Contacts of the helix formed by residues 68 - 90 (chain D) in PDB entry 5DIR
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 TRP 68 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 3.3 53.2 - + + -
66D SER* 3.3 9.6 - - - +
67D GLY* 1.3 76.4 - - - +
69D GLN* 1.3 58.4 + - - +
70D ARG 3.1 1.8 - - - -
71D TRP* 2.9 31.8 + + + -
72D LEU* 2.7 53.6 + - + +
75D LEU* 6.0 6.3 - - + -
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Residues in contact with GLN 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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55D THR 4.9 8.5 - - - +
57D ALA 3.6 4.1 + - - +
59D PHE* 3.5 29.9 - - - +
60D SER* 3.9 6.4 + - - -
63D ALA* 3.1 44.1 - - + +
64D ASP* 4.5 1.3 - - - +
66D SER* 4.4 2.7 - - - +
67D GLY 3.5 0.8 - - - -
68D TRP* 1.3 79.0 - - - +
70D ARG* 1.3 66.7 + - - +
72D LEU* 3.6 22.8 - - - +
73D PHE* 2.8 67.6 + - + -
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Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D THR 5.8 0.4 + - - -
66D SER 5.2 0.6 + - - -
67D GLY* 3.4 17.3 + - - +
69D GLN* 1.3 79.2 - - - +
71D TRP* 1.3 87.8 + - + +
73D PHE* 5.1 0.7 - - - -
74D ALA* 3.2 22.7 + - - +
116D ARG* 2.8 41.1 + - + +
117D MET 2.9 25.7 + - - -
118D VAL 4.3 3.2 + - - -
119D LEU 3.6 12.8 + - - -
120D GLY* 4.0 26.7 - - - +
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Residues in contact with TRP 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 4.4 9.4 - + - -
67D GLY 3.4 22.8 + - - -
68D TRP* 2.9 41.0 + + + +
70D ARG* 1.3 116.2 - - + +
72D LEU* 1.3 56.2 + - - +
73D PHE 3.1 1.8 - - - -
74D ALA* 3.3 12.4 - - + +
75D LEU* 2.4 38.4 + - - +
117D MET* 4.0 35.9 - - + -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PHE* 5.6 0.4 - - + +
60D SER* 6.2 2.2 - - - -
68D TRP* 2.7 38.9 + - + +
69D GLN* 3.6 30.1 - - - +
71D TRP* 1.3 71.1 - - - +
73D PHE* 1.3 64.1 + - + +
75D LEU* 3.3 18.8 + - + +
76D ILE* 2.9 49.9 + - + +
302F OLC 6.1 0.9 - - - +
205G 5BV 4.3 24.9 - - + -
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Residues in contact with PHE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D THR 4.8 1.6 - - - -
56D GLY* 4.2 17.3 - - - -
57D ALA 3.9 0.9 - - - -
59D PHE* 3.4 23.6 - + - -
69D GLN* 2.8 55.5 + - + +
70D ARG* 5.1 0.7 - - - -
72D LEU* 1.3 85.5 - - + +
74D ALA* 1.3 60.5 + - - +
76D ILE* 4.4 3.6 - - + +
77D ALA* 2.9 30.1 + - - +
116D ARG* 3.4 40.1 - - - +
201G MLE 3.7 11.9 - - - -
205G 5BV 3.4 44.2 - - + -
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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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70D ARG 3.2 19.6 + - - +
71D TRP* 3.0 24.0 + - + +
73D PHE* 1.3 77.1 - - - +
75D LEU* 1.3 64.5 + - - +
77D ALA* 3.4 1.8 + - - +
78D ILE* 3.0 35.0 + - + +
113D LEU* 3.7 21.9 - - + +
116D ARG* 4.3 5.8 - - + +
117D MET* 4.5 7.4 - - + -
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Residues in contact with LEU 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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68D TRP* 6.0 6.7 - - + -
71D TRP 2.4 25.7 + - - +
72D LEU* 3.3 20.9 - - + +
74D ALA* 1.3 73.2 - - - +
76D ILE* 1.3 60.3 - - + +
78D ILE* 3.3 12.6 + - + +
79D VAL* 2.9 47.7 + - + +
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Residues in contact with ILE 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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72D LEU* 2.9 42.1 + - + +
73D PHE* 3.9 8.5 - - + +
75D LEU* 1.3 79.3 - - + +
77D ALA* 1.3 57.5 + - - +
79D VAL* 3.8 6.0 - - + +
80D VAL* 2.8 36.5 + - + +
201G MLE 4.6 4.0 - - + -
205G 5BV 3.7 53.6 - - + -
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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 PHE 2.9 18.3 + - - +
74D ALA* 3.7 4.5 - - - +
75D LEU 3.2 0.2 - - - -
76D ILE* 1.3 77.4 - - - +
78D ILE* 1.3 51.4 + - - +
80D VAL* 3.4 1.0 - - - +
81D SER* 2.6 44.4 + - - +
109D ALA 4.3 6.1 - - - +
113D LEU* 4.1 28.0 - - + -
116D ARG* 5.7 2.0 - - - +
201G MLE 3.7 26.4 - - + +
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Residues in contact with ILE 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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74D ALA* 3.0 24.9 + - + +
75D LEU* 3.6 11.2 - - + +
77D ALA* 1.3 76.3 - - - +
79D VAL* 1.3 59.0 + - + +
81D SER* 3.6 5.8 - - - -
82D ALA* 3.0 29.6 + - + +
113D LEU* 3.8 26.0 - - + -
117D MET* 4.8 11.0 - - - -
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ALA* 6.1 3.1 - - + -
157C MET* 5.2 1.2 - - - +
75D LEU* 2.9 39.2 + - + +
76D ILE* 3.8 6.3 - - + +
78D ILE* 1.3 79.2 - - + +
80D VAL* 1.3 62.4 + - + +
82D ALA* 3.3 7.4 + - - +
83D SER* 3.1 21.3 + - - -
302F OLC 3.9 30.2 - - + +
