Contacts of the strand formed by residues 136 - 141 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113K LYS 3.4 6.1 + - - +
114K VAL* 4.5 12.8 - - + -
115K VAL 3.0 22.1 + - - -
134K ALA* 3.9 0.5 - - - +
135K LYS* 1.3 95.7 - - + +
137K VAL* 1.3 66.3 + - - +
138K PHE* 4.1 28.9 - - + -
159K ASP 5.1 0.6 + - - -
160K ASN 3.2 22.4 + - - -
161K ILE* 3.1 32.8 + - - +
163K THR* 3.6 21.9 + - - -
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Residues in contact with VAL 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K VAL* 3.3 20.9 - - + +
117K ASP* 4.8 2.2 - - + -
126K SER* 3.6 38.1 - - - +
129K ALA* 4.0 4.5 - - + -
130K ALA* 4.0 17.9 - - + +
134K ALA* 3.8 20.4 - - + -
136K LYS* 1.3 81.1 - - - +
138K PHE* 1.3 69.7 + - - +
161K ILE* 2.9 18.8 + - + +
162K ILE* 3.2 11.6 - - + +
163K THR 2.9 26.3 + - - +
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Residues in contact with PHE 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K VAL* 3.9 23.8 - - + -
115K VAL 2.8 13.3 + - - +
116K LEU* 3.3 10.7 - - + +
117K ASP 2.9 24.8 + - - -
136K LYS* 4.1 38.8 - - + -
137K VAL* 1.3 82.1 - - - +
139K GLY* 1.3 59.8 + - - +
163K THR* 3.4 12.8 - - - -
165K PHE* 3.9 22.9 - + + -
174K LEU* 4.1 26.5 - - + -
175K PRO* 3.6 26.5 - - + -
176K VAL* 3.9 24.2 - - + -
179K VAL* 4.8 3.1 - - + -
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Residues in contact with GLY 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K ASP* 3.5 11.9 - - - -
120K SER* 3.7 17.3 - - - -
126K SER* 4.3 2.4 + - - -
137K VAL 4.0 1.2 + - - -
138K PHE* 1.3 73.5 - - - +
140K ILE* 1.3 59.8 + - - -
162K ILE* 5.0 0.2 - - - +
163K THR 3.0 9.7 + - - -
164K ILE* 3.4 11.7 - - - +
165K PHE* 2.7 34.1 + - - +
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Residues in contact with ILE 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K LEU* 3.8 26.0 - - + -
117K ASP 3.1 9.2 + - - +
118K VAL* 5.3 0.9 - - + -
119K GLY* 3.0 13.9 + - - -
120K SER 2.8 19.3 + - - -
139K GLY* 1.3 76.4 - - - +
141K GLU* 1.3 64.1 + - - +
165K PHE* 3.6 12.1 - - + +
167K GLY 3.4 17.7 - - - +
169K VAL* 3.4 39.0 - - + +
172K VAL* 3.6 28.9 - - + -
174K LEU* 4.3 7.6 - - + -
207K TRP* 4.1 19.1 - - + -
401K SAH 3.9 1.0 + - + -
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Residues in contact with GLU 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K SER* 3.2 17.2 + - - +
121K GLY 2.8 20.4 + - - +
139K GLY 4.2 0.2 - - - -
140K ILE* 1.3 78.9 - - - +
142K CYS* 1.3 63.7 + - - +
143K SER* 3.0 28.2 + - - +
145K ILE* 3.6 23.1 - - + -
146K SER* 4.1 11.5 - - - +
164K ILE* 5.0 1.1 - - + -
165K PHE 3.3 5.2 + - - +
166K LYS* 3.5 8.5 - - - +
167K GLY 3.1 17.9 + - - -
401K SAH 2.6 58.4 + - - +
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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