Contacts of the helix formed by residues 36 - 54 (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 LYS 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 1.3 79.5 - - - +
37A GLU* 1.3 85.9 + - - +
39A ARG* 3.3 34.3 + - - +
40A GLU* 3.3 26.1 + - - +
71A GLU* 5.2 1.3 - - - +
75A TYR* 6.1 0.8 - - - -
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Residues in contact with GLU 37 (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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35A SER* 4.6 7.3 - - - +
36A LYS* 1.3 103.2 + - - +
38A GLU* 1.3 68.0 + - - +
39A ARG 3.4 0.2 + - - -
40A GLU* 3.4 9.5 + - - +
41A THR* 3.3 18.9 + - - -
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Residues in contact with GLU 38 (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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31A GLN* 4.2 20.2 + - + +
34A PRO* 3.9 10.3 - - + -
35A SER* 2.8 43.3 + - - +
37A GLU* 1.3 77.3 - - - +
39A ARG* 1.3 67.0 - - - +
41A THR* 2.9 20.6 + - - -
42A LEU* 3.1 21.2 + - + +
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Residues in contact with ARG 39 (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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34A PRO* 3.4 34.5 + - + -
35A SER 3.0 12.6 + - - +
36A LYS* 3.3 46.7 - - - +
38A GLU* 1.3 77.9 - - - +
40A GLU* 1.3 57.8 + - + +
42A LEU* 3.0 25.4 + - - +
43A VAL* 3.1 15.7 + - - +
71A GLU* 2.8 40.0 + - + +
74A VAL* 3.6 27.7 - - + +
75A TYR* 3.3 45.8 - - - +
78A PHE* 5.7 0.2 - - - -
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Residues in contact with GLU 40 (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 3.3 15.2 + - - +
37A GLU* 3.7 10.5 - - - +
38A GLU 3.2 0.4 - - - -
39A ARG* 1.3 73.0 - - - +
41A THR* 1.4 64.7 + - - +
43A VAL* 3.5 14.1 + - - +
44A GLU* 3.4 15.9 + - - +
71A GLU* 3.6 38.2 - - - +
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Residues in contact with THR 41 (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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37A GLU 3.3 11.6 + - - -
38A GLU* 2.9 17.6 + - - -
40A GLU* 1.4 69.2 - - - +
42A LEU* 1.3 73.3 + - + +
43A VAL 2.9 1.9 + - - -
44A GLU* 2.9 19.0 + - + +
45A GLU* 3.1 29.2 + - + +
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Residues in contact with LEU 42 (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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23A ILE* 4.0 21.5 - - + +
24A LEU* 4.2 18.6 - - + -
27A ALA* 4.1 26.2 - - + -
34A PRO* 4.8 5.2 - - + -
38A GLU* 3.1 36.6 + - + +
39A ARG* 3.0 10.7 + - - +
41A THR* 1.3 85.1 - - + +
43A VAL* 1.3 57.8 + - - +
45A GLU* 3.7 6.9 - - + -
46A CYS* 2.9 36.0 + - - -
74A VAL* 4.2 7.2 - - + -
78A PHE* 4.6 11.0 - - + -
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Residues in contact with VAL 43 (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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39A ARG 3.1 10.2 + - - +
40A GLU* 3.6 19.7 - - - +
41A THR 2.9 1.4 + - - -
42A LEU* 1.3 73.8 - - - +
44A GLU* 1.3 69.1 + - - +
46A CYS* 3.0 13.2 + - - +
47A ASN* 3.0 24.8 + - - +
69A VAL* 3.5 21.3 - - + +
71A GLU* 3.4 39.0 - - + +
74A VAL* 3.7 18.4 - - + -
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Residues in contact with GLU 44 (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 GLU 3.4 7.6 + - - +
41A THR* 2.9 12.9 + - + +
43A VAL* 1.3 83.3 - - - +
45A GLU* 1.3 89.0 - - - +
46A CYS 2.9 4.3 + - - -
47A ASN* 3.0 13.7 + - - +
48A ARG* 3.0 40.4 + - - +
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Residues in contact with GLU 45 (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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23A ILE* 3.9 22.4 - - + +
41A THR* 3.1 28.5 + - + +
42A LEU* 3.9 11.0 - - + +
44A GLU* 1.3 100.8 - - - +
46A CYS* 1.3 58.4 + - - +
48A ARG* 4.4 15.4 + - - -
49A ALA* 3.2 26.7 + - - +