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Residues in contact with VAL 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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76D ILE* 2.8 27.6 + - + +
77D ALA 3.4 5.6 - - - +
79D VAL* 1.3 74.5 - - + +
81D SER* 1.3 67.4 + - - +
83D SER* 2.9 12.0 + - - +
84D LEU* 2.9 47.5 + - + +
105D VAL* 6.0 0.2 - - + -
109D ALA* 4.8 1.3 - - + -
302F OLC 6.0 0.2 - - - -
201G MLE 3.5 36.6 - - + -
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Residues in contact with SER 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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77D ALA 2.6 26.5 + - - -
78D ILE* 3.6 6.1 - - - -
80D VAL* 1.3 75.3 - - - +
82D ALA* 1.3 59.9 + - - +
84D LEU* 3.1 4.7 + - - +
85D VAL* 2.8 35.5 + - - +
106D LEU* 3.5 22.6 - - - +
109D ALA* 3.9 11.8 - - - +
110D LEU* 3.5 25.9 - - - +
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Residues in contact with ALA 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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157C MET* 3.7 30.7 - - + -
78D ILE* 3.0 16.0 + - + +
79D VAL* 3.5 11.2 - - - +
81D SER* 1.3 75.8 - - - +
83D SER* 1.3 63.1 + - - +
85D VAL* 3.1 9.3 + - - +
86D VAL* 3.0 29.0 + - + +
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Residues in contact with SER 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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157C MET* 4.6 6.6 - - - -
79D VAL 3.1 6.9 + - - -
80D VAL* 2.9 32.1 + - - +
82D ALA* 1.3 78.8 - - - +
84D LEU* 1.3 57.7 + - - +
86D VAL* 3.9 7.2 - - - +
87D TRP* 2.9 32.6 + - - +
302F OLC 4.3 20.5 - - - +
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Residues in contact with LEU 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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80D VAL* 2.9 40.4 + - + +
81D SER* 3.4 5.4 - - - +
83D SER* 1.3 77.2 + - - +
85D VAL* 1.3 59.9 + - - +
87D TRP* 3.7 17.5 - - + +
88D LEU* 2.8 30.3 + - - +
102D LEU* 3.7 38.2 - - + +
105D VAL* 3.6 33.0 - - + +
106D LEU* 4.2 24.5 - - + +
109D ALA* 5.6 0.4 - - + -
153D LEU* 5.6 2.5 - - + -
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Residues in contact with VAL 85 (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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13D LEU* 5.5 11.0 - - + -
81D SER* 2.8 21.6 + - - +
82D ALA* 3.5 8.7 - - - +
84D LEU* 1.3 74.1 - - - +
86D VAL* 1.3 62.8 + - + +
88D LEU* 3.0 8.5 + - + +
89D LYS* 2.9 53.9 + - + +
106D LEU* 3.8 25.8 - - + -
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Residues in contact with VAL 86 (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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156C ASP* 5.4 4.0 - - - +
157C MET* 4.5 23.8 - - + -
82D ALA* 3.0 20.9 + - - +
83D SER* 3.9 6.5 - - - +
85D VAL* 1.3 79.9 - - + +
87D TRP* 1.3 61.6 + - - +
89D LYS* 3.4 9.3 + - + +
90D ARG* 3.3 55.6 + - + +
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Residues in contact with TRP 87 (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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90C ARG* 5.8 5.2 - - - -
83D SER 2.9 22.6 + - - +
84D LEU* 4.1 15.7 - - + +
86D VAL* 1.3 78.5 - - + +
88D LEU* 1.3 59.7 + - - +
90D ARG* 4.0 14.8 + - + +
91D LEU* 3.0 35.1 + - + +
98D LEU* 4.4 19.6 - - + +
102D LEU* 3.9 20.9 - - + -
153D LEU* 3.6 35.2 - - + -
157D MET* 5.8 5.8 - - + -
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Residues in contact with LEU 88 (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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12D TRP* 4.8 18.6 - - + +
13D LEU* 3.5 34.8 - - + +
84D LEU 2.8 20.0 + - - +
85D VAL* 3.0 7.8 + - + +
87D TRP* 1.3 76.7 - - - +
89D LYS* 1.3 66.6 + - + +
91D LEU* 3.3 21.2 - - + +
99D ALA* 3.8 34.5 - - + +
102D LEU* 4.1 20.4 - - + +
103D ALA* 4.8 7.6 - - + +
106D LEU* 5.0 6.7 - - + -
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Residues in contact with LYS 89 (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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13D LEU* 6.3 2.7 - - - -
85D VAL* 2.9 38.8 + - + +
86D VAL* 3.4 9.6 + - + +
88D LEU* 1.3 79.9 - - + +
90D ARG* 1.3 60.4 + - + +
91D LEU 3.0 10.7 + - - +
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Residues in contact with ARG 90 (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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87C TRP* 5.2 8.3 - - - +
92C LYS* 6.2 1.8 - - - +
95C GLU* 3.5 11.2 + - - -
98C LEU* 4.5 13.7 - - - +
156C ASP* 4.0 10.5 + - - -
159C ARG* 3.2 38.2 - - - +
86D VAL* 3.3 39.3 + - + +
87D TRP* 4.3 15.4 - - + +
88D LEU 3.4 0.4 - - - -
89D LYS* 1.3 75.7 - - + +
91D LEU* 1.3 63.2 + - - +
92D LYS* 5.2 2.9 - - - +
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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