Contacts of the strand formed by residues 224 - 229 (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 THR 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TRP* 3.4 8.9 - - - +
219A ASN* 2.8 42.8 + - - +
222A THR* 2.9 23.0 + - - +
223A ASP* 1.3 79.8 - - - +
225A LEU* 1.3 59.3 + - - +
226A VAL 3.5 0.3 + - - -
277A SER* 3.4 10.4 - - - +
280A TYR* 3.4 37.5 - - + -
289A PHE* 3.8 29.8 - - + -
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Residues in contact with LEU 225 (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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188A GLY* 5.6 0.4 - - - -
216A ARG* 3.2 48.5 - - + +
217A LEU 3.5 15.9 - - - +
218A TRP* 3.8 27.7 - - + -
224A THR* 1.3 71.1 - - - +
226A VAL* 1.3 58.1 + - - +
227A ALA 3.6 15.5 - - - +
228A ILE* 3.9 14.8 - - + -
289A PHE* 3.5 13.2 - - - +
291A SER* 2.7 39.2 + - - +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 4.6 6.3 - - + -
217A LEU* 2.7 25.9 + - + +
218A TRP 4.1 2.9 - - - +
219A ASN* 3.9 19.7 - - + +
224A THR 4.2 0.2 - - - +
225A LEU* 1.3 71.3 - - - +
227A ALA* 1.3 57.3 + - - +
270A MET* 4.2 9.2 - - + -
273A ALA* 3.8 34.1 - - + +
274A ILE* 3.8 15.9 - - + +
277A SER* 3.7 25.4 - - - +
289A PHE* 4.2 9.5 - - - -
291A SER* 3.6 1.6 - - - -
292A GLN* 2.9 24.5 + - - +
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Residues in contact with ALA 227 (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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216A ARG* 3.4 3.6 - - - -
217A LEU* 3.0 27.5 + - + +
225A LEU* 3.5 6.5 - - - +
226A VAL* 1.3 81.5 - - - +
228A ILE* 1.3 63.0 + - - +
229A PHE* 3.9 14.8 - - + -
270A MET* 3.9 34.5 - - + -
291A SER* 4.6 0.7 - - - -
292A GLN* 3.3 14.8 - - + +
294A ILE* 4.2 3.8 - - + -
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Residues in contact with ILE 228 (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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214A ALA* 4.0 22.7 - - + -
215A LEU 3.5 5.2 - - - +
216A ARG* 4.0 25.6 - - + +
225A LEU* 3.9 27.4 - - + -
227A ALA* 1.3 77.4 - - - +
229A PHE* 1.3 64.5 + - - +
230A GLY* 3.8 5.1 + - - +
291A SER* 4.3 6.5 - - - -
292A GLN 2.8 8.1 + - - +
293A LYS* 3.7 30.6 - - + +
294A ILE* 2.8 28.1 + - - +
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Residues in contact with PHE 229 (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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207A LEU* 4.5 8.3 - - + -
213A HIS 4.4 0.5 - - - +
214A ALA* 3.4 6.9 - - - -
215A LEU* 2.9 61.1 + - + +
217A LEU* 3.9 19.7 - - + -
227A ALA* 3.9 14.4 - - + -
228A ILE* 1.3 71.0 - - - +
230A GLY* 1.3 57.2 + - - +
235A HIS 5.7 0.2 + - - -
251A ILE* 4.6 3.8 - - + -
263A TRP* 3.5 56.2 - + + -
264A ARG 5.2 1.6 - - - -
265A ILE* 4.0 17.7 - - + -
270A MET* 4.0 28.0 - - + -
294A ILE* 3.5 27.8 - - + -
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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