Contacts of the helix formed by residues 45 - 60 (chain A) in PDB entry 4LWU
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 THR 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLU* 5.9 5.4 - - - +
22A LYS 3.8 12.3 - - - +
23A LEU* 3.7 18.1 - - + +
24A VAL* 4.6 0.2 - - - -
44A PHE* 1.3 77.1 - - - +
46A MET* 1.3 65.3 + - - +
47A LYS* 3.5 11.1 + - - +
48A GLU* 2.9 51.0 + - - +
49A VAL* 3.0 11.0 + - - +
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Residues in contact with MET 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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22A LYS 4.4 4.4 + - - -
24A VAL* 4.0 19.8 - - + +
44A PHE 3.9 0.8 + - - -
45A THR* 1.3 73.0 - - - +
47A LYS* 1.3 63.9 + - + +
49A VAL* 3.1 7.1 + - + +
50A LEU* 2.9 24.2 + - + +
96A TYR* 3.4 40.6 - - + +
99A ILE* 4.0 26.5 - - + -
100A SER* 5.6 2.9 - - - +
103A LEU* 3.9 27.8 - - + -
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Residues in contact with LYS 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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45A THR* 3.1 9.7 + - - +
46A MET* 1.3 79.0 - - + +
48A GLU* 1.3 57.3 + - + +
50A LEU* 3.3 12.4 + - + +
51A TYR* 2.9 28.2 + - - +
96A TYR* 6.2 0.2 - - - +
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Residues in contact with GLU 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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23A LEU* 4.9 1.7 - - - +
41A LYS* 2.8 41.0 + - - -
44A PHE* 3.4 18.3 - - + -
45A THR* 2.9 48.2 + - - +
47A LYS* 1.3 72.5 - - + +
49A VAL* 1.3 67.0 + - - +
51A TYR* 3.1 7.0 + - - +
52A HIS* 2.9 38.5 + - + +
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Residues in contact with VAL 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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24A VAL* 3.9 18.8 - - + -
26A PRO* 4.7 6.3 - - + -
30A LEU* 4.6 5.8 - - + -
34A LEU* 4.6 14.8 - - + -
44A PHE* 3.6 24.0 - - + -
45A THR 3.0 14.5 + - - +
46A MET* 3.5 11.4 - - + +
48A GLU* 1.3 76.3 - - - +
50A LEU* 1.3 58.6 + - - +
52A HIS* 3.8 2.7 - - - +
53A LEU* 2.9 49.1 + - + +
99A ILE* 4.0 21.1 - - + -
103A LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 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 MET* 2.9 19.7 + - + +
47A LYS* 3.6 12.3 - - + +
49A VAL* 1.3 77.1 - - - +
51A TYR* 1.3 58.5 + - - +
53A LEU* 3.5 1.1 + - - -
54A GLY 3.0 15.6 + - - -
95A ILE* 4.1 1.6 - - + -
96A TYR* 3.6 26.5 - - + +
99A ILE* 3.7 27.1 - - + -
201A 20U 2.8 96.7 + - + +
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Residues in contact with TYR 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 LYS 2.9 15.1 + - - +
48A GLU* 3.1 11.2 + - - +
50A LEU* 1.3 77.0 - - - +
52A HIS* 1.3 81.5 + + - +
54A GLY* 3.1 3.3 + - - -
55A GLN* 3.0 52.7 + - + +
201A 20U 5.0 2.0 - - - -
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Residues in contact with HIS 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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34A LEU* 3.7 27.1 + - + +
37A ALA* 3.4 14.4 + - - +
38A GLY 4.4 4.8 - - - -
39A ALA* 3.6 41.5 + - + +
40A GLN 5.1 0.8 + - - -
41A LYS* 5.8 0.6 - - - -
44A PHE* 3.9 20.4 - + - -
48A GLU* 2.9 34.9 + - + +
49A VAL* 4.9 0.4 - - - -
51A TYR* 1.3 93.0 - + - +
53A LEU* 1.3 58.2 + - - +
