Contacts of the strand formed by residues 150 - 152 (chain K) in PDB entry 6R1U
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 TRP 150 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K TRP* 3.7 15.0 - - + -
140K VAL 3.4 21.8 - - - -
141K GLN* 3.3 47.2 - - + +
148K ARG 4.5 0.9 - - - -
149K LYS* 1.3 71.7 - - - +
151K ARG* 1.3 67.8 + - - +
189K GLU* 2.9 29.1 + - - +
190K ASP* 4.8 2.1 + - - +
193K VAL* 3.7 35.6 - - + +
332K ILE* 5.6 1.6 - - + -
342K ARG* 3.5 29.6 - - + -
343K ILE* 3.6 43.4 - - + +
346K VAL* 3.9 31.9 - - + -
347K GLN* 5.2 5.1 - - + +
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Residues in contact with ARG 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K TRP* 3.3 9.7 - - - -
140K VAL* 2.9 36.9 + - - +
149K LYS* 3.6 15.0 - - - +
150K TRP* 1.3 80.9 + - - +
152K GLN* 1.3 66.7 + - - +
153K LEU 3.7 0.7 + - - -
167K TYR* 3.5 31.9 - - + +
169K CYS* 3.1 30.8 - - + +
170K GLY 5.6 0.2 - - - +
184K HIS 2.8 28.8 + - - -
185K CYS* 4.0 1.4 - - - +
187K LEU* 3.0 23.3 + - - +
188K PRO 3.1 28.3 + - - -
189K GLU* 3.9 7.1 - - - +
190K ASP 4.8 1.4 - - - +
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Residues in contact with GLN 152 (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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66K PHE* 5.4 5.1 - - - +
137K PRO* 3.4 31.2 - - + +
138K TYR 3.7 4.0 - - - +
139K TRP* 3.5 35.1 - - + -
151K ARG* 1.3 75.8 - - - +
153K LEU* 1.3 71.3 + - - +
154K THR* 4.0 2.3 + - - +
167K TYR* 5.6 0.2 + - - -
190K ASP* 4.6 1.4 - - - +
192K ARG* 3.5 24.9 + - - +
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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
------------------------------------------------------------
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