - - +
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Residues in contact with CYS 165 (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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120G LEU 4.1 0.2 - - - +
121G SER* 3.5 1.9 - - - -
122G CYS* 2.9 30.9 + - - +
124G TRP* 3.9 9.6 - - + -
138G LEU* 4.6 5.2 - - + -
151G CYS* 2.0 49.6 - - + -
153G HIS 3.2 29.4 - - - -
154G TYR* 3.5 23.1 - - + -
155G LYS* 5.0 2.3 - - - +
164G GLY* 1.3 75.0 - - - +
166G ARG* 1.3 63.2 + - - +
407G EDT 5.0 1.5 - - - +
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Residues in contact with ARG 166 (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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115G HIS* 5.4 0.4 - - - -
119G PHE* 3.7 26.5 - - - -
120G LEU 3.2 12.3 - - - +
121G SER* 3.5 11.0 - - - +
151G CYS* 3.4 14.9 - - - -
153G HIS* 3.0 40.0 + - + +
165G CYS* 1.3 78.0 - - - +
167G PHE* 1.3 60.5 + - - +
168G ASP* 2.9 27.5 + - - +
402G CIT 4.7 0.7 - - - +
407G EDT 2.8 61.8 + - - +
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Residues in contact with PHE 167 (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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118G ASP 3.8 0.3 - - - +
119G PHE* 3.3 7.6 - - - +
120G LEU* 2.9 63.3 + - + +
122G CYS* 5.7 1.1 - - - -
138G LEU* 3.6 24.2 - - + -
140G LEU* 3.8 21.1 - - + -
149G TYR* 3.9 8.5 - - + -
150G GLU 4.0 6.5 - - - -
151G CYS* 3.5 40.2 - - + -
166G ARG* 1.3 75.8 - - - +
168G ASP* 1.3 61.5 + - - +
169G ASP 3.4 1.1 + - - +
170G ILE* 4.6 6.1 - - + -
173G LEU* 3.4 30.1 - - + -
402G CIT 3.6 23.3 - - + +
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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