Contacts of the helix formed by residues 48 - 69 (chain A) in PDB entry 5LLU
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 ASN 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.2 47.6 + - + +
47A ARG* 1.4 82.9 - - - +
49A ALA* 1.4 52.8 + - - +
50A LEU 3.5 2.5 - - - -
51A LEU* 3.2 27.2 + - + +
52A LEU* 2.8 46.2 + - + +
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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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45A LEU 3.6 13.7 + - - +
46A ARG* 3.7 17.0 - - - +
47A ARG 3.2 4.5 + - - +
48A ASN* 1.4 75.3 - - - +
50A LEU* 1.3 61.7 + - - +
52A LEU* 4.1 3.4 - - - +
53A LEU* 3.2 35.4 + - + +
267A TRP* 5.6 7.4 - - + -
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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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47A ARG 5.1 0.6 + - - -
48A ASN 3.5 0.4 - - - -
49A ALA* 1.3 75.0 - - - +
51A LEU* 1.4 63.9 + - - +
53A LEU* 3.5 5.9 + - + +
54A THR* 3.2 23.5 + - + +
266A MET* 3.4 44.4 - - + +
267A TRP* 3.6 48.2 - - + +
270A PRO* 3.8 17.9 - - + -
334A GLN* 3.7 23.8 - - - +
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Residues in contact with LEU 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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44A PHE* 6.1 2.7 - - + -
48A ASN* 3.2 32.3 + - + +
50A LEU* 1.4 76.9 - - - +
52A LEU* 1.3 65.6 + - + +
54A THR* 2.7 21.6 + - - +
55A VAL* 3.1 25.4 - - + +
330A ALA 3.7 12.6 - - - +
331A GLY 5.2 1.1 - - - +
333A LEU* 3.7 44.6 - - + -
334A GLN* 3.8 29.2 - - + +
337A ILE* 5.2 1.8 - - + -
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Residues in contact with LEU 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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44A PHE* 3.7 41.7 - - + +
45A LEU* 3.8 32.5 - - + +
48A ASN* 2.8 29.1 + - + +
49A ALA* 4.2 3.1 - - - +
51A LEU* 1.3 74.2 - - + +
53A LEU* 1.4 60.7 + - - +
55A VAL* 3.2 15.2 + - + +
56A LEU* 2.9 30.5 + - - +
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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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49A ALA* 3.2 27.6 + - + +
50A LEU* 3.8 9.4 - - + +
51A LEU 3.3 0.2 - - - -
52A LEU* 1.4 75.6 - - - +
54A THR* 1.4 56.8 + - - +
56A LEU* 3.7 23.5 - - + +
57A ALA* 3.0 24.8 + - - +
267A TRP* 4.9 13.5 - - + -
270A PRO* 3.7 24.3 - - + +
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Residues in contact with THR 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* 3.2 13.9 + - + +
51A LEU* 2.7 23.6 + - - -
53A LEU* 1.4 74.5 - - - +
55A VAL* 1.4 62.5 + - - +
57A ALA* 3.3 17.7 - - - +
58A VAL* 3.4 5.9 + - - +
266A MET 5.2 0.7 - - - +
269A ALA* 4.3 9.9 - - + -
270A PRO* 3.7 34.1 - - + -
273A ILE* 5.2 4.0 - - + -
334A GLN* 4.6 11.8 - - + +
337A ILE* 3.4 36.1 - - + +
338A THR* 5.5 3.8 - - + -
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Residues in contact with VAL 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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51A LEU* 3.1 31.0 + - + +
52A LEU* 3.2 15.5 + - + +
54A THR* 1.4 73.1 - - - +
56A LEU* 1.4 57.3 + - - +
58A VAL* 3.0 21.6 + - + +
59A ILE* 3.1 31.7 + - + +
333A LEU* 5.2 3.1 - - + -
337A ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 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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52A LEU 2.9 17.4 + - - +
53A LEU* 3.7 26.7 - - + +
55A VAL* 1.4 76.1 - - - +
57A ALA* 1.4 52.3 + - - +
59A ILE* 4.4 11.4 - - + -
60A LEU* 2.8 57.7 + - + +
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Residues in contact with ALA 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 3.0 15.9 + - - +
54A THR* 3.3 16.8 - - - +
56A LEU* 1.4 77.4 - - - +
58A VAL* 1.3 55.9 + - - +
61A GLY* 3.0 24.9 + - - -
270A PRO* 3.2 28.7 - - + +
273A ILE* 4.3 6.7 - - + -
274A LEU* 3.4 26.0 - - - +
277A ILE* 4.2 0.3 - - - +
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Residues in contact with VAL 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 THR 3.5 13.9 - - - +
55A VAL* 3.0 9.2 + - + +
57A ALA* 1.3 74.0 - - - +
59A ILE* 1.4 67.5 + - + +
62A VAL* 3.0 43.8 + - + +
273A ILE* 3.9 12.3 - - + -
277A ILE* 3.4 13.3 - - + +
337A ILE* 3.8 21.1 - - + -
340A LEU* 3.8 30.1 - - + -
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Residues in contact with ILE 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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55A VAL* 3.1 29.7 + - + +
