Contacts of the helix formed by residues 42 - 60 (chain T) in PDB entry 3LUE
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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43T TRP* 1.3 78.6 + - - +
44T GLU* 3.1 6.1 + - - +
45T LYS* 3.2 9.9 + - - +
46T GLN* 2.7 37.7 + - + +
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Residues in contact with TRP 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ARG 6.0 2.0 - - - -
92J ASN 4.6 8.5 - - - -
93J GLU* 4.2 23.1 - - + +
42T ALA* 1.3 88.8 - - - +
44T GLU* 1.3 90.1 + - + +
46T GLN* 3.2 8.4 + - - +
47T GLN* 2.8 77.3 + - - +
135T LYS* 4.7 27.4 - - + -
138T LEU* 5.1 4.7 - - + -
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Residues in contact with GLU 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T ALA 3.1 3.5 - - - +
43T TRP* 1.3 109.6 + - + +
45T LYS* 1.3 62.2 + - - +
47T GLN* 4.6 1.3 - - - -
48T ARG* 3.1 24.9 + - - +
134T LEU* 3.2 37.0 - - + +
135T LYS* 3.7 31.6 + - - +
138T LEU* 3.9 12.3 - - + +
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Residues in contact with LYS 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T ALA* 3.2 6.6 + - - +
44T GLU* 1.3 78.2 - - - +
46T GLN* 1.3 76.5 + - - +
48T ARG* 3.5 10.5 + - - +
49T LYS* 3.2 21.8 + - + +
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Residues in contact with GLN 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T ALA* 2.7 39.3 + - + +
43T TRP* 3.2 8.0 + - - +
45T LYS* 1.3 91.6 - - - +
47T GLN* 1.3 67.1 + - - +
49T LYS* 2.9 18.7 + - - +
50T THR* 2.9 29.4 + - - +
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Residues in contact with GLN 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ASN 4.3 1.8 + - - +
93J GLU 4.4 2.2 + - - -
95J ARG* 2.3 61.3 + - + +
43T TRP* 2.8 55.0 + - - +
44T GLU* 4.0 3.8 - - - +
46T GLN* 1.3 73.8 - - - +
48T ARG* 1.3 57.2 + - - +
50T THR* 4.6 3.4 - - - +
51T PHE* 2.9 52.3 + - + -
138T LEU* 4.0 17.1 - - + +
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Residues in contact with ARG 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU 3.1 17.8 + - - +
45T LYS* 3.6 11.3 + - - +
46T GLN 3.1 0.8 - - - -
47T GLN* 1.3 77.0 - - - +
49T LYS* 1.3 56.5 + - - +
51T PHE* 4.2 0.5 - - - +
52T THR* 2.5 41.5 + - - +
67T GLU 4.6 2.3 + - - -
68T ASN* 3.0 30.0 - - - +
69T ILE* 3.7 17.9 - - + +
70T GLU* 2.5 42.7 + - - -
134T LEU* 4.2 15.9 - - - -
138T LEU* 3.9 16.5 - - + +
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Residues in contact with LYS 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T LYS* 3.2 9.2 + - + +
46T GLN* 2.9 20.0 + - - +
48T ARG* 1.3 83.6 - - - +
50T THR* 1.3 73.2 + - - +
52T THR* 3.6 4.4 - - - -
53T ALA* 3.0 30.7 + - + +
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Residues in contact with THR 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46T GLN* 2.9 17.6 + - - +
47T GLN* 4.1 4.7 - - - -
49T LYS* 1.3 90.6 + - - +
51T PHE* 1.3 68.6 + - + +
53T ALA* 3.3 6.6 + - - +
54T TRP* 2.9 30.3 + - + +
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Residues in contact with PHE 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ARG* 0.8 150.3 - - + -
47T GLN* 2.9 39.9 + - + +
50T THR* 1.3 83.4 - - + +
52T THR* 1.3 57.8 + - - +
54T TRP* 3.2 6.9 + - - +
55T CYS* 2.8 33.8 + - - -
69T ILE* 4.0 15.9 - - + -
138T LEU* 3.3 29.2 - - + -
141T ILE* 4.0 13.9 - - + -
142T TRP* 3.7 3.6 - + + -
145T ILE* 3.7 15.5 - - + -
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Residues in contact with THR 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T ARG* 2.5 28.3 + - - +
