Contacts of the strand formed by residues 223 - 229 (chain A) in PDB entry 3U78
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 LEU 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A VAL* 3.8 21.5 - - + -
195A ILE 3.2 12.3 - - - +
196A ASP* 3.8 16.6 - - + +
203A SER* 5.6 2.7 - - - +
205A MET* 4.5 13.9 - - + -
210A TYR* 2.7 27.3 + - + -
213A TYR* 2.8 50.1 + - + -
221A LYS* 3.9 23.6 - - + -
222A VAL* 1.3 82.4 - - - +
224A ASN* 1.3 55.3 + - - +
274A VAL* 3.8 11.8 + - - +
277A SER* 4.2 3.1 - - - -
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Residues in contact with ASN 224 (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 VAL* 3.4 8.0 - - - +
195A ILE* 2.8 46.3 + - + +
197A VAL* 4.0 9.8 - - + +
210A TYR* 4.1 0.7 - - - -
223A LEU* 1.3 73.6 - - - +
225A VAL* 1.3 68.7 + - - +
226A ILE* 3.3 14.6 - - - +
272A MET 3.3 1.7 - - - +
273A GLY* 3.2 20.1 - - - -
277A SER* 3.4 25.9 - - - -
278A TYR 4.4 5.3 + - - +
279A THR* 3.8 6.9 + - - -
299A LYS* 5.1 2.3 + - - -
358A THR* 4.3 3.7 + - - -
701A AKG 3.2 25.3 + - - -
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Residues in contact with VAL 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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192A ILE* 3.9 16.8 - - + -
193A ASP 4.1 10.8 - - - +
194A VAL* 4.1 6.1 - - + -
210A TYR* 3.6 38.6 - - + -
224A ASN* 1.3 77.3 + - - +
226A ILE* 1.3 62.3 + - - +
227A SER 4.5 0.2 - - - +
228A LEU* 3.8 30.3 - - + +
270A CYS 4.2 2.9 - - - +
271A LEU* 3.2 7.6 - - - +
272A MET* 2.8 53.5 + - + +
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Residues in contact with ILE 226 (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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193A ASP 4.9 1.0 + - - -
195A ILE* 3.8 24.2 - - + +
224A ASN* 3.3 32.7 + - - +
225A VAL* 1.3 77.2 - - - +
227A SER* 1.3 70.6 + - - +
228A LEU 3.7 2.0 - - - -
269A TYR* 4.4 9.8 - - - +
270A CYS 4.8 0.4 - - - -
271A LEU* 4.1 24.8 - - + +
279A THR* 4.0 13.5 - - + +
292A TYR* 5.2 1.7 + - - -
701A AKG 3.4 40.4 - - - +
707A E67 4.1 23.1 - - + +
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Residues in contact with SER 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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193A ASP* 4.7 24.8 + - - -
225A VAL* 3.7 1.0 - - - +
226A ILE* 1.3 93.5 + - - +
228A LEU* 1.3 60.2 + - - +
229A GLU* 2.9 9.8 + - - +
269A TYR* 3.3 17.3 - - - -
395A LYS* 3.5 30.5 + - - -
707A E67 5.2 3.6 - - - +
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Residues in contact with LEU 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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182A VAL* 4.5 10.1 - - + -
186A VAL* 4.5 10.1 - - + -
190A LYS* 3.5 34.8 - - + +
192A ILE* 4.2 16.4 - - + -
193A ASP 6.3 0.2 - - - +
207A LEU* 4.2 26.2 - - + -
225A VAL* 3.8 13.1 - - + +
226A ILE 3.7 1.6 - - - -
227A SER* 1.3 74.7 - - - +
229A GLU* 1.3 64.3 + - - +
230A PHE* 3.6 7.1 + - + -
269A TYR* 3.7 3.5 - - - -
270A CYS* 2.9 45.0 + - + +
272A MET* 4.3 15.5 - - + -
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Residues in contact with GLU 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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190A LYS* 4.1 12.0 + - - +
227A SER 2.9 7.6 + - - +
228A LEU* 1.3 78.4 - - - +
230A PHE* 1.3 58.6 + - - +
231A SER* 2.7 46.5 + - - -
232A ASP* 4.3 9.0 - - - +
233A THR* 5.2 0.3 - - - +
265A PHE* 3.3 29.6 - - - +
266A VAL* 4.0 1.1 - - - -
267A GLN 3.4 6.4 + - - -
268A LYS 3.2 35.2 + - - +
269A TYR* 3.5 25.1 - - + -
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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