Contacts of the strand formed by residues 239 - 244 (chain B) in PDB entry 5GSA
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ASN* 3.0 19.4 + - - -
209B VAL* 3.4 30.0 - - + +
210B SER 2.8 18.4 + - - +
213B HIS 3.4 35.0 - - - +
214B ALA 3.8 8.5 - - - +
215B LEU* 3.9 15.3 - - + -
235B HIS* 3.8 23.6 - - + -
238B GLU* 1.3 71.5 - - - +
240B LEU* 1.3 59.2 + - - +
241B SER 3.8 8.5 - - - +
253B SER* 4.1 2.0 - - - -
254B CYS 3.4 15.7 - - - +
255B GLY* 4.3 0.9 - - - -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ASN* 3.3 20.3 - - - +
195B GLU* 4.3 1.4 - - - +
209B VAL* 3.6 3.7 - - - +
238B GLU* 4.2 6.5 - - + +
239B VAL* 1.3 75.9 - - - +
241B SER* 1.3 56.9 + - - +
254B CYS 2.7 9.5 + - - +
255B GLY* 3.7 2.7 - - - -
256B MET* 3.6 37.2 - - + +
308B TYR* 4.1 9.9 - - + -
309B VAL 3.2 32.5 - - - +
310B ASP* 3.7 17.5 - - + +
364B TRP* 5.7 1.8 - - + -
365B TYR* 3.5 37.5 - - + +
501B 73K 3.2 24.4 - - + -
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 2.7 24.8 + - - -
209B VAL* 3.7 7.8 - - - +
239B VAL* 3.8 5.0 - - - +
240B LEU* 1.3 79.8 - - - +
242B ALA* 1.3 65.9 + - - +
253B SER* 3.4 1.0 - - - -
254B CYS* 3.0 35.4 + - - +
310B ASP 3.8 2.7 - - - -
311B CYS* 3.6 25.3 - - - -
312B VAL* 3.4 7.9 + - - -
313B ARG* 3.0 15.6 + - - -
367B ARG* 5.3 0.6 - - - -
501B 73K 5.1 0.4 - - - -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLU* 3.7 4.7 + - - +
197B LYS* 3.1 26.5 + - + +
207B LEU* 3.8 11.9 - - + -
209B VAL* 3.6 22.9 - - + +
215B LEU* 3.7 20.6 - - + -
241B SER* 1.3 78.0 + - - +
243B ASP* 1.3 62.2 + - - +
251B ILE* 4.2 1.6 - - + -
252B MET 3.2 13.2 - - - +
253B SER* 4.2 1.1 - - - -
312B VAL* 4.0 3.6 - - - -
313B ARG* 3.6 4.3 + - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LYS* 3.2 22.9 + - - +
207B LEU* 5.0 0.6 - - - +
242B ALA* 1.3 78.1 - - - +
244B TYR* 1.3 70.7 + - - +
251B ILE* 3.4 4.4 - - - +
252B MET 3.0 20.5 + - - +
312B VAL* 3.4 16.8 - - + +
313B ARG* 3.4 16.5 - - - +
314B TRP* 2.7 53.3 + - + +
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Residues in contact with TYR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LYS* 3.2 35.2 - - + +
198B PHE 3.5 13.2 - - - -
199B HIS* 3.4 39.7 - + - +
200B PRO* 3.9 10.8 - - + -
205B LEU 3.4 12.5 + - - -
207B LEU* 3.2 25.6 - - + +
217B LEU* 3.3 17.5 - - + +
243B ASP* 1.3 92.8 + - - +
245B ASP* 1.3 70.1 + - - +
248B GLY* 4.6 2.5 - - - -
250B LYS 3.3 9.6 - - - -
251B ILE* 3.7 28.0 - - + +
265B ILE* 4.0 10.1 - - + -
314B TRP* 3.3 3.0 - - - +
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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