Contacts of the strand formed by residues 65 - 71 (chain A) in PDB entry 3BUC
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE* 4.1 23.6 - - + -
61A ARG* 3.4 10.9 - - - +
62A ALA* 2.9 35.8 + - + +
64A GLY* 1.3 77.5 - - - +
66A ASP* 1.3 65.6 + - - +
67A SER* 4.1 12.1 - - - +
197A PHE* 4.3 14.1 - - + -
214A VAL* 4.0 17.5 - - + -
230A THR* 3.7 18.6 - - + +
234A TRP* 3.6 54.3 - - + +
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Residues in contact with ASP 66 (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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59A HIS* 5.8 1.4 + - - -
60A ILE 3.9 1.6 - - - -
61A ARG* 4.3 18.1 + - + +
64A GLY 4.1 0.6 - - - -
65A LEU* 1.3 75.0 - - - +
67A SER* 1.3 66.4 + - - +
227A ASN* 2.8 39.0 + - + -
228A HIS 3.9 19.1 - - - +
229A PRO* 4.6 3.4 - - + -
230A THR* 2.6 29.9 + - - +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 3.5 4.9 + - - +
60A ILE* 2.7 48.5 + - - +
61A ARG* 5.3 0.7 + - - +
65A LEU* 4.1 5.8 - - - -
66A ASP* 1.3 78.6 + - - +
68A SER* 1.3 60.4 + - - +
197A PHE* 4.0 5.6 - - - -
224A LEU* 4.5 10.5 - - - -
225A MET 3.0 17.6 + - - -
226A MET* 3.6 17.5 - - - +
227A ASN* 3.5 4.7 - - - +
230A THR* 3.7 9.5 - - - +
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Residues in contact with SER 68 (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* 3.5 22.5 - - - -
58A ARG 3.3 6.7 - - - -
59A HIS* 3.7 24.7 - - - -
60A ILE* 5.2 0.2 - - - -
67A SER* 1.3 79.3 - - - +
69A TYR* 1.3 60.7 + - - +
223A LEU 3.6 1.0 - - - +
224A LEU* 3.4 6.2 - - - +
225A MET* 2.8 51.3 + - - +
227A ASN* 4.3 4.6 + - - -
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Residues in contact with TYR 69 (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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56A SER 4.1 0.7 - - - +
57A TRP* 3.5 3.2 - - - -
58A ARG* 2.9 49.5 + - + +
60A ILE* 5.0 1.8 - - + -
68A SER* 1.3 75.9 - - - +
70A THR* 1.3 64.7 + - - +
71A VAL* 4.5 16.4 - - + +
216A LEU* 4.0 17.0 - - + -
217A PRO 4.0 11.3 + - - -
218A LEU* 3.8 26.7 - - + -
219A ALA* 3.2 32.4 + - - +
222A SER* 3.3 30.0 - - - -
223A LEU 3.3 12.3 - - - -
224A LEU* 4.1 9.6 - - + -
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Residues in contact with THR 70 (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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56A SER 3.0 22.9 + - - -
57A TRP* 3.5 37.8 - - + -
69A TYR* 1.3 81.5 - - - +
71A VAL* 1.3 74.9 + - - +
72A LEU* 4.3 13.9 - - + -
148A VAL* 5.4 1.1 - - + -
222A SER* 3.4 4.7 - - - -
223A LEU* 2.8 44.1 + - + -
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Residues in contact with VAL 71 (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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69A TYR* 4.5 20.6 - - + +
70A THR* 1.3 85.5 + - - +
72A LEU* 1.3 60.7 + - - +
73A PHE 3.5 22.4 - - - +
74A GLY* 5.7 0.2 - - - -
219A ALA* 5.7 3.6 - - + -
220A HIS 4.5 6.5 - - - +
221A GLY 3.7 13.2 - - - +
222A SER* 4.3 1.1 - - - +
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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