Contacts of the helix formed by residues 71 - 86 (chain A) in PDB entry 1LFB
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 GLU 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LYS* 5.2 1.4 - - - +
39A ARG* 2.8 36.8 + - - -
40A GLU* 3.6 43.2 - - + +
43A VAL* 3.4 22.6 - - + +
69A VAL 3.8 0.2 + - - -
70A THR* 1.3 68.2 - - - +
72A VAL* 1.3 75.4 + - + +
74A VAL* 3.3 3.8 + - + +
75A TYR* 3.0 18.2 + - - +
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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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70A THR* 3.2 11.3 - - - +
71A GLU* 1.3 86.1 - - + +
73A ARG* 1.3 62.4 + - + +
75A TYR* 3.1 7.5 + - + +
76A ASN* 2.8 45.8 + - - +
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Residues in contact with ARG 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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14A PHE* 3.4 54.0 - - + +
16A TRP* 3.4 30.4 - - + -
66A SER 3.9 6.3 + - - -
68A LEU* 3.6 11.9 + - - +
70A THR* 3.0 47.2 + - - +
72A VAL* 1.3 81.9 - - + +
74A VAL* 1.3 57.8 + - - +
76A ASN* 3.9 6.5 - - - +
77A TRP* 3.0 22.9 + - - +
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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
----------------------------------------------------------
16A TRP* 4.2 8.7 - - + -
24A LEU* 4.3 13.7 - - + -
39A ARG* 3.6 34.1 - - + +
42A LEU* 4.2 6.3 - - + +
43A VAL* 3.7 20.0 - - + +
69A VAL* 3.6 26.2 - - + -
70A THR 3.6 1.2 + - - -
71A GLU* 3.3 7.7 + - - +
72A VAL 3.2 0.2 - - - -
73A ARG* 1.3 74.1 - - - +
75A TYR* 1.3 69.0 + - - +
77A TRP* 3.4 4.8 + - - +
78A PHE* 3.2 43.8 + - + -
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Residues in contact with TYR 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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36A LYS* 6.1 0.4 - - - -
39A ARG* 3.3 52.9 - - - +
71A GLU* 3.0 10.4 + - - +
72A VAL* 3.3 12.8 - - + +
74A VAL* 1.3 75.4 - - - +
76A ASN* 1.3 79.8 + - - +
78A PHE* 2.9 8.5 + - + +
79A ALA* 2.9 35.2 + - + +
82A ARG* 4.9 11.5 + - - -
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Residues in contact with ASN 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* 2.8 39.0 + - - +
73A ARG* 4.0 6.1 - - - +
75A TYR* 1.3 87.6 - - - +
77A TRP* 1.3 62.6 + - - +
79A ALA* 3.0 9.6 + - - +
80A ASN* 2.8 29.5 + - + +
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Residues in contact with TRP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.9 25.7 - + + -
21A GLN* 4.7 14.3 - - - +
24A LEU* 3.7 30.4 - - + +
25A PHE* 3.6 60.8 - + - -
28A TYR* 4.0 7.9 - - + -
73A ARG 3.0 22.6 + - - +
74A VAL* 3.5 7.2 - - - +
75A TYR 3.3 0.2 - - - -
76A ASN* 1.3 68.8 - - - +
78A PHE* 1.3 102.9 + + - +
80A ASN* 4.6 1.1 - - - -
81A ARG* 2.9 70.6 + - + +
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Residues in contact with PHE 78 (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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24A LEU* 4.0 20.6 - - + -
27A ALA* 4.1 13.2 - - + -
28A TYR* 3.7 33.6 - + + -
31A GLN 4.1 5.4 - - - -
32A LYS 3.9 3.4 - - - -
34A PRO* 3.6 34.8 - - + -
39A ARG* 5.7 0.2 - - - -
42A LEU* 4.6 6.5 - - + -
74A VAL* 3.2 35.6 + - + -
75A TYR* 2.9 8.5 + - + +
77A TRP* 1.3 103.6 - + - +
79A ALA* 1.3 66.3 + - - +
81A ARG* 3.0 4.3 + - - +
82A ARG* 2.9 43.1 + - - +
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Residues in contact with ALA 79 (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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75A TYR* 2.9 24.0 + - + +
76A ASN* 3.3 15.5 - - - +
78A PHE* 1.3 76.6 - - - +
80A ASN* 1.3 57.4 + - - +
82A ARG* 3.1 29.8 + - - +
83A LYS* 3.0 26.9 + - - +
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Residues in contact with ASN 80 (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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76A ASN* 2.8 21.4 + - + +
77A TRP 3.9 2.9 - - - +
79A ALA* 1.3 73.3 - - + +
81A ARG* 1.3 79.8 + - - +
83A LYS* 3.3 35.9 + - - +
84A GLU* 3.3 34.1 + - - +
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Residues in contact with ARG 81 (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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16A TRP* 5.4 3.8 - - - +
21A GLN* 6.3 0.2 - - - -
25A PHE* 4.5 15.0 - - + -
28A TYR* 3.3 31.4 + - + -
77A TRP* 2.9 80.1 + - + +
78A PHE 3.6 2.9 - - - +
80A ASN* 1.3 91.3 - - - +
82A ARG* 1.3 62.1 + - - +
84A GLU* 2.9 47.8 + - - +
85A GLU* 3.7 3.3 + - - +
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Residues in contact with ARG 82 (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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28A TYR* 4.0 14.8 - - + +
32A LYS* 2.9 41.4 + - + +
33A ASN* 3.4 35.6 - - - +
34A PRO* 4.3 1.8 - - - +
75A TYR* 4.9 14.6 + - - -
78A PHE* 2.9 25.2 + - - +
79A ALA* 3.3 33.4 + - - +
81A ARG* 1.3 74.1 - - - +
83A LYS* 1.3 66.0 + - - +
85A GLU* 3.0 17.3 + - - +
86A ALA* 3.3 9.2 + - - +
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Residues in contact with LYS 83 (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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79A ALA 3.0 14.8 + - - +
80A ASN* 3.3 35.3 + - - +
82A ARG* 1.3 73.2 - - - +
84A GLU* 1.3 58.3 + - + +
86A ALA* 2.7 42.7 + - - +
88A ARG* 5.2 0.9 + - - -
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Residues in contact with GLU 84 (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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80A ASN* 3.3 27.7 + - - +
81A ARG* 2.9 46.1 + - - +
82A ARG 3.1 1.2 - - - -
83A LYS* 1.3 79.1 - - + +
85A GLU* 1.3 59.3 + - - +
86A ALA 4.8 0.9 - - - -
87A PHE* 4.3 15.1 - - - +
88A ARG* 5.5 2.8 + - - +
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Residues in contact with GLU 85 (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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28A TYR* 2.9 29.2 + - - +
32A LYS* 2.9 33.0 + - - +
81A ARG 3.7 2.4 + - - -
82A ARG* 3.0 11.2 + - - +
84A GLU* 1.3 76.4 - - - +
86A ALA* 1.3 58.9 + - - +
87A PHE* 2.7 29.9 + - + -
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Residues in contact with ALA 86 (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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82A ARG 3.3 6.7 + - - +
83A LYS* 2.7 27.7 + - - +
85A GLU* 1.3 65.5 - - - +
87A PHE* 1.3 59.8 + - - +
88A ARG* 3.3 11.8 + - - -
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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