49T LYS* 3.6 5.2 - - - -
51T PHE* 1.3 77.1 - - - +
53T ALA* 1.3 63.2 + - - +
55T CYS* 3.2 2.4 + - - +
56T ASN* 2.9 39.8 + - - +
66T ILE* 4.0 16.2 - - + +
67T GLU 4.0 20.8 + - - +
69T ILE* 3.6 25.2 + - + +
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Residues in contact with ALA 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T LYS* 3.0 19.4 + - + +
50T THR* 3.6 6.1 - - - +
52T THR* 1.3 77.4 - - - +
54T TRP* 1.3 62.7 + - - +
56T ASN* 3.4 7.3 + - - +
57T SER* 3.0 24.4 + - - -
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Residues in contact with TRP 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T THR* 2.9 17.2 + - + +
51T PHE* 3.5 9.9 - - - +
52T THR 3.2 0.2 - - - -
53T ALA* 1.3 77.6 - - - +
55T CYS* 1.3 85.6 + - - +
57T SER* 2.7 25.8 + - - -
58T HIS* 3.5 35.8 + + - -
82T LEU* 4.1 25.6 - - + -
86T ILE* 4.1 26.2 - - + -
141T ILE* 4.9 1.3 - - + -
144T ILE* 4.2 5.4 - - + -
145T ILE* 3.6 46.1 - - + +
148T PHE 5.8 0.2 - - - -
149T ALA* 4.2 24.3 - - + +
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Residues in contact with CYS 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T PHE 2.8 27.5 + - - +
52T THR 3.6 4.3 - - - +
54T TRP* 1.3 82.0 - - - +
56T ASN* 1.3 58.7 + - - +
58T HIS* 3.1 5.2 + - - +
59T LEU* 2.9 34.6 + - + +
66T ILE* 4.1 14.6 - - + -
69T ILE* 4.7 1.6 - - - -
73T PHE* 3.9 13.7 - - + -
82T LEU* 3.7 26.6 - - + +
141T ILE* 3.8 31.2 - - - -
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Residues in contact with ASN 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T THR* 2.9 26.7 + - - +
53T ALA* 3.7 7.0 + - - +
55T CYS* 1.3 72.6 - - - +
57T SER* 1.3 56.2 + - - +
58T HIS 3.0 5.6 - - - -
59T LEU* 4.2 4.5 - - - +
60T ARG* 3.0 19.8 + - - +
65T GLN* 2.7 47.8 + - - +
66T ILE* 2.7 53.7 - - - +
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Residues in contact with SER 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53T ALA 3.0 14.8 + - - -
54T TRP* 2.7 25.4 + - - -
56T ASN* 1.3 75.4 - - - +
58T HIS* 1.3 65.5 + - - +
60T ARG* 2.9 43.6 + - - +
61T LYS* 3.5 11.4 + - - -
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Residues in contact with HIS 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T TRP* 3.5 57.1 + + - -
55T CYS 3.1 6.4 + - - +
56T ASN 3.0 0.4 - - - -
57T SER* 1.3 85.7 + - - +
59T LEU* 1.3 66.3 + - - +
60T ARG 3.1 1.8 - - - -
61T LYS* 3.0 47.9 + - - +
62T ALA 4.1 0.5 + - - -
82T LEU* 3.8 13.7 - - + -
85T VAL* 3.6 17.6 - - + +
86T ILE* 3.5 20.2 - - + +
149T ALA* 5.8 1.0 - - - +
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Residues in contact with LEU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T CYS* 2.9 24.2 + - + +
56T ASN* 4.2 10.3 - - - +
58T HIS* 1.3 76.8 - - - +
60T ARG* 1.3 53.3 + - - +
62T ALA* 2.7 29.7 + - - +
63T GLY 3.3 6.4 + - - -
64T THR* 3.3 35.2 + - + +
65T GLN* 4.2 2.0 - - - +
66T ILE* 3.8 29.8 - - + +
73T PHE* 4.4 13.5 - - + -
78T LYS* 3.6 12.1 - - + +
81T LEU* 4.3 8.7 - - + +
82T LEU* 3.6 35.2 - - + +
85T VAL* 5.0 2.0 - - + -
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Residues in contact with ARG 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T ASN 3.0 19.4 + - - +
57T SER* 2.9 37.2 + - - +
59T LEU* 1.3 76.5 - - - +
61T LYS* 1.3 66.5 + - + +
63T GLY* 3.1 17.9 + - - +
64T THR 3.3 10.7 + - - +
65T GLN* 3.5 12.8 - - + +
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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
------------------------------------------------------------
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