Contacts of the helix formed by residues 79 - 92 (chain L) in PDB entry 1DZH
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 SER 79 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78L LEU* 1.3 74.1 - - - +
80L PRO* 1.3 63.9 - - - +
82L SER* 2.8 39.2 + - - -
83L ILE* 3.3 4.9 + - - +
219L ILE* 3.6 9.6 - - - +
369L HIS* 3.1 23.9 + - - -
384L ALA* 3.6 18.0 - - - +
421L ILE 2.9 17.4 + - - -
422L PHE* 4.0 9.9 - - - -
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Residues in contact with PRO 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ASN* 5.3 1.6 - - - +
58L PHE* 4.8 7.1 - - + -
59L ALA* 3.5 39.0 - - + +
62L PHE* 5.9 0.4 - - + -
78L LEU* 3.5 28.0 - - + +
79L SER* 1.3 79.5 - - - +
81L LEU* 1.3 66.5 + - - +
83L ILE* 3.0 20.9 + - + +
84L SER* 3.0 15.3 + - - -
420L ILE* 3.6 22.0 - - + +
421L ILE 3.3 11.7 - - - +
423L MET* 4.1 10.5 - - + -
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ASN* 4.5 23.8 - - + +
79L SER* 3.7 7.4 - - - +
80L PRO* 1.3 81.1 - - - +
82L SER* 1.3 64.4 + - - +
84L SER* 3.6 4.0 + - - -
85L THR* 3.0 31.8 + - - +
123L PHE* 4.6 9.0 - - + -
126L LEU* 4.7 3.4 - - + -
127L ASN* 5.2 0.2 - - - +
130L LEU* 3.9 23.3 - - + -
131L TYR* 3.3 26.5 - - + +
140L LEU* 6.0 0.2 - - + -
219L ILE* 3.8 10.3 - - + -
419L THR* 4.7 10.3 - - + +
420L ILE 3.9 13.8 + - - +
421L ILE* 4.0 23.3 - - + +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L SER* 2.8 33.4 + - - -
81L LEU* 1.3 75.2 - - - +
83L ILE* 1.3 65.0 + - - +
85L THR 2.9 8.5 + - - -
86L ALA 3.0 12.1 + - - -
217L ASN* 3.1 23.9 + - - +
218L THR 4.8 0.2 + - - -
219L ILE* 3.5 9.3 - - - +
369L HIS* 3.9 2.9 - - - -
384L ALA* 4.4 4.9 + - - -
385L SER* 3.9 5.9 - - - -
386L THR* 2.8 32.4 + - - -
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Residues in contact with ILE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L PHE* 3.9 11.9 - - + -
62L PHE* 3.7 31.6 - - + -
78L LEU* 4.3 7.4 - - + -
79L SER 3.3 7.2 + - - +
80L PRO* 3.0 12.2 + - + +
82L SER* 1.3 72.7 - - - +
84L SER* 1.3 63.5 + - - +
86L ALA* 3.2 1.2 + - - -
87L PHE* 2.9 34.3 + - + -
106L PHE* 3.8 14.1 - - + -
329L PHE* 4.9 0.7 - - + -
331L LEU* 3.5 35.2 - - + -
335L LEU* 4.9 0.2 - - + -
369L HIS* 3.5 27.1 - - + -
386L THR* 3.3 8.2 + - - +
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Residues in contact with SER 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ASN* 3.2 29.9 + - - -
58L PHE* 4.1 13.9 - - - +
80L PRO 3.0 13.1 + - - -
81L LEU* 3.8 8.1 - - - -
83L ILE* 1.3 72.8 - - - +
85L THR* 1.3 54.1 + - - +
87L PHE* 3.1 1.0 + - - +
88L ALA* 2.7 35.9 + - - +
106L PHE* 3.5 26.9 + - - +
108L PHE* 4.4 5.5 - - - -
123L PHE* 3.9 9.1 - - - -
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Residues in contact with THR 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L LEU* 3.0 15.2 + - - +
82L SER 2.9 5.8 + - - -
84L SER* 1.3 68.1 - - - +
86L ALA* 1.3 61.5 + - - +
88L ALA* 2.9 15.0 + - - +
89L MET* 2.9 21.1 + - + +
123L PHE* 3.1 28.9 - - + -
127L ASN* 4.1 7.7 + - - +
131L TYR* 5.1 2.3 + - - -
142L SER* 5.6 0.7 - - - +
144L ASN* 3.5 24.7 - - - +
166L TYR* 4.6 9.9 - - + -
217L ASN* 3.1 31.5 + - - +
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L SER 3.0 9.9 + - - -
83L ILE 3.9 1.3 - - - +
85L THR* 1.3 71.2 - - - +
87L PHE* 1.3 57.9 + - - +
89L MET* 3.3 23.3 - - + +
90L THR* 3.0 30.7 + - - -
