Contacts of the helix formed by residues 42 - 60 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43K TRP* 1.3 79.0 + - - +
44K GLU* 3.1 6.0 + - - +
45K LYS* 3.2 10.5 + - - +
46K GLN* 2.7 38.2 + - + +
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Residues in contact with TRP 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 6.1 1.6 - - - -
92A ASN 4.6 8.3 - - - -
93A GLU* 4.2 22.9 - - - +
42K ALA* 1.3 88.5 - - - +
44K GLU* 1.3 90.4 + - + +
46K GLN* 3.6 8.7 - - - +
47K GLN* 2.8 77.2 + - - +
135K LYS* 4.7 26.9 - - + -
138K LEU* 5.1 5.8 - - + -
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Residues in contact with GLU 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ALA* 3.1 4.0 - - - +
43K TRP* 1.3 110.3 + - + +
45K LYS* 1.3 62.0 + - - +
47K GLN* 4.6 1.3 - - - -
48K ARG* 3.1 24.9 + - - +
134K LEU* 3.2 37.4 - - + +
135K LYS* 3.7 31.4 + - + +
138K LEU* 3.9 12.4 - - + +
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Residues in contact with LYS 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ALA* 3.2 7.0 + - - +
44K GLU* 1.3 78.9 - - - +
46K GLN* 1.3 78.7 + - - +
48K ARG* 3.5 10.8 + - - +
49K LYS* 3.2 21.8 + - + +
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Residues in contact with GLN 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K ALA* 2.7 39.8 + - + +
43K TRP* 3.3 7.8 + - - +
45K LYS* 1.3 91.6 - - - +
47K GLN* 1.3 66.2 + - - +
49K LYS* 2.9 18.4 + - - +
50K THR* 2.9 29.2 + - - +
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Residues in contact with GLN 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN 4.3 1.8 + - - +
93A GLU 4.4 2.0 + - - -
95A ARG* 2.4 60.6 + - + +
43K TRP* 2.8 56.6 + - - +
44K GLU 4.0 3.1 - - - +
46K GLN* 1.3 73.6 - - - +
48K ARG* 1.3 56.8 + - - +
50K THR* 4.6 3.6 - - - +
51K PHE* 2.9 52.7 + - + -
138K LEU* 4.0 16.3 - - + +
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Residues in contact with ARG 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K GLU 3.1 18.7 + - - +
45K LYS* 3.6 11.1 + - - +
46K GLN 3.1 0.4 - - - -
47K GLN* 1.3 78.5 - - - +
49K LYS* 1.3 57.6 + - - +
51K PHE* 4.2 0.5 - - - +
52K THR* 2.5 40.6 + - - +
67K GLU 4.6 2.1 + - - -
68K ASN* 3.0 29.8 - - - +
69K ILE* 3.7 17.5 - - + +
70K GLU* 2.5 43.1 + - - -
134K LEU* 4.2 16.4 - - - -
138K LEU* 3.9 16.1 - - + +
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Residues in contact with LYS 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K LYS* 3.2 10.1 + - + +
46K GLN* 2.9 19.3 + - - +
48K ARG* 1.3 81.8 - - - +
50K THR* 1.3 73.6 + - - +
52K THR* 3.6 4.7 - - - -
53K ALA* 3.0 30.6 + - + +
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Residues in contact with THR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K GLN* 2.9 18.0 + - - +
47K GLN* 4.1 4.5 - - - -
49K LYS* 1.3 89.8 + - - +
51K PHE* 1.3 69.0 + - + +
53K ALA* 3.3 6.9 + - - +
54K TRP* 2.9 29.6 + - + +
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Residues in contact with PHE 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 0.9 146.9 - - + -
47K GLN* 2.9 40.6 + - + +
50K THR* 1.3 81.8 - - + +
52K THR* 1.3 57.7 + - - +
54K TRP* 3.2 6.0 + - - +
55K CYS* 2.8 34.0 + - - -
69K ILE* 4.0 16.4 - - + -
138K LEU* 3.3 29.6 - - + -
141K ILE* 4.0 14.1 - - + -
142K TRP* 3.7 2.9 - + + -
145K ILE* 3.7 15.7 - - + -
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Residues in contact with THR 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K ARG* 2.5 29.5 + - - +
