Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 5H15
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASN* 2.9 23.9 + - - +
209A VAL* 3.6 32.5 - - + +
210A SER 2.9 13.0 + - - +
213A HIS 3.4 32.8 - - - +
214A ALA 3.9 10.1 - - - +
215A LEU* 4.2 3.6 - - + -
235A HIS* 3.6 20.6 - - + -
238A GLU* 1.3 70.8 - - - +
240A LEU* 1.3 59.3 + - - +
241A SER 3.8 9.6 - - - +
253A SER* 4.1 14.8 - - - -
254A CYS 3.4 16.6 - - - +
255A GLY* 4.3 0.7 - - - -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASN* 3.7 16.8 - - - +
195A GLU* 3.9 1.6 - - - +
209A VAL* 3.9 2.9 - - - -
238A GLU* 3.6 5.1 + - + +
239A VAL* 1.3 73.9 - - - +
241A SER* 1.3 59.9 + - - +
254A CYS 3.0 6.3 + - - -
255A GLY* 4.1 1.1 - - - -
256A MET* 3.6 31.9 - - + +
308A TYR* 4.2 7.0 - - + -
309A VAL 3.7 24.0 - - - +
310A ASP* 3.9 12.1 - - + -
365A TYR* 3.7 31.0 - - + -
367A ARG* 2.8 26.2 + - - -
501A LQD 3.7 40.2 - - + -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU* 2.7 21.6 + - - -
209A VAL* 4.0 6.9 - - - +
239A VAL* 3.7 4.1 - - - +
240A LEU* 1.3 79.1 - - - +
242A ALA* 1.3 62.3 + - - +
253A SER* 3.5 0.7 - - - -
254A CYS* 3.0 40.5 + - - +
310A ASP 3.5 9.9 - - - -
311A CYS* 3.8 1.3 - - - -
312A VAL* 3.3 17.6 + - - +
313A ARG* 3.4 9.5 + - - -
367A ARG* 3.4 13.0 + - - -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU* 3.0 9.2 + - - +
197A LYS* 3.2 28.6 + - + +
207A LEU* 3.8 11.9 - - + -
209A VAL* 3.5 24.5 - - + +
215A LEU* 3.8 17.3 - - + -
241A SER* 1.3 76.1 + - - +
243A ASP* 1.3 62.2 + - - +
251A ILE* 4.1 0.9 - - + -
252A MET 3.1 13.9 - - - +
253A SER* 4.0 0.7 - - - -
312A VAL* 3.8 4.7 - - - -
313A ARG* 4.1 0.7 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LYS* 2.9 27.6 + - - +
207A LEU* 5.4 0.4 - - - -
242A ALA* 1.3 76.5 - - - +
244A TYR* 1.3 76.3 + - - +
251A ILE* 3.2 6.2 - - - -
252A MET 2.9 32.3 + - - +
312A VAL* 3.5 16.2 - - + +
313A ARG* 3.3 18.1 - - - +
314A TRP* 2.9 36.2 + - + +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LYS* 3.6 21.1 - - + +
198A PHE 3.4 17.5 - - - -
199A HIS* 3.3 45.8 - + - +
200A PRO* 3.8 11.4 - - + -
205A LEU 3.4 11.8 + - - -
207A LEU* 3.5 19.6 - - + +
217A LEU* 3.2 26.5 - - + +
243A ASP* 1.3 94.3 + - - +
245A ASP* 1.3 69.8 + - - +
248A GLY* 4.6 3.1 - - - -
250A LYS 3.4 6.3 - - - -
251A ILE* 3.7 20.2 - - + +
265A ILE* 3.7 16.2 - - + -
314A TRP* 3.4 2.1 - - - +
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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