Contacts of the helix formed by residues 52 - 71 (chain D) in PDB entry 3BUW
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 ASP 52 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 3.7 10.7 + - + +
51D VAL* 1.3 74.6 - - - +
53D LYS* 1.3 65.9 + - - +
54D LYS* 2.7 40.7 + - - +
55D MET* 3.3 24.3 + - - +
56D VAL* 3.3 15.3 + - - +
106D MET* 4.7 3.6 - - - -
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ASP* 1.3 72.2 - - - +
54D LYS* 1.3 60.6 + - + +
56D VAL* 3.5 9.3 - - + +
57D GLU* 2.9 58.7 + - + +
60D TRP* 4.5 5.8 - - - -
99D LEU* 3.5 30.3 - - - +
106D MET* 4.1 24.7 - - + +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ASP* 2.7 29.0 + - - +
53D LYS* 1.3 71.3 - - + +
55D MET* 1.3 57.2 + - - +
57D GLU* 2.7 37.6 + - + +
58D LYS* 3.2 5.0 + - - +
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Residues in contact with MET 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLY* 4.5 7.4 - - - +
50D THR 3.0 27.6 - - - +
51D VAL* 3.8 28.9 - - + -
52D ASP* 3.3 17.4 + - - +
54D LYS* 1.3 78.5 - - - +
56D VAL* 1.3 60.4 + - - +
58D LYS* 3.2 12.1 + - + +
59D CYS* 2.8 29.6 + - - +
116D ARG 6.0 0.2 - - - +
119D MET* 4.4 3.4 - - - -
120D GLU* 5.6 1.3 - - - -
123D MET* 3.7 25.5 - - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 3.8 21.1 - - + -
52D ASP 3.3 17.9 - - - +
53D LYS* 3.5 11.9 - - + +
54D LYS 2.9 0.4 + - - -
55D MET* 1.3 76.0 - - - +
57D GLU* 1.3 63.4 + - - +
59D CYS* 3.2 4.2 - - - +
60D TRP* 3.0 43.5 + - + +
95D LEU* 5.5 3.1 - - + -
99D LEU* 3.7 37.9 - - + -
106D MET* 5.2 0.9 - - + -
115D PHE* 5.0 2.9 - - + -
119D MET* 4.0 18.6 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LYS* 2.9 47.8 - - + +
54D LYS* 2.7 16.6 + - + +
56D VAL* 1.3 68.4 - - - +
58D LYS* 1.3 65.1 + - - +
60D TRP* 3.1 37.5 + - - +
61D LYS* 3.0 32.5 + - + +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LYS 3.2 3.9 + - - +
55D MET* 3.5 17.5 - - + +
57D GLU* 1.3 79.4 - - - +
59D CYS* 1.3 56.5 + - - +
61D LYS* 3.4 15.5 + - + +
62D LEU* 3.1 66.6 + - + +
123D MET* 5.4 4.9 - - + -
127D LYS* 4.6 10.6 - - - +
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Residues in contact with CYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D MET 2.8 8.2 + - - +
56D VAL 3.2 10.1 - - - +
57D GLU 3.1 0.2 - - - -
58D LYS* 1.3 75.5 - - - +
60D TRP* 1.3 61.6 + - + +
62D LEU* 3.1 6.8 + - - +
63D MET* 2.9 35.2 + - - +
95D LEU* 4.7 1.3 - - - -
119D MET* 3.8 13.5 - - + -
122D LEU* 3.0 44.6 - - - -
123D MET* 3.0 30.0 - - - -
126D THR* 5.7 0.9 - - - -
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LYS* 4.5 5.6 - - - -
56D VAL* 3.0 20.8 + - + +
57D GLU* 3.1 35.4 + - - +
59D CYS* 1.3 76.5 - - + +
61D LYS* 1.3 58.2 + - + +
63D MET* 3.4 22.5 + - + +
64D ASP* 2.9 36.1 + - - +
92D TYR* 3.3 40.2 - + + -
95D LEU* 3.7 23.4 - - + +
96D ARG* 3.8 30.7 - - + -
99D LEU* 3.4 33.7 - - + -
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU* 3.0 19.4 + - + +
58D LYS* 3.7 18.6 - - + +
59D CYS 3.2 0.2 - - - -
60D TRP* 1.3 75.0 - - + +
62D LEU* 1.3 65.7 + - + +
64D ASP* 3.4 9.0 + - - +
65D LYS* 3.1 22.5 + - - +
68D ARG* 4.6 2.6 + - - -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 3.1 45.5 + - + +
59D CYS* 3.1 6.3 + - - +
61D LYS* 1.3 74.6 - - + +
63D MET* 1.3 65.9 + - - +
65D LYS* 3.2 6.1 + - + +
66D VAL* 3.1 24.3 + - - +
