Contacts of the helix formed by residues 68 - 90 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 2.9 40.6 + - + -
60C SER* 4.9 2.0 - - - +
62C LEU* 4.5 13.7 - - + -
63C ALA* 3.3 22.1 - - + +
65C SER* 3.0 37.7 + - - +
66C SER 3.4 1.8 + - - -
67C GLY* 1.3 77.6 - - - +
69C GLN* 1.3 111.2 + - + +
70C ARG 3.2 0.7 - - - -
71C TRP* 3.2 17.8 + - - +
72C LEU* 3.2 42.3 + - + +
73C PHE* 4.2 7.4 - + - -
205F 5BV 6.2 0.9 - - + -
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR* 3.4 20.4 + - - +
56C GLY 3.0 26.4 + - - +
59C PHE* 4.9 0.9 - - + -
60C SER* 3.1 20.8 + - - +
65C SER 5.3 0.6 + - - -
66C SER* 5.3 2.4 - - - +
67C GLY* 3.4 13.6 + - - +
68C TRP* 1.3 137.5 + - + +
70C ARG* 1.3 63.1 + - - +
71C TRP 3.2 0.9 + - - -
72C LEU* 4.7 0.7 - - - +
73C PHE* 3.2 48.1 + - + +
116C ARG* 4.3 0.8 + - - -
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR* 5.0 2.1 + - - +
67C GLY* 3.8 14.2 + - - +
68C TRP 3.2 0.2 - - - -
69C GLN* 1.3 80.7 + - - +
71C TRP* 1.3 93.6 + - + +
74C ALA* 3.2 22.9 + - - +
116C ARG* 2.9 35.5 + - + +
117C MET 2.9 25.3 + - - -
118C VAL 4.7 2.4 + - - -
119C LEU 4.9 0.4 - - - -
120C GLY* 3.6 33.1 - - - +
203C OLC 3.1 22.2 + - - -
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Residues in contact with TRP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY 3.8 18.3 + - - -
68C TRP* 3.2 7.9 + - - +
69C GLN 3.2 0.4 - - - -
70C ARG* 1.3 123.7 - - + +
72C LEU* 1.3 55.1 + - - +
73C PHE 3.3 1.6 - - - -
74C ALA* 3.2 2.5 + - + +
75C LEU* 2.6 37.2 + - - +
117C MET* 3.9 35.0 - - + -
203C OLC 4.3 20.2 - - - -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TRP* 3.2 43.5 + - + +
69C GLN 4.5 0.2 - - - +
71C TRP* 1.3 79.4 - - - +
73C PHE* 1.3 65.1 + - + +
75C LEU* 3.2 19.5 + - + +
76C ILE* 2.8 48.4 + - + +
205F 5BV 4.7 15.0 - - + -
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY* 4.7 2.5 - - - -
59C PHE* 3.8 23.6 - + - -
68C TRP* 4.2 13.7 - + - -
69C GLN* 3.2 38.8 + - + +
72C LEU* 1.3 87.9 - - + +
74C ALA* 1.3 61.1 + - - +
76C ILE* 3.9 12.8 - - + -
77C ALA* 2.9 27.4 + - - +
116C ARG* 3.5 28.0 + - - +
201F MLE 3.5 11.0 - - - -
204F ALO 3.5 17.3 - - - -
205F 5BV 3.6 49.1 - - + -
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG 3.2 21.6 + - - +
71C TRP* 3.2 8.2 + - + +
73C PHE* 1.3 76.5 - - - +
75C LEU* 1.3 58.0 + - - +
77C ALA* 3.2 4.0 + - - +
78C ILE* 2.9 37.5 + - + +
113C LEU* 3.5 21.9 - - + +
116C ARG* 3.9 10.2 - - + +
117C MET* 3.8 19.7 - - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TRP 2.6 21.2 + - - +
72C LEU* 3.3 22.0 - - + +
74C ALA* 1.3 73.1 - - - +
76C ILE* 1.3 62.9 + - + +
78C ILE* 3.2 18.3 + - + +
79C VAL* 3.0 37.2 + - + +
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 2.8 35.3 + - + +
73C PHE* 3.7 25.8 - - + +
75C LEU* 1.3 73.1 - - + +
77C ALA* 1.3 58.2 + - - +
79C VAL* 3.5 4.8 + - - +
80C VAL* 3.0 48.6 + - + +
201F MLE 3.9 4.3 - - - -
205F 5BV 3.8 56.3 - - + -
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PHE 2.9 14.9 + - - +
74C ALA* 3.4 9.6 - - - +
76C ILE* 1.3 78.2 - - - +
78C ILE* 1.3 52.0 + - - +
80C VAL* 4.0 0.3 - - - +
81C SER* 2.7 43.7 + - - +
109C ALA 4.3 7.4 - - - +
113C LEU* 4.0 26.9 - - + +
116C ARG* 5.8 1.8 - - - +
201F MLE 3.7 23.7 - - + +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 2.9 25.3 + - + +
75C LEU* 3.2 16.8 + - + +
77C ALA* 1.3 76.3 - - - +
79C VAL* 1.3 66.9 + - + +
81C SER* 3.8 3.5 - - - -
82C ALA* 3.0 25.9 + - + +
113C LEU* 4.0 11.9 - - + -
117C MET* 5.1 11.0 - - + -
203C OLC 3.5 48.6 - - + +
