Contacts of the strand formed by residues 136 - 141 (chain G) in PDB entry 5DST
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 136 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LYS 3.5 6.8 + - - +
114G VAL* 3.6 12.3 - - + -
115G VAL 3.1 21.4 + - - -
134G ALA* 3.8 1.0 - - - +
135G LYS* 1.3 93.7 - - + +
137G VAL* 1.3 68.6 + - - +
138G PHE* 4.1 27.3 - - + -
159G ASP 4.9 1.4 + - - -
160G ASN 3.3 22.2 + - - -
161G ILE* 2.8 35.4 + - - +
163G THR* 3.7 20.1 + - - -
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Residues in contact with VAL 137 (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 VAL* 3.4 20.0 - - + +
117G ASP* 4.8 1.3 - - + -
126G SER* 3.6 49.4 - - - +
129G ALA* 4.1 4.3 - - + -
130G ALA 4.1 4.5 - - - +
134G ALA* 3.8 18.6 - - + -
136G LYS* 1.3 82.0 - - - +
138G PHE* 1.3 72.2 + - - +
161G ILE* 3.0 18.2 + - + +
162G ILE* 3.3 12.1 - - + +
163G THR 3.0 24.6 + - - -
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Residues in contact with PHE 138 (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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114G VAL* 4.0 24.2 - - + -
115G VAL 2.9 8.9 + - - +
116G LEU* 3.4 10.2 - - + +
117G ASP* 2.7 32.4 + - - +
136G LYS* 4.1 34.1 - - + -
137G VAL* 1.3 83.7 - - - +
139G GLY* 1.3 53.4 + - - +
163G THR* 3.4 12.3 - - - -
165G PHE* 3.9 24.0 - + + -
174G LEU* 4.1 26.2 - - + -
175G PRO* 3.4 31.9 - - + -
176G VAL* 4.1 18.2 - - + -
179G VAL* 4.9 3.4 - - + -
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Residues in contact with GLY 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ASP* 3.5 11.7 - - - -
120G SER* 3.6 18.6 - - - -
126G SER* 4.3 1.9 + - - -
137G VAL* 4.2 0.6 - - - +
138G PHE* 1.3 73.7 - - - +
140G ILE* 1.3 58.5 + - - -
162G ILE* 4.9 0.4 - - - +
163G THR 3.0 9.5 + - - -
164G ILE* 3.4 11.3 - - - +
165G PHE* 2.7 35.2 + - - +
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Residues in contact with ILE 140 (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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116G LEU* 3.8 25.6 - - + -
117G ASP 3.1 8.1 + - - +
118G VAL* 5.3 0.9 - - + -
119G GLY* 2.9 14.4 + - - -
120G SER 2.9 18.5 + - - -
139G GLY* 1.3 77.1 - - - +
141G GLU* 1.3 63.8 + - - +
165G PHE* 3.5 11.0 - - + +
167G GLY 3.3 18.4 - - - +
169G VAL* 3.5 33.9 - - + -
172G VAL* 3.5 30.7 - - + -
174G LEU* 4.2 8.7 - - + -
207G TRP* 4.1 21.8 - - + -
401G SAH 4.0 1.4 + - + -
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Residues in contact with GLU 141 (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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119G GLY 3.7 1.2 - - - -
120G SER* 3.3 15.9 - - - +
121G GLY 2.9 19.7 + - - +
140G ILE* 1.3 76.1 - - - +
142G CYS* 1.3 64.6 + - - +
143G SER* 2.9 28.3 + - - +
145G ILE* 3.6 23.1 - - + -
146G SER* 4.0 12.8 - - - +
164G ILE* 5.0 1.1 - - + -
165G PHE 3.3 6.6 + - - +
166G LYS* 3.6 7.4 - - - -
167G GLY 3.1 18.7 + - - -
401G SAH 2.5 58.0 + - - +
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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