Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 1BL8
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 TYR 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.3 73.4 - + + +
48A VAL* 3.4 28.8 - - + +
49A LEU* 3.9 21.2 - - + +
52A ARG* 4.6 13.9 - - - -
61A THR* 1.3 71.1 - - - +
63A PRO* 1.3 67.9 - - + +
64A ARG 2.9 5.5 + - - -
65A ALA* 3.1 11.7 + - - +
66A LEU* 3.3 17.9 + - - +
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Residues in contact with PRO 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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45A TYR* 5.6 1.8 - - - +
61A THR* 3.2 22.7 - - + -
62A TYR* 1.3 95.2 - - + +
64A ARG* 1.3 55.7 + - - -
66A LEU* 4.3 18.6 - - + +
67A TRP* 4.6 5.4 + - - +
86B LEU* 6.1 0.7 - - - +
89B ARG* 5.5 2.6 + - - -
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Residues in contact with ARG 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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58A GLN* 3.5 43.1 - - - +
59A LEU* 4.8 0.9 - - - -
61A THR* 2.9 18.0 + - + +
63A PRO* 1.3 79.2 - - - +
65A ALA* 1.3 66.4 + - - +
66A LEU 3.1 1.9 + - - -
67A TRP* 3.5 7.0 + - - +
68A TRP* 3.3 16.6 + - - +
81A LEU* 3.8 16.1 - - + +
89B ARG* 5.8 3.4 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.1 36.6 - - - +
47A ALA* 4.9 0.4 - - + -
48A VAL* 3.4 19.7 - - + +
59A LEU* 3.8 20.4 - - + +
61A THR 2.9 5.9 + - - -
62A TYR 3.1 2.9 + - - +
64A ARG* 1.3 76.6 - - - +
66A LEU* 1.3 51.4 + - - +
68A TRP* 2.8 8.7 + - + +
69A SER* 2.7 35.9 + - - -
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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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40A LEU* 5.2 0.7 - - + -
41A LEU* 3.8 22.9 - - + -
44A SER* 2.8 38.3 + - - +
45A TYR* 3.6 22.7 - - + +
62A TYR 3.3 12.0 + - - +
63A PRO* 4.3 13.7 - - + +
65A ALA* 1.3 72.4 - - - +
67A TRP* 1.3 56.4 + - - +
68A TRP 2.7 5.1 + - - -
69A SER* 2.6 25.9 + - - -
70A VAL* 2.9 17.6 + - + +
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 4.9 4.0 - - - +
64A ARG 3.5 8.1 + - - +
66A LEU* 1.3 77.9 - - - +
68A TRP* 1.3 57.7 + - - +
70A VAL* 3.9 17.4 - - + +
71A GLU* 3.2 25.8 + - + +
78A TYR* 3.4 33.9 - + - -
80A ASP* 3.5 28.8 + - - -
81A LEU* 4.3 9.2 - - + -
82B TYR* 4.8 1.3 - - + -
83B PRO* 3.8 16.1 + - + -
89B ARG* 3.2 81.8 - - + +
92B ALA* 3.6 22.0 - - + -
93B VAL* 4.9 6.7 - - + -
96B MET* 5.5 4.0 - - + -
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Residues in contact with TRP 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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43A GLY 4.4 2.2 - - - -
47A ALA* 3.6 27.1 - - + -
59A LEU* 3.7 23.6 - - + -
64A ARG 3.3 6.8 + - - +
65A ALA* 2.8 25.7 + - + +
66A LEU 2.7 1.6 + - - -
67A TRP* 1.3 79.4 - - - +
69A SER* 1.3 70.5 - - - -
70A VAL 3.2 0.2 - - - -
71A GLU* 3.9 4.2 - - + +
72A THR* 2.7 53.7 + - - -
80A ASP* 6.1 0.4 - - - -
81A LEU* 3.7 30.3 - - + -
82A TYR* 4.3 1.1 - - - -
83A PRO* 3.8 17.4 - - + +
88A GLY 4.2 2.7 - - - -
91A VAL* 4.1 8.5 - - + -
92A ALA* 3.5 45.5 - - + -
95A VAL* 4.0 8.3 - - + -
78D TYR* 2.7 22.3 + + - -
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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
----------------------------------------------------------
40A LEU* 3.5 27.2 + - - -
43A GLY 4.0 1.2 - - - -
44A SER* 2.9 36.2 + - - -
65A ALA 2.7 8.1 + - - -
66A LEU 2.6 14.6 + - - -
68A TRP* 1.3 83.8 - - - +
70A VAL* 1.3 51.5 + - - -
72A THR* 4.4 0.2 - - - -
73A ALA* 2.6 38.3 + - - +
95A VAL* 3.5 13.9 - - - +
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Residues in contact with VAL 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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40A LEU* 4.0 22.0 - - + -
66A LEU* 2.9 16.4 + - + +
67A TRP* 3.9 17.3 - - + +
69A SER* 1.3 73.1 - - - +
71A GLU* 1.3 54.7 + - - +
73A ALA* 3.2 5.4 + - - +
74A THR* 2.7 48.9 + - - +
93B VAL* 3.4 32.8 - - + -
96B MET* 4.3 6.7 - - + -
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Residues in contact with GLU 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 TRP* 3.2 21.5 + - + +
68A TRP* 3.9 5.6 - - + +
70A VAL* 1.3 77.8 - - - +
72A THR* 1.3 59.4 + - - +
74A THR 3.3 1.0 + - - -
75A THR 2.8 22.7 + - - -
76A VAL* 3.0 14.5 + - + +
77A GLY* 4.5 10.5 - - - +
78A TYR* 4.5 26.0 - - + +
80A ASP* 5.3 3.4 - - - +
96B MET* 3.9 14.4 - - + -
78D TYR* 6.3 1.6 - - + -
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Residues in contact with THR 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 TRP* 2.7 35.6 + - + -
69A SER 3.6 3.6 - - - -
71A GLU* 1.3 77.1 - - - +
73A ALA* 1.3 54.4 + - - +
75A THR* 2.6 29.9 + - - +
77A GLY 5.3 0.2 - - - +
92A ALA* 3.9 0.7 - - - +
95A VAL* 3.4 29.4 - - + -
96A MET* 3.6 31.3 - - + +
76D VAL* 4.4 6.5 - - + +
78D TYR* 2.7 29.9 + - + +
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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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36A LEU* 4.4 14.8 - - + -
40A LEU* 3.6 21.1 - - + -
69A SER 2.6 22.1 + - - +
70A VAL* 3.6 4.3 - - - +
72A THR* 1.3 74.8 - - - +
74A THR* 1.3 60.8 + - - +
75A THR* 3.0 8.2 + - - +
95A VAL 3.4 21.5 + - - +
96A MET 4.3 0.8 - - - +
99A GLY* 3.4 21.1 - - - -
103A PHE* 4.8 4.2 - - + -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 2.7 27.9 + - - +
73A ALA* 1.3 68.3 - - - +
75A THR* 1.3 77.3 + - - +
76A VAL* 3.4 13.9 - - + -
103A PHE* 5.1 5.2 - - - -
75B THR* 3.7 9.3 + - - +
96B MET* 3.0 39.4 - - + +
100B ILE* 3.2 37.1 - - + +
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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