56A LEU* 3.9 11.7 - - + +
58A VAL* 1.4 83.9 - - + +
60A LEU* 1.3 59.1 + - - +
62A VAL* 3.8 4.6 + - - +
63A VAL* 3.3 29.3 + - + +
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Residues in contact with LEU 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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56A LEU* 2.8 40.0 + - + +
59A ILE* 1.3 72.0 - - - +
61A GLY* 1.3 57.1 + - - +
63A VAL* 3.4 16.1 + - + +
64A LEU* 2.9 31.6 + - + +
274A LEU* 3.7 20.0 - - + -
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Residues in contact with GLY 61 (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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57A ALA 3.0 22.5 + - - -
58A VAL 3.3 1.1 + - - -
60A LEU* 1.3 74.5 - - - +
62A VAL* 1.4 61.8 + - - +
64A LEU* 3.8 2.0 + - - -
65A GLY 3.3 16.8 + - - -
274A LEU* 3.5 23.5 - - - +
277A ILE* 3.6 8.5 - - - -
278A ALA* 3.3 16.5 - - - +
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Residues in contact with VAL 62 (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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58A VAL* 3.0 28.7 + - + +
59A ILE* 4.1 5.6 - - - +
61A GLY* 1.4 71.7 - - - +
63A VAL* 1.4 66.6 + - + +
66A PHE* 3.3 33.7 + - + -
277A ILE* 3.7 13.5 - - + -
281A ILE* 3.3 33.5 - - + +
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Residues in contact with VAL 63 (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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59A ILE* 3.3 19.9 + - + +
60A LEU* 3.4 22.4 + - + +
61A GLY 3.4 0.4 - - - -
62A VAL* 1.4 77.0 - - + +
64A LEU* 1.3 65.4 + - - +
66A PHE* 3.5 4.9 + - - +
67A LEU* 3.2 29.8 + - + +
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Residues in contact with LEU 64 (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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60A LEU* 2.9 19.9 + - + +
61A GLY 3.9 3.1 - - - +
62A VAL 3.5 0.2 - - - -
63A VAL* 1.3 76.0 - - - +
65A GLY* 1.3 56.9 + - - +
67A LEU* 3.4 11.1 - - + +
68A LEU* 3.1 54.3 + - + +
81A PHE* 3.8 28.5 - - + -
274A LEU* 3.8 26.2 - - + -
275A PHE* 4.4 9.9 - - + -
278A ALA* 3.8 11.0 - - + -
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Residues in contact with GLY 65 (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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61A GLY 3.3 8.8 + - - -
62A VAL 3.6 0.2 + - - -
63A VAL 3.4 0.4 - - - -
64A LEU* 1.3 79.1 - - - +
66A PHE* 1.4 50.0 + - - +
68A LEU* 3.3 2.3 + - - -
69A ARG* 2.8 32.3 + - - +
81A PHE* 5.1 0.7 - - - -
278A ALA* 3.8 20.6 - - - -
281A ILE* 3.6 19.3 - - - -
282A VAL* 3.4 13.5 - - - +
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Residues in contact with PHE 66 (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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62A VAL* 3.3 43.7 + - + +
63A VAL* 4.1 4.7 - - - +
65A GLY* 1.4 72.2 - - - +
67A LEU* 1.3 62.8 + - - +
69A ARG* 3.9 21.8 + - + +
70A PRO* 3.8 13.0 - - - +
281A ILE* 3.4 24.0 - - + +
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Residues in contact with LEU 67 (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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63A VAL* 3.2 21.2 + - + +
64A LEU* 3.4 15.9 - - + +
66A PHE* 1.3 76.6 - - - +
68A LEU* 1.4 70.0 + - + +
70A PRO* 3.5 9.4 - - - +
71A TYR* 3.3 22.0 - - + +
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Residues in contact with LEU 68 (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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64A LEU* 3.1 47.4 + - + +
65A GLY 3.6 3.1 - - - +
67A LEU* 1.4 88.6 - - + +
69A ARG* 1.4 61.2 + - - +
70A PRO* 3.6 1.3 - - - -
71A TYR* 3.4 31.8 - - + +
73A LEU* 5.8 0.3 - - - +
81A PHE* 3.7 29.2 - - + -
282A VAL* 4.5 11.3 - - + +
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Residues in contact with ARG 69 (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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65A GLY 2.8 15.3 + - - +
66A PHE* 4.0 25.3 - - + +
67A LEU 3.5 0.2 - - - -
68A LEU* 1.4 75.0 - - - +
70A PRO* 1.4 67.0 - - + +
71A TYR 3.3 2.8 + - - +
73A LEU* 3.5 27.0 - - + +
281A ILE* 2.8 39.9 + - - +
282A VAL* 3.8 26.3 + - - +
283A GLU 3.6 18.8 + - - -
453A TRP* 6.0 2.0 - - - -
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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