Contacts of the helix formed by residues 65 - 77 (chain A) in PDB entry 1BX4
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY* 1.3 69.5 - - - -
66A THR* 1.3 64.6 + - - +
68A ASN* 3.3 5.2 + - - +
69A SER* 3.1 23.5 + - - -
166A TYR* 4.8 4.3 + - - -
168A ALA* 4.3 7.8 - - - +
170A PHE* 3.8 36.0 - - - -
196A ASN* 5.5 2.1 + - - -
198A SER* 5.2 0.3 + - - -
300A ASP* 2.7 35.2 + - - -
350A ADN 3.2 17.9 + - - -
380A CL 4.1 2.2 - - - +
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Residues in contact with THR 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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11A GLY* 4.2 3.6 - - - -
12A MET 3.4 34.7 + - - +
65A SER* 1.3 76.4 + - - +
67A GLN* 1.3 63.9 + - - +
69A SER* 3.2 3.3 + - - -
70A ILE* 2.9 23.3 + - + +
86A PHE* 3.9 12.1 - - + -
166A TYR* 4.0 29.8 - - + +
168A ALA* 3.1 24.6 + - - +
380A CL 3.1 20.5 - - - +
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Residues in contact with GLN 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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14A ASN 5.6 0.4 + - - -
15A PRO* 4.1 13.9 - - + +
63A GLY 2.9 26.2 + - - +
64A GLY* 3.3 10.2 + - - +
65A SER 3.3 0.8 - - - -
66A THR* 1.3 78.9 - - - +
68A ASN* 1.3 61.5 + - - +
70A ILE* 3.3 3.9 + - + +
71A LYS* 3.0 56.7 + - + +
86A PHE* 3.5 40.1 - - + -
99A LEU* 4.4 16.5 + - - +
103A ALA* 4.5 3.6 - - + +
108A VAL* 6.5 0.4 - - + -
112A TYR* 2.6 30.6 + - - -
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Residues in contact with ASN 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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18A ASP* 5.1 0.4 + - - -
62A ALA 4.1 5.2 - - - +
63A GLY* 3.6 16.1 - - - -
64A GLY 2.9 14.7 + - - +
65A SER 3.5 7.6 - - - +
66A THR 3.3 0.2 - - - -
67A GLN* 1.3 77.3 - - - +
69A SER* 1.3 62.1 + - - +
71A LYS* 3.3 13.6 + - - +
72A VAL* 3.0 28.3 + - - +
297A GLY* 5.0 0.2 - - - -
300A ASP* 3.1 23.7 + - + +
335A GLY 5.7 0.2 - - - -
336A CYS* 3.7 33.5 - - - +
350A ADN 3.1 27.7 + - - -
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Residues in contact with SER 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 SER 3.1 9.9 + - - -
66A THR 3.2 7.4 + - - -
68A ASN* 1.3 79.3 - - - +
70A ILE* 1.3 57.2 + - - +
72A VAL* 3.4 1.2 + - - -
73A ALA* 2.9 25.5 + - - +
166A TYR* 3.9 25.5 + - - -
300A ASP* 2.8 37.1 + - - +
303A VAL* 3.9 8.8 - - - +
304A GLY* 3.3 17.3 - - - -
307A LEU* 5.0 2.0 - - - +
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Residues in contact with ILE 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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9A LEU* 4.0 28.3 - - + -
10A PHE 4.4 0.7 - - - +
11A GLY* 4.0 32.5 - - - +
66A THR* 2.9 25.6 + - + +
67A GLN* 3.8 6.5 - - + +
69A SER* 1.3 74.3 - - - +
71A LYS* 1.3 60.2 + - - +
73A ALA* 3.4 3.3 + - - +
74A GLN* 3.0 28.6 + - - +
84A ALA* 3.7 13.3 - - + +
85A THR 4.1 8.7 - - - +
86A PHE* 4.4 7.6 - - + -
108A VAL* 3.7 29.4 - - + -
166A TYR* 5.1 8.5 - - + -
307A LEU* 5.1 1.3 - - + -
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Residues in contact with LYS 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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62A ALA* 3.7 33.7 + - - +
67A GLN* 3.0 42.7 + - + +
68A ASN* 3.3 13.9 + - - +
70A ILE* 1.3 75.0 - - - +
72A VAL* 1.3 59.0 + - + +
74A GLN* 3.5 3.5 + - - +
