Contacts of the helix formed by residues 59 - 75 (chain A) in PDB entry 3BA6
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU 4.5 0.5 - - - +
56A GLN* 3.2 31.4 + - - +
57A PHE 2.8 18.3 + - - +
58A GLU* 1.3 82.9 - - - +
60A LEU* 1.3 75.8 + - + +
62A VAL* 4.3 11.6 - - + +
63A ARG* 3.0 23.7 - - - +
246A LYS* 5.1 6.8 + - - -
312A PRO* 4.0 21.2 - - + +
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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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59A ASP* 1.3 82.6 - - + +
61A LEU* 1.3 82.1 + - + +
62A VAL 2.7 13.8 + - - -
63A ARG* 3.1 17.9 + - - +
64A ILE* 3.8 8.1 + - - +
246A LYS* 5.0 2.0 - - - +
253A LEU 5.0 0.4 - - - +
254A ASP* 3.0 57.9 - - - +
257A GLY* 4.9 2.0 - - - -
258A GLU* 4.7 7.9 - - + +
311A LEU* 6.2 1.6 - - + -
312A PRO* 3.6 24.0 - - + -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 1.3 97.5 - - + +
62A VAL* 1.3 60.1 + - - +
64A ILE* 4.1 13.7 - - + -
65A LEU* 4.0 6.4 + - - +
257A GLY* 3.4 39.9 - - - +
258A GLU* 5.1 1.3 - - - -
260A LEU* 5.8 0.2 - - + -
261A SER* 5.3 5.6 - - - -
307A ILE* 3.7 23.7 - - + +
308A PRO* 3.3 48.0 - - + +
309A GLU* 3.7 18.5 - - - +
311A LEU* 4.7 8.7 - - + -
312A PRO* 4.5 7.3 - - + +
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Residues in contact with VAL 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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56A GLN 4.2 13.2 - - - +
57A PHE* 3.6 41.5 - - + -
59A ASP* 4.3 20.6 - - + +
60A LEU 2.7 1.2 + - - -
61A LEU* 1.3 78.6 - - - +
63A ARG* 1.3 63.0 + - - +
64A ILE 3.1 1.6 - - - -
65A LEU 3.6 0.9 + - - +
66A LEU* 2.9 27.0 + - + +
98A LEU* 4.0 20.1 - - + +
309A GLU 3.8 22.2 - - - +
312A PRO* 4.4 10.3 - - + -
313A ALA* 6.6 0.4 - - + -
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Residues in contact with ARG 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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58A GLU* 3.1 56.7 + - - +
59A ASP 3.0 19.9 + - - +
60A LEU* 3.1 5.8 + - - +
62A VAL* 1.3 76.4 - - - +
64A ILE* 1.3 60.7 + - + +
66A LEU* 3.1 20.7 - - + +
67A LEU* 2.8 31.4 + - - +
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Residues in contact with ILE 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 LEU 4.0 12.6 - - - +
61A LEU* 4.2 12.3 - - + +
62A VAL 3.1 0.4 - - - -
63A ARG* 1.3 77.9 - - + +
65A LEU* 1.3 63.1 + - + +
67A LEU* 3.0 7.4 + - - +
68A ALA* 2.9 30.1 + - + +
261A SER* 5.4 10.5 - - - +
303A ALA* 5.7 6.7 - - + -
304A VAL* 5.9 1.1 - - + +
307A ILE* 3.4 33.2 - - + -
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Residues in contact with LEU 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 LEU 4.0 2.9 - - - +
62A VAL 3.6 4.2 + - - +
63A ARG 3.5 0.2 - - - -
64A ILE* 1.3 83.7 - - + +
66A LEU* 1.3 63.4 + - - +
68A ALA* 3.9 5.4 - - - -
69A ALA* 3.4 8.3 + - - +
94A ILE* 3.1 31.3 - - + +
97A ILE* 4.5 4.0 - - + -
98A LEU* 4.2 18.1 - - + +
304A VAL* 3.5 42.0 - - + -
307A ILE* 3.6 32.8 - - + -
309A GLU* 3.0 42.8 - - + +
796A ASN* 4.1 2.2 - - - +
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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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57A PHE* 4.0 33.4 - - + -
62A VAL 2.9 16.4 + - - +
63A ARG* 3.1 29.6 - - + +
64A ILE 3.0 0.2 - - - -
65A LEU* 1.3 77.3 - - - +
67A LEU* 1.3 61.0 + - - +
69A ALA* 3.4 17.2 + - - +
70A CYS* 3.6 11.1 + - - -
95A LEU* 5.1 10.9 - - + +
98A LEU* 4.0 19.0 - - + +
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Residues in contact with LEU 67 (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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63A ARG 2.8 18.4 + - - +
