Contacts of the strand formed by residues 222 - 226 (chain A) in PDB entry 3BU0
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 SER 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.2 36.6 - - - -
70A THR 3.5 7.6 - - - -
71A VAL* 4.1 5.2 - - - +
72A LEU* 4.7 0.9 - - - -
186A SER 3.8 0.7 + - - +
187A VAL* 3.3 11.4 - - - +
188A SER* 3.2 30.1 + - - -
218A LEU* 3.8 5.2 - - - +
219A ALA* 2.8 29.3 + - - -
220A HIS 3.4 0.2 - - - -
221A GLY* 1.3 79.4 - - - +
223A LEU* 1.3 60.2 + - - +
224A LEU 4.3 0.4 + - - -
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Residues in contact with LEU 223 (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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57A TRP* 3.8 26.2 - - + -
68A SER 3.6 1.2 - - - +
69A TYR* 3.4 7.9 - - - -
70A THR* 2.7 39.0 + - + +
72A LEU* 3.7 36.5 - - + +
145A VAL* 4.4 7.0 - - + -
148A VAL* 4.8 1.6 - - + -
149A THR* 4.3 14.8 - - + -
185A ALA* 3.8 28.5 - - + -
186A SER 3.4 11.2 - - - +
187A VAL* 3.9 11.0 - - + -
222A SER* 1.3 75.3 - - - +
224A LEU* 1.3 68.8 + - - +
225A MET* 4.2 4.7 - - + -
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Residues in contact with LEU 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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60A ILE* 4.6 1.1 - - + -
67A SER* 4.1 16.2 - - - -
68A SER 3.3 19.7 - - - +
69A TYR* 4.2 6.5 - - + -
184A ILE 3.6 2.4 - - - +
185A ALA* 3.7 0.7 - - - -
186A SER* 2.8 49.5 + - - +
195A PHE* 3.7 36.6 - - + -
197A PHE* 4.5 3.1 - - + -
216A LEU* 3.8 21.8 - - + -
218A LEU* 4.2 21.5 - - + -
222A SER* 5.2 0.4 + - - -
223A LEU* 1.3 74.1 - - - +
225A MET* 1.3 64.0 + - - +
226A MET* 3.9 20.4 + - + +
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Residues in contact with MET 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.8 26.7 - - + -
67A SER* 3.2 9.7 - - - -
68A SER* 2.7 45.2 + - - +
149A THR* 3.6 31.4 - - + +
151A GLN* 4.4 5.2 - - + -
153A PHE* 4.6 6.1 - - + -
183A PRO* 3.7 33.7 - - + -
184A ILE 3.5 2.7 - - - +
185A ALA* 3.8 24.2 - - - -
223A LEU* 4.2 6.5 - - + -
224A LEU* 1.3 71.9 - - - +
226A MET* 1.3 62.0 + - - +
227A ASN* 3.8 12.2 + - - +
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Residues in contact with MET 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.6 17.7 - - - +
173A ASP* 4.7 7.0 - - - +
182A SER 4.6 1.0 - - - +
183A PRO* 3.4 2.8 - - - +
184A ILE* 2.8 65.3 + - + +
186A SER* 4.2 22.4 - - - -
195A PHE* 4.3 16.8 - - + -
197A PHE* 4.0 25.1 - - + -
224A LEU* 4.1 9.6 - - + -
225A MET* 1.3 71.6 - - - +
227A ASN* 1.3 65.9 + - - +
230A THR* 4.5 4.9 - - + -
231A ASN* 4.2 16.5 - - - +
236A HIS* 4.5 13.7 - - + +
252A THR* 5.0 4.0 - - + -
301A AKG 5.7 2.5 - - + +
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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