Contacts of the helix formed by residues 65 - 84 (chain D) in PDB entry 6MUO
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 PHE 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 4.2 23.1 - - + -
59C THR* 4.0 27.4 - - + -
62C ILE* 4.5 24.9 - - + -
87C ILE* 6.0 1.1 - - + -
93C LEU* 5.8 0.4 - - + -
96C LEU* 4.4 8.5 - - + -
97C LEU* 3.7 33.2 - - + -
61D ILE* 2.8 18.8 + - + +
62D MET* 4.5 13.5 - - - -
64D SER* 1.3 80.0 - - - +
66D VAL* 1.3 62.3 + - + +
67D ASN 3.4 0.2 - - - -
68D ASP* 3.4 1.7 + - - +
69D ILE* 3.1 49.7 + - + +
98F TYR* 3.7 24.9 - + + -
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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
----------------------------------------------------------
25C PHE* 4.6 4.7 - - + -
55C LEU* 3.9 27.3 - - + +
59C THR* 4.1 24.9 - - + -
37D TYR* 3.5 40.1 - - + -
41D VAL* 5.5 1.8 - - + -
62D MET 3.3 17.0 + - - +
63D ASN* 3.0 17.3 + - - +
65D PHE* 1.3 79.5 - - + +
67D ASN* 1.3 63.4 + - - +
69D ILE* 3.6 2.6 + - - -
70D PHE* 3.0 25.6 + - - +
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Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.5 3.6 - - - +
37D TYR* 4.2 19.6 + - - -
63D ASN* 3.0 27.5 + - - +
64D SER* 4.8 4.0 - - - -
66D VAL* 1.3 79.2 - - - +
68D ASP* 1.3 54.8 + - - +
70D PHE* 3.5 13.7 - - + +
71D GLU* 2.6 39.9 + - + +
101F GLY 5.2 6.4 + - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 5.0 0.2 - - - +
100C VAL* 4.8 0.3 - - - +
64D SER 3.3 21.0 + - - +
65D PHE 3.4 2.3 + - - +
66D VAL 3.3 0.4 - - - -
67D ASN* 1.3 76.0 - - - +
69D ILE* 1.3 67.2 + - - +
71D GLU* 4.4 3.8 - - - +
72D ARG* 3.3 52.3 + - - +
91F LYS* 3.9 17.1 + - - +
96F THR* 3.8 18.9 + - + +
98F TYR* 2.8 28.2 + - + +
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Residues in contact with ILE 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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55C LEU* 3.8 17.5 - - + -
58C LEU* 3.8 19.3 - - + -
96C LEU* 3.9 37.2 - - + -
97C LEU* 5.0 1.8 - - + -
65D PHE* 3.1 40.9 + - + +
66D VAL* 4.1 0.9 - - - +
68D ASP* 1.3 82.3 - - - +
70D PHE* 1.3 63.9 + - - +
72D ARG* 3.6 12.7 + - + +
73D ILE* 3.2 44.3 + - + +
101D LEU* 6.5 0.2 - - + -
102D LEU* 6.2 0.7 - - + -
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Residues in contact with PHE 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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30C VAL* 4.2 12.8 - - + -
33C LEU* 4.4 32.3 - - + -
34C LEU* 4.2 21.5 - - + -
39C TYR* 5.1 12.1 - + - -
51C LEU* 3.6 24.9 - - + -
55C LEU* 3.8 28.2 - - + +
37D TYR* 5.2 6.7 - - + +
66D VAL 3.0 19.7 + - - +
67D ASN* 3.1 17.7 + - - +
69D ILE* 1.3 77.5 - - - +
71D GLU* 1.3 66.6 + - + +
73D ILE* 4.3 2.2 - - - +
74D ALA* 3.3 30.5 + - + +
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Residues in contact with GLU 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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39C TYR* 3.9 24.6 + - - +
67D ASN* 2.6 21.8 + - + +
68D ASP* 4.6 3.8 - - - +
70D PHE* 1.3 75.9 - - + +
72D ARG* 1.3 67.7 + - - +
75D GLY* 3.4 15.1 + - - +
91F LYS* 3.5 27.8 + - - -
79H ARG* 5.0 14.2 + - - +