49K LYS* 3.6 5.3 - - - -
51K PHE* 1.3 76.1 - - - +
53K ALA* 1.3 63.8 + - - +
55K CYS* 3.2 2.8 + - - +
56K ASN* 2.9 38.9 + - - +
66K ILE* 4.0 16.4 - - + +
67K GLU 4.0 20.9 + - - +
69K ILE* 3.6 24.3 + - + +
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Residues in contact with ALA 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K LYS* 3.0 19.2 + - + +
50K THR* 3.6 6.1 - - + +
52K THR* 1.3 77.9 - - - +
54K TRP* 1.3 63.0 + - - +
56K ASN* 3.7 6.6 - - - +
57K SER* 3.0 24.3 + - - -
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Residues in contact with TRP 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K THR* 2.9 17.6 + - + +
51K PHE* 3.5 9.6 - - - +
52K THR 3.2 0.2 - - - -
53K ALA* 1.3 76.9 - - - +
55K CYS* 1.3 85.3 + - - +
57K SER* 2.7 26.1 + - - -
58K HIS* 3.5 35.9 + + - -
82K LEU* 4.1 25.6 - - + -
86K ILE* 4.1 25.4 - - + -
141K ILE* 4.9 1.1 - - + -
144K ILE* 4.2 5.2 - - + -
145K ILE* 3.6 45.7 - - + +
148K PHE 5.8 0.4 - - - -
149K ALA* 4.2 25.5 - - + +
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Residues in contact with CYS 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K PHE 2.8 26.9 + - - +
52K THR 3.6 4.3 - - - +
54K TRP* 1.3 82.9 - - - +
56K ASN* 1.3 58.9 + - - +
58K HIS* 3.1 5.4 + - - +
59K LEU* 2.9 34.4 + - + +
66K ILE* 4.1 15.3 - - + -
69K ILE* 4.7 2.2 - - - -
73K PHE* 3.9 13.5 - - + -
82K LEU* 3.7 26.8 - - + +
141K ILE* 3.8 31.0 - - - -
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Residues in contact with ASN 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K THR* 2.9 26.1 + - - +
53K ALA* 3.7 7.5 - - - +
55K CYS* 1.3 73.7 - - - +
57K SER* 1.3 56.4 + - - +
58K HIS 3.0 5.4 - - - -
59K LEU* 4.2 3.9 - - - +
60K ARG* 3.0 19.3 + - - +
65K GLN* 2.7 48.3 + - - +
66K ILE* 2.7 54.8 - - - +
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Residues in contact with SER 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K ALA 3.0 15.2 + - - -
54K TRP* 2.7 25.7 + - - -
56K ASN* 1.3 74.7 - - - +
58K HIS* 1.3 65.0 + - - +
60K ARG* 2.9 42.8 + - - +
61K LYS* 3.5 11.6 + - - -
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Residues in contact with HIS 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K TRP* 3.5 57.0 + + - -
55K CYS 3.1 6.4 + - - +
56K ASN 3.0 0.6 - - - -
57K SER* 1.3 84.2 + - - +
59K LEU* 1.3 65.2 + - - +
60K ARG 3.1 1.8 - - - -
61K LYS* 3.0 46.7 + - - +
62K ALA 4.1 0.5 + - - -
82K LEU* 3.8 14.4 - - + -
85K VAL* 3.6 17.2 - - + +
86K ILE* 3.5 21.5 - - + +
149K ALA* 5.8 1.2 - - - +
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Residues in contact with LEU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K CYS* 2.9 22.6 + - + +
56K ASN* 4.2 10.8 - - - +
58K HIS* 1.3 76.0 - - - +
60K ARG* 1.3 53.9 + - - +
62K ALA* 2.7 29.5 + - - +
63K GLY 3.3 6.8 + - - -
64K THR* 3.3 34.1 + - + +
65K GLN* 4.2 1.6 - - - +
66K ILE* 3.8 29.8 - - + +
73K PHE* 4.4 13.7 - - + -
78K LYS* 3.6 12.6 - - + +
81K LEU* 4.3 8.5 - - + +
82K LEU* 3.6 35.2 - - + +
85K VAL* 5.0 2.2 - - + -
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Residues in contact with ARG 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K ASN 3.0 18.5 + - - +
57K SER* 2.9 37.7 + - - +
59K LEU* 1.3 77.0 - - - +
61K LYS* 1.3 66.3 + - + +
63K GLY* 3.1 17.4 + - - +
64K THR 3.3 11.1 + - - +
65K 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
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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