Contacts of the strand formed by residues 237 - 239 (chain A) in PDB entry 4K2S
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 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.6 17.5 - + - -
149A ARG* 5.9 0.4 - - - +
210A VAL 4.0 1.0 + - - -
211A LEU* 3.3 32.1 - - + +
212A HIS 3.1 20.3 + - - -
235A LEU* 3.9 13.1 - - - +
236A PHE* 1.3 91.4 - + - +
238A LEU* 1.3 59.0 + - - +
239A GLU* 3.1 33.8 + - + +
260A PRO 3.4 11.2 - - - +
262A ALA* 3.4 18.2 - - + +
284A TYR* 3.5 42.8 - + + -
286A ARG* 3.6 30.3 - - - -
313A GLY* 3.9 7.6 - - - -
340A ILE* 3.4 32.1 - - + -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 5.3 1.3 - - + -
212A HIS* 3.5 20.0 - - + -
214A VAL* 3.7 25.6 - - + -
223A ALA 4.6 2.9 - - - +
226A LEU* 4.2 16.2 - - + -
227A GLY* 4.0 31.0 - - - +
230A VAL* 4.6 2.7 - - + -
235A LEU* 4.0 16.8 - - + -
237A TRP* 1.3 72.8 - - - +
239A GLU* 1.3 60.4 + - - +
240A ASP 4.2 0.2 + - - -
241A CYS* 3.8 20.3 - - - -
259A THR* 3.9 11.9 - - + -
260A PRO 2.9 13.9 + - - +
261A LEU* 3.4 15.1 - - + +
262A ALA 3.0 20.6 + - - +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 4.0 3.5 + - - -
149A ARG* 4.9 4.3 + - - -
212A HIS 2.9 12.6 + - - +
213A ASP* 2.9 31.5 + - - +
214A VAL* 2.8 30.0 + - - +
237A TRP* 3.1 30.9 + - + +
238A LEU* 1.3 71.8 - - - +
240A ASP* 1.3 77.7 + - - +
241A CYS 3.3 3.2 + - - -
262A ALA* 3.3 10.8 - - + +
265A GLU* 2.9 26.7 - - - +
286A ARG* 3.0 29.3 + - - +
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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