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Residues in contact with ARG 72 (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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96C LEU* 3.2 44.5 + - - +
97C LEU* 5.3 1.2 - - - +
98C GLY 5.5 1.4 - - - +
99C ARG* 5.6 4.0 - - - +
100C VAL* 4.7 13.7 - - - +
68D ASP* 3.3 42.8 + - - +
69D ILE* 3.8 11.3 - - + +
70D PHE 3.2 0.4 - - - -
71D GLU* 1.3 79.3 - - - +
73D ILE* 1.3 54.3 + - + +
75D GLY 3.0 4.6 + - - -
76D GLU* 2.6 39.9 + - + +
101D LEU* 3.7 30.0 - - + +
91F LYS* 6.3 1.1 - - - +
96F THR* 5.7 1.6 + - - -
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Residues in contact with ILE 73 (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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51C LEU* 3.7 32.1 - - + -
54C VAL* 4.4 17.5 - - + -
55C LEU* 5.1 2.9 - - + -
58C LEU* 5.8 0.2 - - + -
69D ILE* 3.2 36.5 + - + +
70D PHE* 3.4 2.6 + - - +
72D ARG* 1.3 77.9 - - + +
74D ALA* 1.3 55.9 + - - +
76D GLU* 3.1 4.2 + - - +
77D ALA* 2.7 35.2 + - - +
94D ILE* 4.2 16.8 - - + -
97D ALA* 4.4 13.5 - - + +
98D VAL* 4.9 7.9 - - + -
101D LEU* 4.6 22.7 - - + -
102D LEU* 6.3 2.9 - - + -
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Residues in contact with ALA 74 (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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34C LEU* 4.2 27.4 - - + -
39C TYR* 3.2 36.5 - - + +
51C LEU* 5.1 3.0 - - + +
70D PHE* 3.3 21.0 + - + +
73D ILE* 1.3 80.0 - - - +
75D GLY* 1.3 57.6 + - - +
77D ALA* 4.1 6.4 - - - +
78D SER* 3.3 21.0 + - - -
89D ILE* 5.0 2.3 - - + +
94D ILE* 5.4 2.9 - - + -
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Residues in contact with GLY 75 (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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39C TYR* 3.6 17.5 - - - -
71D GLU* 3.4 17.7 + - - -
72D ARG 3.0 9.8 + - - -
74D ALA* 1.3 77.4 - - - +
76D GLU* 1.3 56.2 + - - +
78D SER* 4.4 7.5 - - - -
79D ARG* 5.0 11.1 + - - +
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Residues in contact with GLU 76 (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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72B TYR* 3.1 25.3 + - - -
92B ARG* 4.5 13.7 - - + +
72D ARG* 2.6 18.3 + - - +
73D ILE 3.9 2.2 - - - +
75D GLY* 1.3 76.0 - - - +
77D ALA* 1.3 62.5 + - - +
78D SER 3.2 1.6 - - - -
79D ARG* 3.2 33.4 + - - +
80D LEU* 3.8 10.7 - - - +
97D ALA* 3.4 26.5 - - - +
100D LEU* 3.6 11.7 - - - +
101D LEU* 4.0 24.2 - - + +
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Residues in contact with ALA 77 (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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73D ILE 2.7 21.8 + - - +
74D ALA* 4.3 3.8 - - - +
76D GLU* 1.3 72.5 + - - +
78D SER* 1.3 64.7 + - - +
79D ARG 3.1 1.2 + - - -
80D LEU* 3.5 15.4 + - - +
81D ALA* 3.5 12.5 + - - +
89D ILE* 4.4 12.1 - - + +
93D GLU* 3.4 27.8 - - - +
94D ILE* 3.7 18.8 - - + -
97D ALA* 4.2 5.8 - - + -
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Residues in contact with SER 78 (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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38C ASN 5.2 0.7 + - - -
39C TYR* 2.8 37.1 + - - +
74D ALA 3.3 17.8 + - - -
