Contacts of the strand formed by residues 239 - 244 (chain H) in PDB entry 5LS6
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 VAL 239 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H ASN* 3.2 19.2 + - - +
209H VAL* 3.6 25.4 - - + +
210H SER 3.0 14.1 + - - +
213H HIS 3.6 30.1 - - - -
214H ALA 3.6 14.6 - - - +
215H LEU* 3.8 15.3 - - + -
235H HIS* 3.6 27.4 - - + -
237H ASP 3.3 0.4 + - - -
238H GLU* 1.3 68.5 - - - +
240H LEU* 1.3 60.0 + - - +
241H SER 3.8 7.9 - - - +
253H SER* 4.1 3.1 - - - -
254H CYS 3.6 16.2 - - - +
255H GLY* 4.3 1.3 - - - -
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Residues in contact with LEU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H ASN* 3.4 34.3 - - + +
195H GLU* 3.7 3.3 - - - +
209H VAL* 4.1 1.3 - - - -
238H GLU* 3.2 20.4 + - + +
239H VAL* 1.3 74.3 - - - +
241H SER* 1.3 60.2 + - - +
254H CYS 3.0 5.3 + - - -
255H GLY* 4.0 2.0 - - - -
256H MET* 4.1 15.9 - - + +
308H TYR* 4.2 9.9 - - + -
309H VAL 3.6 20.6 - - - +
310H ASP* 3.7 30.7 - - + +
364H TRP* 3.7 34.5 - - + -
365H TYR* 5.1 2.9 - - + -
367H ARG* 3.2 24.9 + - - +
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Residues in contact with SER 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H GLU* 2.5 25.1 + - - -
209H VAL* 4.1 8.1 - - - -
239H VAL* 3.7 3.8 - - - +
240H LEU* 1.3 80.3 - - - +
242H ALA* 1.3 70.7 + - - +
253H SER* 3.6 2.8 - - - -
254H CYS* 3.1 38.0 + - - +
310H ASP 3.5 17.7 - - - -
311H CYS* 3.7 3.3 - - - -
312H VAL* 3.5 4.5 + - - -
313H ARG* 3.1 19.1 + - - -
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Residues in contact with ALA 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H GLU* 4.0 3.9 + - - +
197H LYS* 2.7 35.1 + - + +
207H LEU* 4.0 12.1 - - + -
209H VAL* 3.7 23.8 - - + +
215H LEU* 4.0 13.0 - - + -
241H SER* 1.3 82.9 + - - +
243H ASP* 1.3 53.4 + - - +
251H ILE* 4.2 0.7 - - + -
252H MET 3.3 16.6 - - - +
253H SER* 4.0 0.9 - - - -
312H VAL* 3.7 8.1 - - - -
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Residues in contact with ASP 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H LYS* 3.7 19.4 - - - +
207H LEU* 5.4 0.4 - - - -
242H ALA* 1.3 72.5 - - - +
244H TYR* 1.3 92.4 + - - +
251H ILE* 3.5 7.6 - - - +
252H MET* 3.1 30.2 + - - +
312H VAL* 3.4 19.0 + - + +
313H ARG* 3.0 37.7 - - - +
314H TRP* 3.4 11.1 + - + +
374H GLN* 5.8 1.2 + - - -
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Residues in contact with TYR 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H LYS* 3.5 26.0 - - + -
198H PHE 3.4 25.4 - - - +
199H HIS* 3.7 29.3 - + - +
200H PRO* 3.8 20.2 - - + -
205H LEU 3.5 9.7 + - - -
207H LEU* 3.2 22.5 - - + +
217H LEU* 3.1 27.7 - - + +
243H ASP* 1.3 98.6 + - - +
245H ASP* 1.3 70.2 + - - +
248H GLY* 4.7 3.4 - - - -
250H LYS 3.6 6.5 - - - -
251H ILE* 4.2 15.0 - - + +
265H ILE* 3.9 15.3 - - + -
314H TRP* 3.3 7.7 - - - +
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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
------------------------------------------------------------
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