75A TRP* 3.0 26.9 + - - +
99A LEU 5.1 0.8 + - - -
102A LYS* 4.0 24.7 - - - +
103A ALA* 4.1 11.8 - - - +
106A ALA* 3.9 22.0 - - + +
108A VAL* 4.1 13.2 - - + -
336A CYS* 5.9 4.7 - - + +
338A PHE* 4.3 13.5 - - + -
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Residues in contact with VAL 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 ASN 3.0 21.3 + - - +
69A SER 3.8 4.0 - - - +
71A LYS* 1.3 75.8 - - + +
73A ALA* 1.3 64.6 + - - +
75A TRP* 3.2 12.9 + - + +
76A MET* 3.1 24.8 + - + +
301A ALA* 3.7 41.1 - - + +
304A GLY* 4.2 2.2 - - - -
305A GLY 4.0 7.2 - - - +
326A ALA* 3.9 17.7 - - + -
330A ILE* 4.5 11.2 - - + -
336A CYS* 4.8 8.1 - - + +
338A PHE* 4.4 15.9 - - + -
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Residues in contact with ALA 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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9A LEU* 3.6 31.2 - - + -
69A SER 2.9 16.5 + - - +
70A ILE 3.7 3.8 - - - +
72A VAL* 1.3 75.8 - - - +
74A GLN* 1.3 64.3 + - - +
76A MET 3.2 2.1 + - - -
77A ILE* 3.0 30.7 + - + +
304A GLY* 3.4 23.1 + - - +
307A LEU* 4.5 2.5 - - + -
308A SER* 3.7 9.6 - - - +
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Residues in contact with GLN 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 ILE 3.0 17.1 + - - +
71A LYS 3.6 5.2 - - - +
73A ALA* 1.3 76.7 - - - +
75A TRP* 1.3 61.0 + - - +
77A ILE* 3.3 6.6 + - - +
78A GLN* 3.0 29.6 + - - +
80A PRO 3.0 24.8 + - - -
81A HIS* 3.7 10.5 - - - +
82A LYS 4.0 0.4 - - - -
83A ALA* 3.1 26.4 + - - +
84A ALA* 3.2 15.2 + - + +
106A ALA 3.3 23.1 - - - +
107A HIS* 3.5 20.0 + - + +
108A VAL* 4.0 8.7 - - + -
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Residues in contact with TRP 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 LYS 3.0 14.7 + - - +
72A VAL* 3.4 12.8 - - + +
73A ALA 3.2 0.2 - - - -
74A GLN* 1.3 77.8 - - - +
76A MET* 1.3 91.9 + - + +
78A GLN* 2.8 40.0 + - - +
106A ALA 5.4 0.6 + - - -
325A TYR* 4.2 14.6 - + - -
326A ALA* 5.0 3.8 - - + -
329A ILE* 4.3 11.9 - - + -
330A ILE* 4.9 4.9 - - + -
338A PHE* 3.3 51.1 - + + -
339A PRO* 3.0 45.2 + - + -
340A GLU 3.6 6.8 + - - -
342A PRO* 3.6 38.8 - - + +
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Residues in contact with MET 76 (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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72A VAL* 3.1 19.7 + - + +
73A ALA 3.7 1.1 - - - +
75A TRP* 1.3 93.6 - - + +
77A ILE* 1.3 65.5 + - - +
78A GLN* 4.3 4.7 - - - +
305A GLY* 4.4 10.8 - - - -
308A SER* 3.4 25.4 - - - +
309A GLN* 4.5 5.3 - - - +
322A ALA* 3.9 28.3 - - + +
325A TYR* 3.9 26.2 - - + -
326A ALA* 4.6 3.8 - - - -
342A PRO* 4.1 13.7 - - - +
344A PHE* 3.9 31.2 - - + -
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Residues in contact with ILE 77 (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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4A VAL 5.1 8.1 - - - +
8A ILE* 5.2 2.5 - - + -
9A LEU* 4.9 7.9 - - + -
73A ALA* 3.0 29.3 + - + +
74A GLN* 3.3 8.3 + - - +
76A MET* 1.3 77.2 - - - +
78A GLN* 1.3 56.7 + - - +
79A GLN* 2.8 35.9 + - - +
80A PRO* 4.5 3.4 - - + +
83A ALA* 3.9 33.4 - - + -
84A ALA* 5.4 0.7 - - + -
308A SER* 3.9 21.1 - - - +
311A VAL* 3.9 23.3 - - + -
312A SER* 5.5 1.8 - - - +
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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