Contacts of the strand formed by residues 136 - 141 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113L LYS 3.5 4.0 + - - +
114L VAL* 3.4 15.6 - - + -
115L VAL 3.0 22.8 + - - -
134L ALA* 3.9 1.0 - - - +
135L LYS* 1.3 95.2 - - + +
137L VAL* 1.3 66.7 + - - +
138L PHE* 4.2 27.8 - - + -
159L ASP 5.1 0.6 + - - -
160L ASN 3.3 22.4 + - - -
161L ILE* 3.0 29.9 + - - +
163L THR* 3.7 19.9 + - - -
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Residues in contact with VAL 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L VAL* 3.3 17.7 - - + +
117L ASP* 4.8 2.0 - - + -
126L SER* 3.6 38.8 - - - +
129L ALA* 4.0 5.6 - - + -
130L ALA* 3.9 16.8 - - + +
134L ALA* 3.6 21.1 - - + -
136L LYS* 1.3 78.4 - - - +
138L PHE* 1.3 73.1 + - - +
161L ILE* 3.1 16.0 + - + +
162L ILE* 3.4 11.6 - - + +
163L THR 3.0 26.2 + - - -
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Residues in contact with PHE 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 4.0 16.2 - - + -
115L VAL 2.8 11.3 + - - +
116L LEU* 3.3 11.5 - - + +
117L ASP 2.7 31.1 + - - -
136L LYS* 4.2 35.9 - - + -
137L VAL* 1.3 81.6 - - - +
139L GLY* 1.3 55.0 + - - +
163L THR* 3.4 11.9 - - - -
165L PHE* 3.9 23.1 - + + -
174L LEU* 4.0 26.0 - - + -
175L PRO* 3.6 28.0 - - + -
176L VAL* 3.9 30.3 - - + -
179L VAL* 4.8 3.6 - - + -
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Residues in contact with GLY 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ASP* 3.5 11.9 - - - -
120L SER* 3.7 19.1 - - - -
126L SER* 4.2 2.1 + - - -
137L VAL* 4.2 0.8 - - - +
138L PHE* 1.3 72.5 - - - +
140L ILE* 1.3 58.8 + - - -
162L ILE* 5.1 0.2 - - - +
163L THR 3.0 9.1 + - - +
164L ILE* 3.3 12.1 - - - +
165L PHE* 2.7 35.7 + - - +
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Residues in contact with ILE 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 3.8 26.9 - - + -
117L ASP 3.2 7.3 + - - +
118L VAL* 5.8 0.9 - - + -
119L GLY* 3.1 12.3 + - - -
120L SER 2.9 19.8 + - - -
139L GLY* 1.3 77.8 - - - +
141L GLU* 1.3 65.8 + - - +
165L PHE* 3.5 13.0 - - + +
167L GLY 3.3 18.2 - - - +
169L VAL* 3.5 36.8 - - + -
172L VAL* 3.6 28.5 - - + -
174L LEU* 4.4 8.1 - - + -
207L TRP* 4.1 18.8 - - + -
401L SAH 4.1 1.3 + - + -
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Residues in contact with GLU 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L GLY 3.5 3.1 - - - -
120L SER* 3.4 14.4 - - - +
121L GLY 2.8 19.5 + - - +
140L ILE* 1.3 76.7 - - - +
142L CYS* 1.3 63.7 + - - +
143L SER* 3.0 27.0 + - - +
145L ILE* 3.6 24.0 - - + -
146L SER* 4.0 13.1 - - - +
164L ILE* 4.9 1.6 - - + -
165L PHE 3.2 6.6 + - - +
166L LYS* 3.5 7.8 - - - -
167L GLY 3.0 19.4 + - - -
401L SAH 2.4 56.5 + - - -
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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