75D GLY* 4.7 7.0 - - - -
76D GLU 3.2 0.6 - - - -
77D ALA* 1.3 78.9 - - - +
79D ARG* 1.3 56.6 + - - +
81D ALA* 3.6 4.3 + - - +
82D HIS* 3.0 28.1 + - - +
89D ILE* 4.5 5.3 - - - +
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Residues in contact with ARG 79 (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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72B TYR* 5.0 7.5 + - - -
88B TYR 5.7 0.4 + - - -
91B LYS* 4.5 22.9 + - - +
92B ARG* 4.5 26.5 - - - +
75D GLY 5.0 9.8 + - - +
76D GLU* 3.2 28.3 + - - +
77D ALA 3.1 1.0 - - - -
78D SER* 1.3 78.3 - - - +
80D LEU* 1.3 61.2 + - + +
82D HIS* 3.5 6.2 + - + +
83D TYR* 2.9 73.1 + - + -
71H GLU* 4.6 13.7 + - - -
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Residues in contact with LEU 80 (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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72B TYR* 3.8 33.2 - - + +
75B HIS* 3.6 34.1 - - + +
76D GLU* 3.8 28.0 - - - +
77D ALA* 3.5 10.2 + - - +
78D SER 3.3 0.2 - - - -
79D ARG* 1.3 76.3 - - + +
81D ALA* 1.3 59.9 + - - +
82D HIS 3.1 1.6 - - - -
83D TYR* 3.0 23.1 + - + +
84D ASN* 3.0 21.7 + - - +
93D GLU* 4.5 9.8 - - + +
96D THR* 3.3 28.7 - - - +
97D ALA* 5.3 3.4 - - + -
100D LEU* 5.2 1.6 - - + -
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Residues in contact with ALA 81 (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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39C TYR 5.9 0.2 - - - +
40C ALA* 5.2 5.4 - - + -
77D ALA 3.5 9.1 + - - +
78D SER* 4.1 6.3 - - - +
79D ARG 3.5 0.2 - - - -
80D LEU* 1.3 77.4 - - - +
82D HIS* 1.3 57.8 + - - +
84D ASN* 5.6 0.7 - - - -
85D LYS* 3.6 1.7 + - - -
86D ARG* 2.9 45.8 + - + +
87D SER* 5.2 1.3 - - - -
88D THR 4.9 7.0 - - - +
89D ILE* 4.5 14.1 - - + -
93D GLU* 3.4 24.3 + - - +
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Residues in contact with HIS 82 (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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78D SER* 3.0 18.9 + - - +
79D ARG* 3.8 7.3 - - - +
80D LEU 3.1 0.2 - - - -
81D ALA* 1.3 78.5 - - - +
83D TYR* 1.3 73.5 + + - +
85D LYS* 3.8 12.9 + - - +
36G LYS* 3.8 24.0 + - - +
37G GLY* 4.0 18.8 - - - -
38G ASN* 6.1 0.9 - - - -
39G TYR* 5.7 2.8 + - - -
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Residues in contact with TYR 83 (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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72B TYR* 4.7 13.9 - + - -
88B TYR* 3.1 73.7 + + + +
91B LYS* 4.7 8.3 - - - +
79D ARG* 2.9 55.7 + - + +
80D LEU* 3.0 14.7 + - + +
82D HIS* 1.3 85.8 - - - +
84D ASN* 1.3 67.8 + - - +
85D LYS* 3.1 18.1 + - - +
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Residues in contact with ASN 84 (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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75B HIS* 3.1 38.6 + - - -
76B ALA* 3.8 21.8 - - - +
78B ARG* 5.5 2.1 + - - -
80D LEU* 3.0 15.2 + - - +
81D ALA* 5.6 0.2 - - - -
83D TYR* 1.3 77.9 - - - +
85D LYS* 1.3 69.0 + - - +
86D ARG* 3.3 32.4 + - + +
93D GLU* 5.5 1.8 - - - +
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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