Contacts of the helix formed by residues 56 - 74 (chain A) in PDB entry 1BL0
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 LEU 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.4 1.3 - - + -
20A ILE* 3.9 17.3 - - + -
31A GLU* 2.8 29.8 - - + +
34A SER* 3.9 24.2 - - - +
44A LEU* 4.7 16.4 - - + -
45A GLN* 4.7 15.0 + - + +
48A PHE* 3.2 54.3 - - + -
54A HIS 3.3 3.8 + - - -
55A SER* 1.3 72.4 - - - +
57A GLY* 1.3 64.1 + - - +
59A TYR* 3.1 2.4 + - + +
60A ILE* 3.0 33.4 + - + +
417B G 3.9 2.0 + - - +
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.6 9.8 + - - -
56A LEU* 1.3 75.7 - - - +
58A GLN* 1.3 55.1 + - - +
60A ILE* 3.5 7.6 + - - +
61A ARG* 3.2 31.4 + - - +
416B C 3.7 11.4 - - - -
417B G 2.7 27.8 + - - -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 4.6 15.7 - - + -
55A SER* 3.4 20.1 + - - +
56A LEU 3.4 0.4 - - - -
57A GLY* 1.3 70.7 - - - +
59A TYR* 1.3 58.5 + - - +
61A ARG* 3.7 22.0 + - - +
62A SER* 2.3 45.3 + - - +
417B G 3.1 15.6 + - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.0 16.5 - - + +
20A ILE* 4.5 11.4 - - + -
21A GLU* 3.0 12.3 + - - -
48A PHE* 3.7 21.8 - + + -
54A HIS* 4.2 16.2 - + + -
55A SER 3.2 16.5 + - - +
56A LEU* 3.1 4.6 + - + +
58A GLN* 1.3 79.0 - - - +
60A ILE* 1.3 74.5 + - + +
62A SER* 3.1 4.7 + - - -
63A ARG* 2.8 51.0 + - + +
121A LEU* 3.7 21.8 - - + -
123A PRO 2.7 32.7 + - - -
124A LEU* 2.7 30.2 - - - -
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.2 32.3 - - + -
24A LEU* 5.0 2.0 - - + -
29A SER* 3.3 38.8 - - - +
30A LEU 5.4 0.4 - - - -
31A GLU* 4.8 3.4 - - - +
34A SER* 4.7 5.8 - - - +
56A LEU* 3.0 35.5 + - + +
57A GLY* 3.8 7.9 - - - +
59A TYR* 1.3 79.6 - - + +
61A ARG* 1.3 59.4 + - - +
63A ARG* 3.1 7.5 + - - +
64A LYS* 3.0 48.2 + - + +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY 3.2 12.5 + - - +
58A GLN* 3.7 28.7 + - - +
59A TYR 3.2 0.6 - - - -
60A ILE* 1.3 79.1 - - - +
62A SER* 1.3 61.3 + - - +
64A LYS* 3.2 9.1 + - + +
65A MET* 2.9 41.0 + - + +
88A PHE* 5.5 3.4 - - + -
97A THR* 4.7 19.3 + - + +
101A TYR* 5.0 10.3 - - - +
416B C 5.7 1.6 + - - -
417B G 5.4 0.8 + - - -
437C T 5.1 0.4 + - - -
438C T 3.6 46.4 + - - -
439C T 3.5 24.5 - - - -
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 5.8 0.2 - - - -
58A GLN* 2.3 37.4 + - - +
59A TYR 3.5 0.9 - - - -
61A ARG* 1.3 76.0 + - - +
63A ARG* 1.3 50.1 + - - +
65A MET 3.7 0.2 + - - -
66A THR* 2.6 37.7 + - - +
101A TYR* 3.5 33.6 + - - -
121A LEU* 3.3 29.1 - - - +
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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
----------------------------------------------------------
21A GLU* 2.3 52.7 + - - +
24A LEU* 3.9 13.4 - - + +
59A TYR* 2.8 57.3 + - + +
60A ILE* 3.4 8.1 - - - +
62A SER* 1.3 76.5 - - - +
64A LYS* 1.3 60.1 + - - +
66A THR* 3.0 31.7 + - - +
67A GLU* 3.0 43.5 + - - +
70A GLN* 5.1 2.0 + - - -
121A LEU* 2.7 32.1 + - + -
122A HIS* 3.8 5.2 - - - +
123A PRO* 3.4 24.5 - - - +
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.6 30.1 - - + +
27A PRO 2.9 21.0 + - - -
28A LEU* 3.7 19.0 + - - +
29A SER* 4.6 1.6 - - - -
60A ILE* 3.0 34.9 + - + +
61A ARG* 3.8 8.5 - - + +
63A ARG* 1.3 72.6 - - - +
65A MET* 1.4 72.6 + - + +
67A GLU* 3.8 4.3 - - - +
68A ILE* 2.9 35.3 + - - +
86A TYR* 2.9 37.7 + - + +
87A GLY* 4.6 1.6 - - - -
88A PHE* 4.6 13.9 - - + -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.9 25.4 + - + +
62A SER 4.1 0.7 - - - +
64A LYS* 1.4 77.5 - - + +
66A THR* 1.3 67.9 + - - +
68A ILE* 3.4 6.8 + - + +
69A ALA* 3.0 24.1 + - - +
88A PHE* 3.2 30.3 - - + -
94A LEU* 4.0 7.0 - - + -
97A THR* 3.0 37.9 - - + -
98A PHE* 3.8 27.1 - - - -
101A TYR* 3.8 37.9 - - + -
102A PHE* 3.6 8.1 - - + -
