Contacts of the helix formed by residues 58 - 66 (chain A) in PDB entry 6BAA
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 ASP 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ARG 3.4 13.2 + - - +
55A PHE* 4.0 3.8 - - - +
56A LEU 3.1 3.9 - - - -
57A GLN* 1.3 73.8 - - - +
59A VAL* 1.3 55.2 + - - +
60A PHE* 4.1 1.7 + - - +
61A THR* 2.6 41.5 + - - +
62A THR* 2.7 30.0 + - - +
173B GLN 5.7 0.2 - - - +
176B ARG* 4.1 30.0 - - + +
177B ARG* 3.1 29.0 + - - +
180B THR* 5.6 2.5 - - + -
206B ARG* 5.6 3.7 - - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 2.9 22.9 - - - +
57A GLN* 2.8 15.3 + - - +
58A ASP* 1.3 72.2 - - - +
60A PHE* 1.3 78.1 + - + +
62A THR* 3.2 7.3 - - - -
63A LEU* 2.8 46.6 + - + +
46E ILE* 6.0 7.0 - - + -
49E ILE* 4.2 15.0 - - + +
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Residues in contact with PHE 60 (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 GLN 5.8 0.4 - - - -
58A ASP* 3.4 1.7 + - - +
59A VAL* 1.3 88.6 - - + +
61A THR* 1.3 63.1 + - - +
62A THR 3.1 1.6 - - - -
63A LEU* 3.9 11.1 - - + +
64A VAL* 3.0 32.2 + - - +
162A ILE* 3.3 37.0 - - + -
166A CYS* 3.7 18.8 - - - -
169A MET* 4.3 4.7 - - + -
68B TRP* 3.9 37.0 - + - -
170B LYS 5.2 1.8 - - - -
171B THR* 3.7 41.5 - - + +
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Residues in contact with THR 61 (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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58A ASP* 2.6 38.2 + - - +
60A PHE* 1.3 76.7 - - - +
62A THR* 1.3 54.1 + - - +
64A VAL* 3.5 4.5 + - - +
65A ASP* 2.8 50.6 + - - +
174B ALA* 5.5 5.0 - - - +
177B ARG* 4.1 24.7 - - + +
208B SER* 5.0 0.9 - - - +
291B VAL* 5.2 0.5 - - - +
293B THR* 3.4 27.4 + - + +
294B THR* 4.8 10.0 - - - +
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Residues in contact with THR 62 (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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55A PHE* 3.6 20.7 + - + +
56A LEU* 5.2 4.2 - - + -
58A ASP* 2.7 19.3 + - - +
59A VAL* 3.2 11.0 - - - -
61A THR* 1.3 77.7 - - - +
63A LEU* 1.3 65.0 + - - +
65A ASP* 3.0 19.2 + - + +
66A LEU* 3.0 24.8 + - + +
49E ILE* 3.5 32.8 - - + +
53E SER* 5.4 7.2 - - - -
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Residues in contact with LEU 63 (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 VAL* 2.8 38.0 + - + +
60A PHE* 3.9 11.4 - - + +
61A THR 3.4 0.2 - - - -
62A THR* 1.3 72.6 - - - +
64A VAL* 1.3 63.5 + - - +
66A LEU* 3.2 21.2 + - + +
71A THR* 3.7 16.2 + - + +
74A ILE* 3.6 28.0 - - + -
75A PHE* 4.9 11.4 - - + -
162A ILE* 5.4 2.0 - - + -
166A CYS* 3.5 34.5 - - + -
170A LYS* 4.0 2.2 + - - +
49E ILE* 3.3 30.7 - - + -
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Residues in contact with VAL 64 (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 PHE 3.0 18.3 + - - +
61A THR* 3.7 6.1 - - - +
63A LEU* 1.3 77.6 - - + +
65A ASP* 1.3 60.0 + - - +
166A CYS* 4.2 9.4 - - + +
169A MET* 3.6 47.8 - - + +
170A LYS* 2.9 30.3 + - - +
173A GLN* 3.0 42.0 - - + +
293B THR* 4.2 9.4 - - - +
294B THR* 5.5 1.3 - - + -
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Residues in contact with ASP 65 (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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61A THR* 2.8 38.8 + - - +
62A THR* 3.0 11.5 + - + +
64A VAL* 1.3 76.0 - - - +
66A LEU* 1.3 65.4 + - + +
67A LYS* 3.7 2.3 + - - +
173A GLN* 5.0 2.7 - - - +
208B SER* 4.7 10.2 + - - -
292B GLU* 5.2 0.5 - - - +
293B THR* 2.7 31.9 - - - +
56E SER* 6.0 1.6 - - - -
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Residues in contact with LEU 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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62A THR* 3.0 27.4 + - + +
63A LEU* 3.2 23.0 + - + +
65A ASP* 1.3 81.9 - - + +
67A LYS* 1.3 65.3 + - - +
70A HIS* 4.4 13.0 - - + +
71A THR* 4.0 4.5 - - - +
74A ILE* 3.3 34.1 - - + -
170A LYS* 2.6 31.0 + - - -
48E PHE 5.9 0.2 - - - +
49E ILE* 4.5 10.5 - - + +
52E GLY* 4.3 28.0 - - - +
53E SER* 4.6 4.3 - - - +
56E SER* 5.1 8.1 - - - +
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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