215L LEU* 4.6 4.5 - - - +
216L VAL 4.9 1.3 - - - -
217L ASN* 4.1 5.4 - - + +
386L THR* 3.8 40.8 - - + +
388L VAL* 4.2 10.3 - - + +
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Residues in contact with PHE 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L ILE* 2.9 32.0 + - + +
84L SER 3.9 0.7 - - - +
86L ALA* 1.3 72.2 - - + +
88L ALA* 1.3 58.5 + - - +
90L THR* 3.4 7.7 - - - +
91L LYS* 2.9 26.3 + - - +
102L LEU* 4.4 7.1 - - + +
106L PHE* 3.4 32.1 - + + -
108L PHE* 5.4 2.5 - - - -
331L LEU* 3.7 23.6 - - + -
335L LEU* 3.5 15.7 - - + -
340L LEU* 3.9 24.5 - - + -
343L LEU* 4.1 16.4 - - + -
344L PHE* 4.5 5.6 - + - -
367L ALA* 3.7 23.6 - - + -
386L THR* 4.4 3.6 - - + -
388L VAL* 3.9 22.2 - - + -
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Residues in contact with ALA 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L SER 2.7 16.2 + - - +
85L THR 3.4 7.9 - - - +
87L PHE* 1.3 67.5 - - - +
89L MET* 1.3 69.7 + - - +
91L LYS* 2.8 26.0 + - - +
92L LEU 3.3 3.3 + - - -
108L PHE* 4.3 12.9 - - + -
119L ILE* 5.7 1.1 - - + -
120L HIS* 3.9 8.8 - - + -
123L PHE* 3.8 20.6 - - + -
166L TYR* 3.4 23.8 - - + +
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Residues in contact with MET 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L THR* 2.9 14.1 + - + +
86L ALA* 3.3 34.1 - - + +
88L ALA* 1.3 77.7 - - - +
90L THR* 1.3 61.9 + - - +
92L LEU* 3.2 22.0 + - + +
93L GLY 4.6 0.2 + - - -
144L ASN* 3.1 44.0 - - - +
145L ARG 4.8 0.9 - - - -
146L LEU* 5.0 7.4 - - + -
158L TYR* 4.7 3.5 - - - -
162L SER* 5.9 1.3 - - - +
166L TYR* 3.8 31.4 - - + -
168L ALA* 4.3 13.5 - - + -
215L LEU* 3.7 15.1 - - + +
216L VAL 3.6 16.2 - - - +
217L ASN* 3.6 12.8 - - + -
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Residues in contact with THR 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ALA 3.0 11.6 + - - -
87L PHE* 3.4 12.8 - - + +
89L MET* 1.3 77.3 - - - +
91L LYS* 1.3 66.0 + - - +
92L LEU 3.1 1.2 + - - -
93L GLY 3.3 11.8 + - - -
94L ALA 4.0 3.3 + - - -
102L LEU* 4.7 3.1 - - + -
158L TYR* 5.4 1.3 - - - -
215L LEU* 3.4 26.4 - - + +
343L LEU* 4.3 32.3 - - + -
351L LEU* 4.3 12.6 - - + +
354L ILE* 5.4 3.4 - - + +
364L VAL* 4.8 2.9 - - + -
388L VAL* 3.7 23.5 - - + +
390L ILE* 5.6 1.8 - - + -
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Residues in contact with LYS 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PHE 2.9 14.4 + - - +
88L ALA* 2.8 17.8 + - - +
90L THR* 1.3 69.5 - - - +
92L LEU* 1.3 49.6 + - - +
94L ALA* 2.7 33.6 + - - +
99L LEU* 3.6 23.0 - - + +
102L LEU* 3.5 38.4 - - + -
103L MET* 3.4 32.5 - - + +
108L PHE* 4.3 18.2 - - + -
116L SER* 3.1 12.0 + - - -
119L ILE* 4.4 4.3 - - - -
120L HIS* 2.9 39.2 + - - -
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Residues in contact with LEU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L MET* 6.1 1.1 - - + +
19L PRO* 3.5 32.4 - - + +
20L MET* 4.8 2.1 + - - +
88L ALA 3.3 3.0 + - - +
89L MET* 3.2 16.9 + - + +
90L THR 3.1 0.8 + - - -
91L LYS* 1.3 70.6 - - - +
93L GLY* 1.3 55.9 + - - +
94L ALA 3.5 1.8 + - - +
120L HIS* 3.5 44.3 + - + +
158L TYR* 4.2 15.9 - - + +
161L ILE* 3.6 25.4 - - + -
162L SER* 3.8 38.8 - - - +
166L TYR* 4.0 16.4 - - + -
353L GLY* 5.5 0.5 - - - -
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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