123D MET* 3.9 25.4 - - + -
126D THR* 3.4 26.7 - - - +
127D LYS* 4.1 24.5 - - + -
130D ILE* 3.8 23.5 - - + +
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Residues in contact with MET 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D CYS* 2.9 27.1 + - - +
60D TRP* 3.5 35.4 - - + +
62D LEU* 1.3 76.3 - - - +
64D ASP* 1.3 64.6 + - - +
66D VAL* 3.2 3.9 + - - +
67D VAL* 3.0 28.3 + - - +
88D LEU* 3.8 45.2 - - + +
91D THR* 4.1 12.6 - - - -
92D TYR* 4.1 10.3 - - + -
95D LEU* 4.0 7.4 - - + -
122D LEU* 3.9 13.2 - - + -
126D THR* 3.8 23.6 - - + -
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 2.9 23.3 + - - +
61D LYS* 3.4 11.4 - - - +
63D MET* 1.3 77.4 - - - +
65D LYS* 1.3 61.6 + - - +
67D VAL* 3.3 10.5 + - - +
68D ARG* 3.1 39.2 + - - +
92D TYR* 6.1 1.0 - - - -
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LYS 3.1 9.9 + - - +
62D LEU* 3.2 8.5 + - + +
64D ASP* 1.3 76.6 - - - +
66D VAL* 1.3 66.2 + - - +
68D ARG* 3.2 36.4 - - + +
69D LEU* 2.9 37.5 + - + +
130D ILE* 3.9 39.6 - - + +
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU 3.1 14.5 + - - +
63D MET 3.2 2.0 + - - +
65D LYS* 1.3 76.8 - - - +
67D VAL* 1.3 58.3 + - - +
69D LEU* 3.3 8.3 + - - +
70D CYS* 2.8 39.3 + - - -
84D ILE* 4.4 5.6 - - + -
88D LEU* 3.3 29.6 - - + -
126D THR* 3.8 32.3 - - + +
129D THR* 3.8 28.3 - - + +
130D ILE* 3.8 8.5 - - + -
133D PHE* 5.5 0.2 - - + -
158D PHE* 5.1 1.8 - - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D MET 3.0 15.7 + - - +
64D ASP* 3.5 11.7 - - - +
65D LYS 3.2 0.2 - - - -
66D VAL* 1.3 77.0 - - - +
68D ARG* 1.3 64.3 + - - +
70D CYS* 3.1 2.8 + - - -
71D GLN* 2.9 48.4 + - - +
84D ILE* 4.9 1.3 - - - +
85D LEU* 3.7 18.7 - - + +
88D LEU* 3.8 26.7 - - + -
89D PRO* 4.3 19.7 - - + -
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Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LYS 4.6 1.8 + - - -
64D ASP* 3.1 26.7 + - - +
65D LYS* 3.2 58.1 - - + +
67D VAL* 1.3 76.1 - - - +
69D LEU* 1.3 72.5 + - + +
71D GLN* 3.3 27.2 + - - +
72D ASN* 3.8 4.2 + - - +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 2.9 38.2 + - + +
66D VAL* 3.4 7.0 - - - +
67D VAL 3.2 0.2 - - - -
68D ARG* 1.3 85.5 - - + +
70D CYS* 1.3 59.6 + - - +
71D GLN 3.4 0.5 + - - -
72D ASN* 3.4 20.4 + - - +
75D LEU* 3.6 6.4 - - - +
129D THR 5.3 0.2 - - - -
130D ILE* 4.1 23.3 - - + +
133D PHE* 3.6 53.3 - - + -
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Residues in contact with CYS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 2.8 29.6 + - - +
67D VAL 3.6 0.2 - - - -
69D LEU* 1.3 73.4 - - - +
71D GLN* 1.3 59.1 + - - +
72D ASN 3.2 7.5 + - - +
75D LEU* 3.5 11.4 - - - +
77D LEU* 3.4 28.2 - - + +
84D ILE* 3.7 19.7 - - + -
85D LEU* 3.7 24.2 - - + +
133D PHE* 3.7 23.6 - - - -
151D LEU* 4.2 11.7 - - - -
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Residues in contact with GLN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL* 2.9 37.2 + - - +
68D ARG* 3.6 21.7 + - - +
69D LEU 3.2 1.4 - - - -
70D CYS* 1.3 76.6 - - - +
72D ASN* 1.3 65.4 + - - +
73D PRO* 3.1 11.3 - - - +
85D LEU* 3.8 23.0 - - + +
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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
------------------------------------------------------------
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