Contacts of the strand formed by residues 136 - 139 (chain E) in PDB entry 6NQN
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 THR 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E ALA* 3.5 29.9 - - + +
55E ASP* 2.6 28.6 + - - +
130E PRO* 3.9 14.4 - - + +
131E VAL* 4.8 4.0 - - + -
134E LYS 3.5 4.1 - - - +
135E ARG* 1.3 81.6 - - - +
137E VAL* 1.3 63.8 + - - +
161E LEU* 3.9 26.9 - - + -
162E SER 3.8 5.8 - - - -
163E LEU* 4.1 11.2 - - + -
164E GLU* 5.2 2.6 - - - +
169E TYR* 5.0 0.9 - - + -
204E TYR* 5.5 2.9 + - - -
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ASP* 3.7 9.7 - - - +
136E THR* 1.3 75.0 - - - +
138E LYS* 1.3 73.8 + - + +
162E SER* 2.9 25.8 + - - +
163E LEU 3.6 6.3 - - - +
164E GLU* 3.5 36.3 - - + +
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Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASP* 3.9 9.8 + - - -
137E VAL* 1.3 91.8 - - + +
139E TRP* 1.3 84.8 + - - +
140E GLU* 4.5 5.3 + - - +
141E PRO* 4.3 8.5 - - - +
161E LEU* 3.4 9.1 - - - +
162E SER* 2.9 37.4 + - - +
194E HIS* 3.2 28.7 + - - -
195E ILE 5.4 2.5 - - - +
196E GLU* 4.3 20.6 - - - +
197E ILE 6.1 1.3 - - - +
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Residues in contact with TRP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ASP* 2.7 29.8 + - + -
56E ILE* 4.5 2.5 - - - -
58E THR* 3.3 18.8 + - - -
59E THR* 3.8 15.0 - - + +
63E KZ4 4.9 3.6 - - + +
93E MET* 6.0 0.4 - - - -
95E TYR* 3.5 37.2 - + - -
138E LYS* 1.3 96.2 + - - +
140E GLU* 1.3 69.7 + - - +
159E THR* 3.7 29.8 - - + -
160E ALA 3.5 25.1 - - - -
161E LEU* 3.5 22.6 - - + +
171E CYS* 3.9 8.7 - - + -
173E PHE* 3.7 22.7 - + - -
194E HIS* 4.6 0.3 - - - -
195E ILE* 3.9 31.8 + - + +
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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