55A GLN* 3.2 6.6 + - - +
56A TYR* 2.9 23.7 + - - +
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Residues in contact with LEU 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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30A LEU* 3.9 19.5 - - + -
33A LEU* 5.0 4.3 - - + -
34A LEU* 3.7 18.4 - - + -
49A VAL* 2.9 37.1 + - + +
52A HIS* 1.3 73.4 - - - +
54A GLY* 1.3 60.3 + - - +
56A TYR* 3.4 14.7 - - + +
57A ILE* 2.8 36.0 + - - +
78A LEU* 4.3 18.8 - - + -
82A PHE* 4.2 4.9 - - + -
99A ILE* 3.9 19.5 - - + -
201A 20U 3.8 29.4 - - + -
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Residues in contact with GLY 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 LEU 3.0 16.4 + - - -
51A TYR 3.1 4.2 + - - -
53A LEU* 1.3 76.2 - - - +
55A GLN* 1.3 63.7 + - - +
57A ILE* 3.3 4.8 + - - +
58A MET* 3.1 28.9 + - - +
201A 20U 3.8 31.1 - - - +
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Residues in contact with GLN 55 (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 ALA* 4.1 20.9 - - + +
51A TYR* 3.0 52.2 + - + +
52A HIS* 3.5 10.5 - - - +
54A GLY* 1.3 76.6 - - - +
56A TYR* 1.3 58.6 + - - +
58A MET* 3.3 10.7 + - - +
59A ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 56 (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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33A LEU* 3.5 56.2 - - + +
36A SER* 3.5 13.2 - - - -
37A ALA* 3.6 11.4 - - + +
52A HIS 2.9 14.5 + - - +
53A LEU* 3.2 16.6 + - + +
55A GLN* 1.3 77.4 - - - +
57A ILE* 1.3 66.8 + - - +
59A ALA* 3.2 5.1 + - + +
60A LYS* 2.9 53.0 + - + +
62A LEU* 4.3 2.9 - - + -
76A ASP* 2.6 36.1 + - - -
77A PRO* 3.8 7.6 - - - +
78A LEU* 4.0 22.0 - - + -
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Residues in contact with ILE 57 (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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53A LEU 2.8 21.4 + - - +
54A GLY* 3.6 4.3 - - - +
56A TYR* 1.3 79.3 - - + +
58A MET* 1.3 61.8 + - - +
60A LYS 3.5 0.9 + - - -
61A GLN 3.1 3.3 + - - -
62A LEU* 3.0 40.9 + - + -
63A TYR* 3.5 30.0 + - + -
71A VAL* 4.1 18.8 - - + -
78A LEU* 4.0 24.2 - - + -
87A PHE* 4.5 0.2 - - + -
201A 20U 3.7 52.0 - - + -
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Residues in contact with MET 58 (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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54A GLY 3.1 17.1 + - - +
55A GLN* 3.8 11.9 - - - +
57A ILE* 1.3 72.8 - - - +
59A ALA* 1.3 66.6 + - - +
61A GLN* 3.1 18.7 + - - +
63A TYR* 3.8 38.1 - - - +
65A GLU* 4.3 25.1 - - + +
201A 20U 3.8 23.8 - - + -
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Residues in contact with ALA 59 (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 SER 5.8 1.8 - - - +
37A ALA* 5.7 6.1 - - - -
55A GLN 2.9 18.9 + - - +
56A TYR* 3.2 8.7 + - + +
58A MET* 1.3 77.7 - - - +
60A LYS* 1.3 67.1 + - + +
61A GLN* 3.2 6.5 + - - +
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Residues in contact with LYS 60 (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 SER* 5.1 6.3 - - - -
56A TYR* 2.9 57.4 + - + +
59A ALA* 1.3 82.2 - - + +
61A GLN* 1.3 72.9 + - - +
62A LEU* 3.2 24.4 + - + +
76A ASP* 3.6 13.0 - - - +
77A PRO* 6.1 0.7 - - - -
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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