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.0 32.0 + - + +
76C ILE* 4.0 4.9 - - - +
78C ILE* 1.3 79.2 - - + +
80C VAL* 1.3 61.7 + - + +
82C ALA* 3.4 5.7 + - - +
83C SER* 3.0 30.0 + - - -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.0 36.3 + - + +
77C ALA 4.0 1.6 - - - +
79C VAL* 1.3 77.0 - - + +
81C SER* 1.3 60.6 + - - +
83C SER* 3.4 6.7 + - - -
84C LEU* 2.8 46.1 + - + +
201F MLE 4.0 27.1 - - + -
205F 5BV 5.9 0.7 - - + -
302F OLC 6.2 1.1 - - + -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA* 2.7 29.0 + - - +
78C ILE* 3.8 5.2 - - - -
80C VAL* 1.3 71.3 - - - +
82C ALA* 1.3 66.5 + - - +
84C LEU* 3.1 11.4 + - - +
85C VAL* 2.9 28.9 + - - +
106C LEU* 4.5 7.2 + - - +
109C ALA* 3.6 22.0 - - - +
110C LEU* 3.8 23.8 - - - +
203C OLC 4.3 9.4 - - - -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 3.0 19.9 + - + +
79C VAL* 3.5 6.3 - - - +
81C SER* 1.3 75.4 - - - +
83C SER* 1.3 62.4 + - - +
85C VAL* 3.0 16.6 + - - +
86C VAL* 3.1 18.6 + - + +
203C OLC 4.3 15.8 - - + +
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 3.0 20.4 + - - -
80C VAL* 3.7 7.6 - - - -
82C ALA* 1.3 76.6 - - - +
84C LEU* 1.3 60.2 + - - +
86C VAL* 3.6 9.7 + - - +
87C TRP* 3.2 23.0 + - - +
153D LEU* 6.0 0.3 - - - +
157D MET* 4.2 24.4 - - - +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 2.8 36.5 + - + +
81C SER* 3.1 8.7 + - - +
83C SER* 1.3 75.4 - - - +
85C VAL* 1.3 59.4 + - - +
87C TRP* 3.4 18.7 + - + +
88C LEU* 2.9 29.2 + - - +
102C LEU* 3.9 36.9 - - + +
105C VAL* 3.7 30.1 - - + +
106C LEU* 4.1 27.5 - - + +
109C ALA* 5.3 1.8 - - + -
153C LEU* 6.1 1.3 - - + -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C SER 2.9 19.4 + - - +
82C ALA* 3.0 7.6 + - - +
84C LEU* 1.3 74.5 - - - +
86C VAL* 1.3 67.1 + - + +
88C LEU* 3.0 19.5 + - + +
89C LYS* 3.0 37.7 + - + +
106C LEU* 3.7 17.0 - - + -
203C OLC 3.6 44.0 - - + -
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 3.1 16.6 + - + +
83C SER* 3.7 10.1 - - - +
85C VAL* 1.3 78.6 - - + +
87C TRP* 1.3 61.9 + - + +
89C LYS* 3.5 7.9 + - - +
90C ARG* 3.2 62.6 + - - +
157D MET* 4.4 21.1 - - + +
158D PHE* 6.6 0.4 - - + -
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C SER 3.2 14.0 + - - +
84C LEU* 4.0 16.6 - - + +
86C VAL* 1.3 78.9 - - + +
88C LEU* 1.3 61.1 + - - +
90C ARG* 3.6 17.0 + - + +
91C LEU* 3.1 26.2 + - + +
98C LEU* 3.9 27.1 - - + +
102C LEU* 3.7 33.0 - - + -
153C LEU* 3.6 28.3 - - + -
90D ARG* 5.2 9.5 - - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PRO 5.2 5.2 - - - +
13C LEU* 4.7 23.1 - - + -
16C THR* 5.5 0.2 - - - +
84C LEU 2.9 18.9 + - - +
85C VAL* 3.0 10.5 + - + +
87C TRP* 1.3 77.0 - - - +
89C LYS* 1.3 66.2 + - + +
91C LEU* 3.3 22.7 - - + +
99C ALA* 4.0 22.2 - - + +
102C LEU* 3.9 31.0 - - + -
103C ALA* 4.7 8.5 - - + +
106C LEU* 4.5 18.8 - - + -
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PRO* 4.3 23.6 - - + +
13C LEU* 6.2 1.8 - - - +
85C VAL* 3.0 37.2 + - + +
86C VAL* 3.9 7.6 - - - +
88C LEU* 1.3 73.6 - - + +
90C ARG* 1.3 58.4 + - + +
91C LEU* 2.9 16.4 + - - +
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 3.2 36.5 + - - +
87C TRP* 4.0 16.1 - - + +
88C LEU 3.3 0.8 - - - -
89C LYS* 1.3 74.7 - - + +
91C LEU* 1.3 62.4 + - - +
92C LYS* 5.4 2.1 - - - +
87D TRP* 5.8 5.1 - - - -
95D GLU* 4.8 10.2 + - - -
98D LEU* 5.3 5.1 - - - +
156D ASP* 4.5 13.3 + - - -
157D MET* 3.5 36.7 + - - +
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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