Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 1LFD
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 ALA 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 1.3 70.0 - - - +
43A PRO* 1.4 63.9 - - - +
44A THR 3.2 0.2 + - - -
45A VAL* 3.3 1.6 + - - +
46A ILE* 2.9 39.5 + - + +
65A LEU* 5.2 2.2 - - + -
77A ILE* 4.4 6.5 - - + +
78A PRO 3.2 20.2 - - - +
79A GLU* 3.1 26.2 - - - +
81A ALA 2.8 12.3 + - - +
83A VAL* 3.7 15.4 - - + +
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Residues in contact with PRO 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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41A LYS* 3.4 19.3 - - + -
42A ALA* 1.4 88.7 - - - +
44A THR* 1.3 61.0 + - - +
46A ILE* 3.6 8.5 + - + +
47A ARG* 3.1 25.3 + - - +
60A PRO* 4.6 10.5 - - + +
79A GLU 3.1 20.4 - - - +
80A ASN* 3.9 16.4 - - - +
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Residues in contact with THR 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 ASP* 3.9 22.1 - - - +
41A LYS* 2.9 34.5 + - - -
43A PRO* 1.3 76.7 - - - +
45A VAL* 1.3 60.0 + - - +
47A ARG* 3.4 5.7 + - - +
48A LYS* 3.0 28.9 + - - +
265D SER* 4.1 26.0 - - - -
266D ALA* 4.2 14.2 - - + +
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Residues in contact with VAL 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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19A ILE* 4.3 5.2 - - + -
34A ILE* 3.9 20.2 - - + -
36A VAL* 4.2 15.3 - - + -
40A ASP* 3.5 31.9 - - + +
41A LYS 3.2 2.3 + - - +
42A ALA 3.9 4.3 - - - +
44A THR* 1.3 71.5 - - - +
46A ILE* 1.3 60.8 + - - +
48A LYS* 3.4 7.3 - - + +
49A ALA* 2.8 28.9 + - + +
65A LEU* 3.8 21.8 - - + -
83A VAL* 3.5 30.7 - - + -
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Residues in contact with ILE 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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42A ALA* 2.9 31.2 + - + +
43A PRO* 3.9 6.7 - - + +
45A VAL* 1.3 77.5 - - - +
47A ARG* 1.3 57.1 + - - +
49A ALA* 3.3 5.6 + - - +
50A MET* 2.8 53.1 + - - +
60A PRO* 3.8 14.8 - - + +
63A TYR* 3.7 37.0 - - + +
64A GLU* 4.7 0.2 - - - -
65A LEU* 4.1 30.3 - - + +
79A GLU* 5.6 4.3 - - - +
97A LEU* 4.0 9.0 - - + -
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Residues in contact with ARG 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 PRO 3.1 18.4 + - - +
44A THR* 3.9 4.9 - - - +
46A ILE* 1.3 76.6 - - - +
48A LYS* 1.3 58.4 + - - +
50A MET* 3.7 12.6 - - - +
51A ASP* 2.9 57.1 + - - +
55A LEU 3.2 21.4 + - - -
56A ASP* 3.8 12.3 + - - +
58A ASP 2.8 25.1 + - - -
59A GLU* 4.3 0.2 - - - +
60A PRO* 3.3 34.8 - - + +
262D GLU* 4.4 11.2 - - - +
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Residues in contact with LYS 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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34A ILE* 4.3 13.6 - - + +
35A LEU 2.8 17.7 + - - +
37A THR 4.9 0.2 - - - +
40A ASP* 2.6 32.8 + - - -
44A THR* 3.0 24.1 + - - +
45A VAL* 3.4 6.7 - - - +
47A ARG* 1.3 79.2 - - - +
49A ALA* 1.3 60.3 + - - +
51A ASP* 3.9 5.0 - - - +
52A LYS* 3.2 24.4 + - - +
262D GLU* 3.1 36.1 - - + +
263D GLU* 2.7 47.0 + - - +
265D SER* 4.9 1.2 - - - +
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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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21A VAL* 4.0 21.1 - - + -
34A ILE* 4.2 14.3 - - + +
45A VAL* 2.8 19.2 + - + +
46A ILE* 3.7 5.2 - - - +
48A LYS* 1.3 74.2 - - - +
50A MET* 1.3 64.7 + - - +
52A LYS* 3.3 5.3 + - - +
53A HIS* 3.0 31.0 + - - +
65A LEU* 5.3 2.5 - - + -
97A LEU* 3.9 20.6 - - + -
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Residues in contact with MET 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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46A ILE* 2.8 32.0 + - + +
47A ARG* 3.7 12.8 - - - +
48A LYS 3.4 0.2 - - - -
49A ALA* 1.3 76.1 - - - +
51A ASP* 1.3 54.1 - - - +
53A HIS 3.1 3.5 + - - -
54A ASN 2.9 10.6 + - - -
55A LEU* 2.7 56.5 + - + +
58A ASP* 3.4 37.0 - - + +
59A GLU 3.6 7.0 - - - -
60A PRO* 3.5 31.9 - - - -
63A TYR* 3.7 13.0 - - + -
97A LEU* 3.8 19.1 - - + -
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Residues in contact with ASP 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 ARG* 2.9 54.4 + - - +
48A LYS* 3.9 4.7 - - - +
50A MET* 1.3 73.7 - - - +
52A LYS* 1.3 59.4 + - - +
54A ASN* 2.8 17.2 + - - +
55A LEU 4.4 1.1 - - - +
56A ASP* 3.1 24.3 - - - +
231B LYS* 3.0 24.3 + - - +
262D GLU* 3.5 31.1 - - + +
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Residues in contact with LYS 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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32A LYS* 3.0 54.9 + - + +
33A SER 4.0 16.5 + - - +
34A ILE* 3.9 17.7 - - + -
48A LYS 3.2 17.4 + - - +
49A ALA* 3.5 6.5 - - - +
51A ASP* 1.3 78.5 - - - +
53A HIS* 1.3 60.1 + - - +
54A ASN* 3.6 4.5 + - - -
231B LYS* 4.9 0.7 + - - -
233B ASP* 3.0 44.2 + - - +
234B PRO 3.4 18.8 + - - -
235B THR* 4.5 6.9 + - - +
236B ILE* 5.1 0.6 - - - +
238B ASP* 4.5 9.6 + - - +
263D GLU* 5.6 5.7 - - - -
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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