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Residues in contact with CYS 46 (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* 4.7 3.1 - - - -
20A SER* 4.1 25.7 - - - +
23A ILE* 3.6 22.2 - - - -
24A LEU* 3.7 21.3 - - - -
42A LEU 2.9 24.4 + - - +
43A VAL 3.0 5.4 + - - +
44A GLU 2.9 0.2 + - - -
45A GLU* 1.3 75.7 - - - +
47A ASN* 1.3 68.1 + - - +
49A ALA* 3.5 2.8 + - - +
50A GLU* 2.9 30.0 + - - +
69A VAL* 4.1 19.5 - - + -
74A VAL* 4.8 0.4 - - - -
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Residues in contact with ASN 47 (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 VAL* 3.0 28.0 + - - +
44A GLU* 3.7 5.8 - - - +
46A CYS* 1.3 75.7 - - - +
48A ARG* 1.3 51.4 + - - +
50A GLU* 3.0 5.5 + - - +
51A CYS* 2.7 38.8 + - - -
61A ALA* 4.6 15.0 - - + +
64A LEU* 3.6 15.5 - - + +
68A LEU* 3.5 21.8 - - - +
69A VAL* 2.9 42.5 + - - +
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Residues in contact with ARG 48 (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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44A GLU* 3.0 35.6 + - - +
45A GLU* 4.4 15.1 + - - +
47A ASN* 1.3 76.2 - - - +
49A ALA* 1.3 68.7 + - - +
51A CYS* 2.8 23.3 + - - +
52A ILE* 2.9 44.7 + - - +
58A PRO* 3.9 25.9 - - + +
61A ALA* 5.7 0.4 - - - +
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Residues in contact with ALA 49 (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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19A ALA* 4.0 10.0 - - + +
23A ILE* 3.6 23.1 - - + -
45A GLU* 3.2 21.2 + - - +
46A CYS* 3.5 3.3 + - - +
47A ASN 3.5 0.2 - - - -
48A ARG* 1.3 84.2 - - - +
50A GLU* 1.3 61.8 + - - +
52A ILE* 3.8 13.5 - - + +
53A GLN* 3.3 25.1 + - - +
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Residues in contact with GLU 50 (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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15A LYS 4.8 4.5 - - - +
17A GLY* 3.5 18.3 + - - -
19A ALA* 3.2 25.8 - - - +
20A SER* 3.4 26.8 + - - +
46A CYS 2.9 23.0 + - - +
47A ASN* 3.2 7.2 - - - +
49A ALA* 1.3 74.3 - - - +
51A CYS* 1.4 65.6 + - - +
53A GLN* 3.2 15.8 + - - +
54A ARG* 3.3 14.9 + - - +
64A LEU* 4.2 21.3 - - + +
67A ASN* 5.1 10.1 - - - +
69A VAL* 5.5 4.0 - - + -
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Residues in contact with CYS 51 (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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47A ASN 2.7 25.2 + - - -
48A ARG* 2.8 9.3 + - - +
50A GLU* 1.4 63.7 - - - +
52A ILE* 1.3 52.4 + - - +
53A GLN 2.7 4.5 + - - -
54A ARG* 2.6 31.1 + - - -
55A GLY 3.4 4.2 + - - -
56A VAL* 3.4 29.6 + - + +
57A SER 3.7 11.2 - - - -
58A PRO* 3.9 16.8 - - + -
60A GLN 3.9 4.0 - - - -
61A ALA* 3.6 33.7 - - - -
64A LEU* 4.3 10.7 - - - +
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Residues in contact with ILE 52 (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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48A ARG* 2.9 39.4 + - - +
49A ALA* 3.8 15.0 - - + +
51A CYS* 1.3 68.4 - - - +
53A GLN* 1.3 66.1 + - + +
55A GLY* 4.2 6.1 + - - +
56A VAL 4.1 5.8 - - - -
58A PRO* 3.5 31.4 - - + -
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Residues in contact with GLN 53 (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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19A ALA* 3.9 21.8 - - + +
49A ALA 3.3 16.4 + - - +
50A GLU* 3.2 10.9 + - - +
51A CYS 2.7 2.6 + - - -
52A ILE* 1.3 80.4 + - + +
54A ARG* 1.3 60.3 + - + +
55A GLY 3.2 9.0 + - - -
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Residues in contact with ARG 54 (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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50A GLU* 3.3 8.7 + - - +
51A CYS* 2.6 15.4 + - - +
53A GLN* 1.3 73.4 - - + +
55A GLY* 1.3 63.0 + - - +
56A VAL* 3.0 22.8 + - + +
63A GLY 3.3 25.9 + - - -
64A LEU* 3.8 36.5 + - + +
67A ASN* 4.7 12.1 - - - +
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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