Contacts of the strand formed by residues 228 - 232 (chain A) in PDB entry 5HAN
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.1 28.5 - - + -
150A VAL* 3.6 33.0 - - + -
151A LEU* 4.0 32.8 - - + -
161A ILE* 4.6 5.2 - - + -
185A TRP* 3.2 12.1 + - - -
189A ASP 2.8 14.4 + - - +
190A PHE* 3.5 26.6 - - + -
191A ILE 3.0 22.7 + - - -
216A MET* 4.0 0.7 - - - -
227A LYS* 1.3 78.8 - - - +
229A PHE* 1.3 61.1 + - - +
257A ASP 4.9 0.4 - - - +
258A HIS* 3.3 19.7 - - - +
260A ALA* 6.5 0.2 - - + -
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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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177A PHE* 4.0 11.9 - + - -
181A CYS* 3.8 17.3 - - - -
185A TRP* 3.7 19.7 - + + -
190A PHE* 5.3 0.9 - - - -
191A ILE* 3.2 28.9 - - + -
192A KCX 4.2 0.7 - - - -
193A ASN* 4.0 28.3 - - - -
212A VAL* 3.6 15.9 - - + -
216A MET* 3.9 10.6 - - + +
228A LEU* 1.3 74.3 - - - +
230A SER* 1.3 86.8 + - - +
231A PHE* 3.4 48.6 + + + -
258A HIS 3.1 6.3 + - - -
259A ILE* 3.3 9.6 - - + +
260A ALA* 2.9 25.2 + - - +
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Residues in contact with SER 230 (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 PHE* 3.7 26.9 - - - -
191A ILE 2.8 11.0 + - - -
192A KCX 4.0 5.1 - - - +
193A ASN 2.9 26.3 + - - -
229A PHE* 1.3 75.4 - - - +
231A PHE* 1.3 60.3 + - - +
260A ALA* 3.3 13.5 - - - +
262A LEU* 3.7 11.1 + - - +
286A HIS* 3.0 30.9 + - - +
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Residues in contact with PHE 231 (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 ASN* 3.3 13.9 - - - -
205A PHE* 5.2 3.4 - + - -
208A THR* 5.2 3.6 - - + -
209A VAL* 3.8 27.4 - - + -
212A VAL* 3.8 16.8 - - + -
229A PHE* 3.4 36.3 - + - -
230A SER* 1.3 71.9 - - - +
232A ASN* 1.3 60.3 + - - +
233A ILE* 3.3 3.8 + - + +
248A ILE* 3.5 40.6 - - + -
252A PHE* 3.5 40.6 - + - -
259A ILE* 3.7 13.2 - - + -
260A ALA 2.9 9.9 + - - +
261A PHE* 3.5 5.8 - - + -
262A LEU* 2.7 28.5 + - - -
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Residues in contact with ASN 232 (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 ASN* 2.7 22.1 + - + +
195A GLU 3.4 21.0 + - - +
196A PRO 4.3 1.6 - - - -
197A GLN 2.9 30.9 + - - +
198A GLY* 5.0 0.5 - - - -
205A PHE* 4.3 8.3 - - - -
231A PHE* 1.3 69.7 - - - +
233A ILE* 1.3 63.5 + - - +
234A THR* 2.6 39.9 + - - +
244A ARG* 4.0 13.6 + - - +
262A LEU* 3.5 21.3 - - + +
264A ASP* 4.1 0.5 + - - +
92B ASP* 4.2 13.1 + - - -
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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