Contacts of the strand formed by residues 133 - 138 (chain A) in PDB entry 5C16
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 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 5.2 1.1 - - - -
99A PRO* 2.7 29.0 + - - +
100A LEU* 4.1 1.4 - - - +
101A PHE* 4.9 3.8 - - + +
104A GLU* 2.7 34.8 + - - +
129A VAL* 3.8 1.0 - - - -
130A THR* 2.9 41.2 + - + +
132A PHE* 1.3 90.5 - - + +
134A LEU* 1.3 65.4 + - - +
135A TYR* 3.8 28.7 - - + -
148A ASP* 3.6 25.8 - - - +
149A VAL 3.5 18.2 - - - +
150A PRO* 4.0 2.0 - - + -
151A LEU* 3.6 9.8 - - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.3 19.3 - - + -
128A THR 3.4 8.1 - - - +
129A VAL* 4.6 2.5 - - + +
133A LYS* 1.3 77.6 - - - +
135A TYR* 1.3 64.7 + - - +
136A PHE* 5.2 0.9 - - + -
147A LEU* 3.8 11.3 - - + +
148A ASP* 3.8 1.2 - - - -
149A VAL* 2.8 61.5 + - + +
151A LEU* 3.5 7.7 - - + +
154A ILE* 4.2 12.8 - - + -
174A ILE* 3.7 23.1 - - + -
182A LEU* 4.7 7.6 - - + -
184A LEU* 5.6 3.6 - - + -
200A LEU* 3.6 28.7 - - + -
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.5 25.8 - - + -
99A PRO* 3.4 32.9 - - + +
126A THR 3.6 1.6 - - - +
127A LEU* 3.2 6.3 - - - +
128A THR* 2.8 39.9 + - + +
130A THR* 5.8 0.4 - - + -
133A LYS* 3.8 18.4 - - + -
134A LEU* 1.3 74.6 - - - +
136A PHE* 1.3 66.2 + - - +
137A LYS* 4.0 34.0 + - + +
146A ILE* 3.8 32.2 - - + +
147A LEU 3.5 3.4 - - - -
148A ASP* 3.5 31.0 - - + -
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 3.2 41.5 - - + -
115A TYR* 3.9 25.4 - - + -
123A VAL* 4.1 2.9 - - + -
124A SER 3.8 5.6 - - - -
125A GLY* 3.4 28.9 - - - -
126A THR 3.4 14.4 - - - -
127A LEU* 4.2 16.2 - - + -
134A LEU* 5.2 2.0 - - + -
135A TYR* 1.3 77.7 - - - +
137A LYS* 1.3 63.4 + - - +
145A PHE* 3.5 39.2 - + - +
146A ILE* 3.6 3.1 - - - +
147A LEU* 3.0 45.7 + - + +
184A LEU* 5.2 4.5 - - + -
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLY* 3.2 4.9 - - - -
126A THR* 3.0 35.3 + - - +
135A TYR* 4.0 25.9 + - + +
136A PHE* 1.3 76.1 - - - +
138A ASN* 1.3 66.8 + - - +
139A VAL* 4.3 6.4 - - + +
144A HIS* 3.9 36.9 + - + +
145A PHE 3.4 3.8 - - - +
146A ILE* 3.6 33.2 - - + -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.8 20.9 - - + +
124A SER* 2.3 44.6 + - - +
125A GLY* 4.5 1.5 - - - -
136A PHE* 5.0 0.2 - - + -
137A LYS* 1.3 76.1 - - - +
139A VAL* 1.3 73.7 + - - +
144A HIS* 3.2 18.9 - - - -
145A PHE* 3.2 32.4 + - + +
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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