64A ILE* 3.7 4.5 - - - +
66A LEU* 1.3 69.0 - - - +
68A ALA* 1.3 57.0 + - - +
69A ALA 2.9 5.2 - - - -
70A CYS* 2.7 44.3 + - + +
71A ILE* 3.2 22.7 + - + +
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Residues in contact with ALA 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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64A ILE* 2.9 18.5 + - + +
65A LEU 4.0 4.0 - - - +
67A LEU* 1.3 75.6 - - - +
69A ALA* 1.3 58.4 + - - +
71A ILE* 3.1 29.0 - - - +
72A SER* 3.5 11.1 + - - -
94A ILE* 3.9 5.8 - - + +
300A VAL* 3.9 13.3 - - + +
304A VAL* 3.3 34.1 - - + -
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Residues in contact with ALA 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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65A LEU 3.4 9.2 + - - +
66A LEU 3.4 12.2 + - - +
67A LEU 2.9 1.0 - - - -
68A ALA* 1.3 78.7 - - - +
70A CYS* 1.3 63.7 + - - +
72A SER* 3.5 4.1 + - - -
73A PHE* 3.0 22.2 + - - +
91A PRO* 4.1 12.5 - - + +
94A ILE* 4.0 17.2 - - + +
95A LEU* 3.5 30.3 - - + -
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Residues in contact with CYS 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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66A LEU* 4.0 12.3 - - - -
67A LEU* 2.7 32.5 + - + +
69A ALA* 1.3 73.4 - - - +
71A ILE* 1.3 57.4 + - + +
73A PHE* 2.8 24.3 + - - +
74A VAL* 2.9 20.4 + - + +
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Residues in contact with ILE 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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67A LEU* 3.2 22.9 + - + +
68A ALA* 3.1 17.5 - - - +
70A CYS* 1.3 77.1 - - + +
72A SER* 1.3 71.7 + - - +
74A VAL* 2.9 11.8 + - + +
75A LEU* 2.8 40.1 + - + +
296A PHE* 4.1 20.0 - - + -
300A VAL* 3.5 42.8 - - + -
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Residues in contact with SER 72 (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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68A ALA 3.5 14.7 + - - -
69A ALA* 3.7 5.4 - - - -
70A CYS 3.3 0.4 - - - -
71A ILE* 1.3 83.5 - - - +
73A PHE* 1.3 56.7 + - - +
75A LEU* 4.2 11.0 - - - +
76A ALA* 3.4 21.5 + - - +
87A ALA 3.4 8.7 - - - +
90A GLU* 4.0 33.4 + - - +
91A PRO* 3.6 6.7 - - - +
94A ILE* 4.9 5.2 - - - +
297A LYS* 4.9 8.1 + - - +
300A VAL* 5.3 4.7 - - - +
793A LEU* 5.2 2.6 - - - +
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Residues in contact with PHE 73 (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 ALA 3.0 12.9 + - - +
70A CYS* 2.8 15.5 + - - +
72A SER* 1.3 78.7 - - - +
74A VAL* 1.3 64.2 + - + +
76A ALA* 4.0 3.9 - - - +
77A TRP* 3.5 40.0 + + - +
88A PHE* 3.7 32.3 - + - -
91A PRO* 4.1 14.1 - - + -
92A PHE* 6.4 1.3 - + - -
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Residues in contact with VAL 74 (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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70A CYS* 3.1 20.9 - - + +
71A ILE* 2.9 8.7 + - - +
73A PHE* 1.3 81.0 - - + +
75A LEU* 1.3 64.7 + - + +
76A ALA 3.1 1.8 - - - -
77A TRP* 3.0 20.7 + - + +
78A PHE* 3.0 38.1 + - + -
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Residues in contact with LEU 75 (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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71A ILE* 2.8 25.2 + - + +
72A SER* 4.4 5.6 - - - +
74A VAL* 1.3 82.8 - - + +
76A ALA* 1.3 62.0 + - - +
78A PHE* 3.5 11.3 + - + +
79A GLU* 3.3 25.8 + - - +
293A ILE* 4.3 19.5 - - + -
296A PHE* 4.1 21.8 - - + -
297A LYS* 3.3 47.1 - - + +
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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