Contacts of the strand formed by residues 237 - 239 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TYR* 3.6 20.8 - + - -
149B ARG* 5.9 0.4 - - - +
210B VAL 4.0 0.6 + - - -
211B LEU* 3.4 27.1 - - + +
212B HIS 3.2 21.2 + - - +
235B LEU* 3.2 13.4 - - - +
236B PHE* 1.3 91.7 - + - +
238B LEU* 1.3 59.3 + - - +
239B GLU* 3.2 32.3 + - + +
260B PRO 3.3 12.1 - - - +
262B ALA* 3.4 19.1 - - + +
284B TYR* 3.5 42.2 - + + -
286B ARG* 3.5 32.3 - - - -
313B GLY* 3.9 7.2 - - - -
340B ILE* 3.5 31.6 - - + -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 5.2 1.6 - - + -
212B HIS* 3.5 21.3 - - + +
214B VAL* 3.7 24.7 - - + -
223B ALA 4.6 2.0 - - - +
226B LEU* 4.1 17.0 - - + -
227B GLY* 4.0 32.1 - - - +
230B VAL* 4.6 2.2 - - + -
235B LEU* 4.0 17.3 - - + -
237B TRP* 1.3 72.9 - - - +
239B GLU* 1.3 59.8 + - - +
240B ASP 4.1 0.2 + - - -
241B CYS* 3.8 18.4 - - - -
259B THR* 3.9 12.6 - - + -
260B PRO 2.8 12.6 + - - +
261B LEU* 3.5 15.0 - - + +
262B ALA 2.9 20.8 + - - +
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Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 4.1 4.0 + - - -
149B ARG* 4.7 4.7 + - - -
212B HIS 2.9 11.7 + - - +
213B ASP* 3.0 31.9 - - - +
214B VAL* 2.8 30.0 + - - +
237B TRP* 3.2 30.9 + - + +
238B LEU* 1.3 72.2 - - - +
240B ASP* 1.3 76.8 + - - +
241B CYS 3.3 3.1 + - - -
262B ALA* 3.3 7.9 - - + +
265B GLU* 2.8 26.0 - - - +
286B ARG* 2.9 31.6 + - - +
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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