Contacts of the helix formed by residues 53 - 63 (chain A) in PDB entry 1BQ2
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 ARG 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A HIS* 3.4 14.1 - - + +
52A LEU* 1.3 75.8 - - - +
54A SER* 1.3 71.1 + - - +
56A ILE* 4.5 1.1 - - - +
57A HIS* 3.1 41.5 + - - -
75A ASN* 2.7 29.3 + - - +
76A ASN* 4.3 16.9 + - - +
77A VAL* 3.5 18.4 - - - +
244A PHE* 3.4 31.4 - - + -
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Residues in contact with SER 54 (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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51A HIS* 4.0 9.0 + - - +
52A LEU 3.3 0.8 - - - -
53A ARG* 1.3 88.8 + - - +
55A ILE* 1.3 62.8 + - - +
57A HIS* 3.4 2.1 + - - +
58A GLU* 3.0 24.6 + - - +
77A VAL* 4.4 19.9 - - - +
79A ILE* 4.4 18.5 - - - +
176A PHE* 4.1 21.8 - - - -
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Residues in contact with ILE 55 (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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44A LEU* 4.9 5.6 - - + -
50A CYS* 5.4 4.5 - - + -
51A HIS 3.9 17.3 - - - +
52A LEU* 3.0 28.7 + - + +
54A SER* 1.3 75.4 - - - +
56A ILE* 1.3 64.0 + - + +
58A GLU* 3.3 5.3 + - - +
59A LEU* 3.0 22.5 + - - +
175A PRO 5.2 0.4 - - - +
176A PHE* 3.5 47.5 - - + -
179A ALA* 3.8 22.0 - - + +
180A SER* 3.7 31.9 + - - +
183A LEU* 4.9 5.4 - - + -
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Residues in contact with ILE 56 (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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52A LEU* 3.0 43.4 + - + +
53A ARG* 4.8 0.2 - - - -
55A ILE* 1.3 75.3 - - - +
57A HIS* 1.3 63.9 + - - +
59A LEU* 3.0 13.3 + - - +
60A LEU* 3.0 23.5 + - + +
183A LEU* 4.3 20.4 - - + -
244A PHE* 3.5 41.3 - - + +
247A PHE* 4.0 44.9 - - + +
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Residues in contact with HIS 57 (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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53A ARG* 3.1 34.9 + - - +
54A SER 3.9 1.3 - - - +
56A ILE* 1.3 78.8 - - - +
58A GLU* 1.3 60.9 + - - +
60A LEU* 4.2 1.1 - - - -
61A TRP* 3.3 7.8 + - - +
71A TYR* 2.7 53.6 + + + -
72A LEU* 3.3 4.9 - - + +
75A ASN* 3.3 29.4 + - + +
77A VAL* 3.7 32.5 - - + -
244A PHE* 3.3 39.6 - + + +
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Residues in contact with GLU 58 (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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54A SER 3.0 17.9 + - - +
55A ILE 3.4 3.5 - - - +
56A ILE 3.1 0.2 - - - -
57A HIS* 1.3 76.7 - - - +
59A LEU* 1.3 64.3 + - - +
61A TRP* 3.0 20.3 + - + +
62A PHE* 3.0 31.0 + - + -
72A LEU* 4.1 8.5 - - + +
77A VAL* 5.7 0.2 - - + -
79A ILE* 4.1 14.3 - - + +
80A TRP* 2.9 42.0 + - + +
176A PHE* 3.3 22.6 - - - -
180A SER* 4.3 11.6 + - - -
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Residues in contact with LEU 59 (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 ILE 3.0 12.1 + - - +
56A ILE 3.0 8.8 + - - +
58A GLU* 1.3 75.5 + - - +
60A LEU* 1.3 64.9 + - + +
62A PHE* 3.1 16.1 + - + +
63A LEU* 3.0 31.0 + - + +
98A TRP* 4.1 26.7 - - + -
180A SER* 3.7 30.7 - - - +
181A TYR* 6.3 0.4 - - + -
183A LEU* 3.5 29.4 - - + -
184A LEU* 4.0 18.4 - - + +
187A MET* 3.9 18.4 - - + -
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Residues in contact with LEU 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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56A ILE* 3.0 22.4 + - + +
57A HIS 4.5 0.2 - - - +
59A LEU* 1.3 76.1 - - + +
61A TRP* 1.3 62.8 + - - +
63A LEU* 3.5 6.9 + - + +
64A GLN* 3.3 29.4 + - + +
71A TYR* 4.0 24.0 - - + +
183A LEU* 6.1 0.7 - - + -
187A MET* 3.7 30.5 - - + -
239A ILE 5.8 0.4 - - - +
242A TYR* 3.8 25.1 - - + +
243A ARG* 3.9 2.2 - - - -
244A PHE* 3.7 30.7 - - + +
247A PHE* 4.6 6.5 - - + -
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Residues in contact with TRP 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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57A HIS 3.3 15.1 + - - +
58A GLU* 3.0 16.5 + - + +
60A LEU* 1.3 76.9 - - - +
62A PHE* 1.3 93.6 + + - +
64A GLN* 3.0 21.1 + - - +
66A ASP* 2.9 44.0 + - + +
67A THR* 3.9 10.3 - - - -
68A ASN 2.8 27.9 + - - -
71A TYR* 3.6 31.7 - + + -
72A LEU* 3.8 20.3 - - + +
80A TRP* 3.5 31.4 - + - -
90A LEU* 3.4 33.2 - - + -
93A VAL* 5.0 5.8 - - + -
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Residues in contact with PHE 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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58A GLU* 3.0 38.8 + - + -
59A LEU* 3.3 17.5 - - + +
61A TRP* 1.3 104.0 - + - +
63A LEU* 1.3 58.5 + - - +
65A GLY* 2.8 20.6 + - - -
66A ASP 4.6 1.1 - - - -
80A TRP* 4.1 3.4 - + - -
93A VAL* 5.7 0.7 - - + -
94A TYR* 3.6 49.1 - + + -
95A GLY* 3.4 21.7 - - - +
98A TRP* 3.7 39.5 - + + -
99A ARG* 4.1 2.4 - - - +
147A HIS* 5.8 5.6 - + - -
180A SER* 5.0 8.3 - - - -
181A TYR* 5.4 3.4 - + - -
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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 LEU* 3.0 24.0 + - + +
60A LEU* 3.9 9.9 - - + +
62A PHE* 1.3 77.0 - - - +
64A GLN* 1.3 65.3 + - - +
65A GLY 3.2 0.4 - - - -
98A TRP* 4.1 23.1 - - + -
99A ARG* 3.0 28.9 + - - -
112A ILE* 4.0 29.6 - - + -
184A LEU* 4.5 9.9 - - + -
187A MET* 3.9 24.9 - - + -
239A ILE* 3.9 27.6 - - + +
240A PHE* 3.5 11.6 - - + -
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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