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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
----------------------------------------------------------
62A SER 2.6 29.0 + - - +
63A ARG* 3.0 41.7 + - - +
65A MET* 1.3 75.1 - - - +
67A GLU* 1.3 56.7 + - - -
69A ALA* 3.2 8.6 + - - +
70A GLN* 2.9 32.3 + - - +
101A TYR* 4.9 1.5 - - - -
102A PHE* 4.5 5.8 - - - -
119A ARG 5.1 0.2 - - - -
120A PHE* 3.7 23.7 - - - +
121A LEU 3.3 26.9 + - - +
122A HIS* 4.9 1.7 - - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 6.4 0.4 - - - -
24A LEU* 3.6 22.2 - - + +
25A GLU* 4.0 8.7 - - - +
63A ARG* 3.0 39.3 + - - +
64A LYS 3.8 3.4 - - - +
66A THR* 1.3 75.9 - - - +
68A ILE* 1.3 63.8 + - - +
70A GLN* 3.4 18.5 + - - +
71A LYS* 3.3 32.9 + - - +
86A TYR* 3.3 27.9 + - + +
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Residues in contact with ILE 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 LYS 2.9 21.2 + - - +
65A MET* 3.9 8.1 - - + +
67A GLU* 1.3 76.8 - - - +
69A ALA* 1.3 57.9 + - - +
71A LYS* 4.0 5.5 - - - +
72A LEU* 3.0 35.6 + - + +
82A LEU* 4.4 15.0 - - + +
86A TYR* 3.8 30.5 - - + -
88A PHE* 3.8 16.8 - - + -
94A LEU* 3.4 39.3 - - + -
98A PHE* 3.5 21.8 - - + -
106A PRO* 5.6 0.9 - - + -
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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 MET 3.0 14.2 + - - +
66A THR 3.3 10.8 - - - +
68A ILE* 1.3 79.2 - - - +
70A GLN* 1.3 61.0 + - - +
72A LEU* 3.5 8.2 + - - +
73A LYS* 3.5 9.9 + - - +
98A PHE* 3.9 10.1 - - + -
102A PHE* 3.6 26.7 - - + -
109A TYR* 3.6 23.2 + - + +
120A PHE* 3.6 14.0 - - + -
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Residues in contact with GLN 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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63A ARG* 5.1 1.6 + - - -
66A THR* 2.9 25.0 + - - +
67A GLU* 3.4 22.4 + - - +
68A ILE 3.4 0.4 - - - -
69A ALA* 1.3 74.0 - - - +
71A LYS* 1.3 59.2 + - + +
73A LYS* 4.9 1.1 - - - -
74A GLU* 2.9 50.8 + - + +
117A GLU* 5.1 3.4 + - - -
120A PHE* 3.3 32.4 - - + -
122A HIS* 4.5 13.9 + - - -
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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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25A GLU* 3.2 9.7 + - - +
67A GLU* 3.3 18.7 + - - +
68A ILE 4.0 4.0 - - - +
69A ALA 3.3 0.2 - - - -
70A GLN* 1.3 76.0 - - + +
72A LEU* 1.3 67.8 + - - +
73A LYS 2.9 2.2 - - - -
74A GLU* 4.2 3.1 - - - +
75A SER* 2.9 37.9 + - - +
77A GLU* 3.4 14.4 - - - +
82A LEU* 3.6 22.2 - - + -
85A ARG* 3.0 33.2 - - - +
86A TYR* 2.8 30.5 + - + +
110A ARG* 3.6 1.1 + - - -
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Residues in contact with LEU 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 ILE* 3.0 23.0 + - + +
69A ALA* 3.7 5.4 - - - +
70A GLN 3.4 0.4 - - - -
71A LYS* 1.3 78.3 - - - +
73A LYS* 1.3 58.6 + - - +
75A SER 3.5 2.4 - - - +
79A ILE* 4.3 12.1 - - + -
82A LEU* 3.5 23.6 - - + -
98A PHE* 3.3 38.1 - - + -
106A PRO* 3.6 29.8 - - + +
109A TYR* 4.1 7.2 - - + -
110A ARG* 2.8 60.8 + - + +
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Residues in contact with LYS 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 3.5 15.9 + - - +
70A GLN* 3.5 2.5 + - - +
71A LYS 2.9 0.4 - - - -
72A LEU* 1.3 85.9 - - - +
74A GLU* 1.3 74.7 + - - +
75A SER 3.4 1.3 - - - -
109A TYR* 3.8 26.2 - - + +
110A ARG 3.5 19.3 + - - -
112A THR 3.1 30.3 + - - +
113A ASN* 4.6 10.0 + - - +
115A GLN 4.4 10.8 - - - +
120A PHE* 6.5 0.2 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN* 2.9 43.6 + - - +
71A LYS* 4.7 1.8 - - - -
73A LYS* 1.3 95.8 - - - +
75A SER* 1.3 62.5 + - - +
120A PHE* 6.0 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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