Contacts of the helix formed by residues 42 - 60 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43L TRP* 1.3 77.4 + - - +
44L GLU* 3.1 6.7 + - - +
45L LYS* 3.2 10.3 + - - +
46L GLN* 2.7 38.3 + - + +
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Residues in contact with TRP 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG 6.0 1.3 - - - -
92C ASN 4.6 9.0 - - - -
93C GLU* 4.2 23.3 - - - +
42L ALA* 1.3 87.9 - - - +
44L GLU* 1.3 91.3 + - + +
46L GLN* 3.3 8.9 + - - +
47L GLN* 2.8 75.5 + - - +
135L LYS* 4.7 27.4 - - + -
138L LEU* 5.1 5.4 - - + -
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ALA 3.1 3.8 - - - +
43L TRP* 1.3 108.6 + - + +
45L LYS* 1.3 61.8 + - - +
47L GLN* 4.6 0.9 - - - -
48L ARG* 3.1 25.3 + - - +
134L LEU* 3.2 37.6 - - + +
135L LYS* 3.7 30.4 + - + +
138L LEU* 3.9 12.1 - - + +
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Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ALA* 3.2 6.2 + - - +
44L GLU* 1.3 79.2 - - - +
46L GLN* 1.3 77.1 + - - +
48L ARG* 3.5 11.0 + - - +
49L LYS* 3.2 21.4 + - + +
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Residues in contact with GLN 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ALA* 2.7 38.7 + - + +
43L TRP* 3.6 7.2 - - - +
45L LYS* 1.3 91.4 - - - +
47L GLN* 1.3 67.4 + - - +
49L LYS* 2.9 19.5 + - - +
50L THR* 2.9 29.3 + - - +
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Residues in contact with GLN 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASN 4.3 1.2 + - - +
93C GLU 4.4 2.4 + - - -
95C ARG* 2.3 60.4 + - + +
43L TRP* 2.8 55.2 + - - +
44L GLU* 4.0 3.4 - - - +
46L GLN* 1.3 73.3 - - - +
48L ARG* 1.3 57.1 + - - +
50L THR* 4.6 3.8 - - - +
51L PHE* 2.9 52.5 + - + -
138L LEU* 4.0 16.3 - - + +
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Residues in contact with ARG 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L GLU 3.1 18.2 + - - +
45L LYS* 3.6 11.5 + - - +
46L GLN 3.1 0.6 - - - -
47L GLN* 1.3 77.2 - - - +
49L LYS* 1.3 54.6 + - - +
51L PHE* 4.2 0.3 - - - +
52L THR* 2.5 41.6 + - - +
67L GLU 4.6 2.1 + - - -
68L ASN* 3.0 29.6 - - - +
69L ILE* 3.7 17.2 - - + +
70L GLU* 2.5 43.6 + - - -
134L LEU* 4.2 15.9 - - + -
138L LEU* 3.9 15.0 - - + +
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Residues in contact with LYS 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LYS 3.2 9.6 + - - +
46L GLN* 2.9 18.7 + - - +
48L ARG* 1.3 82.9 - - - +
50L THR* 1.3 73.8 + - - +
52L THR* 3.6 4.9 - - - -
53L ALA* 3.0 31.5 + - + +
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Residues in contact with THR 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L GLN* 2.9 17.9 + - - +
47L GLN* 4.1 4.3 - - - -
49L LYS* 1.3 90.6 + - - +
51L PHE* 1.3 67.4 + - + +
53L ALA* 3.3 6.7 + - - +
54L TRP* 2.9 30.6 + - + +
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Residues in contact with PHE 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 0.9 146.0 - - + -
47L GLN* 2.9 41.9 + - + +
50L THR* 1.3 81.8 - - + +
52L THR* 1.3 58.7 + - - +
54L TRP* 3.2 6.6 + - - +
55L CYS* 2.8 33.6 + - - -
69L ILE* 4.0 15.5 - - + -
138L LEU* 3.3 30.3 - - + -
141L ILE* 4.0 13.2 - - + -
142L TRP* 3.7 3.8 - + + -
145L ILE* 3.7 15.9 - - + -
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Residues in contact with THR 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L ARG* 2.5 28.4 + - - +
