Contacts of the strand formed by residues 135 - 139 (chain A) in PDB entry 5NER
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU 4.6 0.2 - - - -
131A GLN* 3.3 4.9 - - - +
132A ASP* 3.0 41.4 + - + +
134A THR* 1.3 83.3 + - - +
136A THR* 1.3 77.8 + - - +
137A VAL* 4.0 18.3 - - + +
192A VAL* 3.9 29.2 + - + +
195A TYR* 4.8 7.7 - - - +
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Residues in contact with THR 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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71A GLU 5.0 3.1 + - - +
72A PHE* 3.5 37.0 - - + +
129A PHE* 4.6 4.7 - - + -
130A LEU 3.2 10.5 - - - +
131A GLN* 3.3 22.6 + - + +
134A THR 4.0 3.9 + - - -
135A LYS* 1.3 88.1 + - - +
137A VAL* 1.3 69.8 + - - +
195A TYR* 4.7 5.0 + - - -
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Residues in contact with VAL 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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129A PHE* 3.4 12.9 - - - +
130A LEU* 2.8 49.6 + - + +
135A LYS* 4.0 11.7 - - + +
136A THR* 1.3 78.8 - - - +
138A GLU* 1.3 61.8 + - - +
191A ILE* 3.7 25.4 - - + +
192A VAL* 3.8 31.2 - - + -
195A TYR* 3.6 36.1 - - + -
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Residues in contact with GLU 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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78A ARG* 3.5 18.6 + - - -
87A GLU* 4.8 1.6 - - - +
89A LYS* 5.9 1.7 - - - -
112A TYR* 4.7 2.8 + - - -
127A THR* 3.0 22.2 + - - +
128A CYS 3.4 12.1 - - - +
129A PHE* 3.8 29.5 - - + -
137A VAL* 1.3 79.4 - - - +
139A TYR* 1.3 64.6 + - - +
140A ALA 4.1 1.2 + - - -
143A ARG* 3.2 37.6 + - - +
191A ILE 4.6 1.4 - - - +
195A TYR* 3.2 38.6 + - + +
202A ILE* 5.0 3.1 - - - +
204A TYR* 4.1 8.3 + - - -
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Residues in contact with TYR 139 (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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106A LEU* 5.1 4.7 - - + -
127A THR* 4.1 0.6 - - - -
128A CYS* 2.9 42.0 + - + +
130A LEU* 5.2 7.2 - - + -
137A VAL 4.3 0.2 + - - -
138A GLU* 1.3 74.3 - - - +
140A ALA* 1.3 59.7 + - - +
141A PRO* 3.3 15.3 - - + +
169A VAL* 4.4 16.2 - - + +
171A LEU* 3.7 28.4 - - + +
184A ILE* 3.6 18.2 + - - +
186A ASP* 2.7 41.5 + - + +
191A ILE* 3.6 40.2 - - + -
204A TYR* 3.6 25.1 - + - -
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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