49L LYS* 3.6 5.2 - - - -
51L PHE* 1.3 77.1 - - - +
53L ALA* 1.3 63.1 + - - +
55L CYS* 3.2 2.8 + - - +
56L ASN* 2.9 39.3 + - - +
66L ILE* 4.0 17.3 - - + +
67L GLU 4.0 19.9 + - - +
69L ILE* 3.6 25.3 + - - +
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L LYS* 3.0 18.8 + - + +
50L THR* 3.6 6.7 - - - +
52L THR* 1.3 77.5 - - - +
54L TRP* 1.3 63.4 + - - +
56L ASN* 3.4 6.9 + - - +
57L SER* 3.0 24.8 + - - -
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Residues in contact with TRP 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L THR* 2.9 17.3 + - + +
51L PHE* 3.5 9.2 - - - +
53L ALA* 1.3 77.5 - - - +
55L CYS* 1.3 85.8 + - - +
57L SER* 2.7 26.2 + - - -
58L HIS* 3.5 34.9 + + - -
82L LEU* 4.1 25.6 - - + -
86L ILE* 4.1 25.4 - - + -
141L ILE* 4.9 0.9 - - + -
144L ILE* 4.2 5.2 - - + -
145L ILE* 3.6 47.3 - - + +
148L PHE 5.8 0.2 - - - -
149L ALA* 4.2 25.4 - - + +
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Residues in contact with CYS 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L PHE 2.8 26.0 + - - +
52L THR 3.6 4.3 - - - +
54L TRP* 1.3 83.2 - - - +
56L ASN* 1.3 58.4 + - - +
58L HIS* 3.1 5.7 + - - +
59L LEU* 2.9 34.7 + - + +
66L ILE* 4.1 14.8 - - + -
69L ILE* 4.7 2.0 - - - -
73L PHE* 3.9 14.1 - - + -
82L LEU* 3.7 25.1 - - + +
141L ILE* 3.8 31.9 - - - -
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Residues in contact with ASN 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L THR* 2.9 27.0 + - - +
53L ALA* 3.7 7.0 - - - +
55L CYS* 1.3 73.3 - - - +
57L SER* 1.3 56.2 + - - +
58L HIS 3.0 5.4 - - - -
59L LEU* 4.2 3.5 - - - +
60L ARG* 3.0 20.1 + - - +
65L GLN* 2.7 49.9 + - - +
66L ILE* 2.7 54.3 - - - +
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Residues in contact with SER 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L ALA 3.0 14.2 + - - -
54L TRP* 2.7 25.0 + - - -
56L ASN* 1.3 75.8 - - - +
58L HIS* 1.3 66.0 + - - +
60L ARG* 2.9 43.7 + - - +
61L LYS* 3.5 11.8 + - - -
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Residues in contact with HIS 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 3.5 56.0 + + - -
55L CYS 3.1 7.0 + - - +
56L ASN 3.0 0.4 - - - -
57L SER* 1.3 84.6 + - - +
59L LEU* 1.3 65.8 + - - +
60L ARG 3.1 1.8 - - - -
61L LYS* 3.0 48.2 + - - +
62L ALA 4.1 0.7 + - - -
82L LEU* 3.8 13.7 - - + -
85L VAL* 3.6 17.3 - - + +
86L ILE* 3.5 20.3 - - + +
149L ALA* 5.8 1.2 - - - +
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Residues in contact with LEU 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L CYS* 2.9 23.1 + - + +
56L ASN* 4.2 10.5 - - - +
58L HIS* 1.3 76.2 - - - +
60L ARG* 1.3 52.9 + - - +
62L ALA* 2.7 28.9 + - - +
63L GLY 3.3 6.2 + - - -
64L THR* 3.3 35.9 + - + +
65L GLN* 4.2 1.3 - - - +
66L ILE* 3.8 28.9 - - + +
73L PHE* 4.4 14.8 - - + -
78L LYS* 3.6 12.1 - - + +
81L LEU* 4.3 8.5 - - + -
82L LEU* 3.6 35.9 - - + +
85L VAL* 5.0 2.0 - - + -
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Residues in contact with ARG 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ASN 3.0 18.8 + - - +
57L SER* 2.9 36.8 + - - +
59L LEU* 1.3 77.6 - - - +
61L LYS* 1.3 67.4 + - + +
62L ALA 3.1 0.2 - - - -
63L GLY* 3.1 17.9 + - - +
64L THR 3.3 10.5 + - - +
65L GLN* 3.5 12.6 - - - +
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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