Contacts of the helix formed by residues 69 - 80 (chain B) in PDB entry 5DYE
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 ASN 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ILE* 5.9 1.3 - - + -
67B HIS* 3.1 9.8 - - - +
68B ILE* 1.3 79.6 - - - +
70B PRO* 1.4 60.8 - - - +
71B ALA* 3.2 22.1 + - - +
72B ILE* 2.8 47.2 + - + +
73B THR* 3.1 10.6 + - - -
94B GLN* 3.7 7.5 - - - +
142B LEU* 4.4 11.9 - - - +
184B MET* 2.6 27.1 + - - +
185B ASN* 3.4 22.0 - - - +
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 1.4 83.6 - - - +
71B ALA* 1.3 57.1 + - - +
73B THR* 3.7 4.5 - - - +
74B LEU* 3.1 41.6 + - + +
91B VAL* 4.2 16.4 - - + -
94B GLN* 3.2 28.0 - - + +
95B LEU* 4.0 13.0 - - + -
185B ASN* 3.7 4.7 - - - +
186B PRO* 4.3 11.7 - - + -
187B ALA* 3.5 38.8 - - + +
207B TRP* 5.1 3.8 - - + -
211B ILE* 6.3 0.2 - - + -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 3.1 15.0 + - - +
70B PRO* 1.3 77.2 - - - +
72B ILE* 1.3 58.2 + - - +
74B LEU* 3.6 3.0 + - - +
75B ALA* 3.0 27.9 + - - +
139B THR* 4.5 4.3 - - + -
186B PRO* 3.8 16.9 - - + +
210B PRO* 4.0 31.0 - - + +
211B ILE* 4.0 15.7 - - + +
214B ALA* 3.5 8.4 - - + +
215B VAL* 5.7 0.3 - - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLY 5.9 0.4 - - - +
67B HIS* 4.8 17.0 - - + +
69B ASN* 2.8 34.1 + - + +
71B ALA* 1.3 71.2 - - - +
73B THR* 1.3 66.4 + - - +
75B ALA* 3.3 3.9 + - - +
76B LEU* 3.1 39.9 + - + +
139B THR* 4.6 10.8 - - + -
142B LEU* 4.8 5.8 - - + -
143B ALA* 3.8 31.0 - - + +
146B ILE* 4.0 35.7 - - + -
147B PHE* 4.7 4.0 - - + -
214B ALA* 4.5 6.1 - - + -
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 3.0 20.2 + - - +
69B ASN 3.1 5.2 + - - -
70B PRO* 3.7 11.0 - - - -
72B ILE* 1.3 77.9 - - - +
74B LEU* 1.3 60.4 + - - +
76B LEU* 3.4 0.9 + - - +
77B LEU* 3.2 18.7 + - - +
82B ILE* 3.6 13.7 - - + +
87B ALA* 3.6 36.6 - - + +
90B TYR* 3.9 12.3 - - + -
91B VAL* 4.0 5.6 - - + -
94B GLN* 2.9 28.7 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PRO* 3.1 25.7 + - + +
71B ALA* 4.0 3.6 - - - +
72B ILE 3.4 0.2 - - - -
73B THR* 1.3 76.0 - - - +
75B ALA* 1.3 63.7 + - - +
77B LEU* 3.5 18.5 + - + +
78B VAL* 3.2 29.2 + - + +
87B ALA* 5.2 3.6 - - + -
91B VAL* 4.5 18.2 - - + -
207B TRP* 6.1 2.7 - - + -
211B ILE* 4.2 35.0 - - + -
215B VAL* 4.9 3.6 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA 3.0 18.6 + - - +
72B ILE* 3.6 7.2 - - - +
73B THR 3.3 0.4 - - - -
74B LEU* 1.3 76.1 - - - +
76B LEU* 1.3 57.0 + - - +
78B VAL* 3.5 2.3 + - - +
79B GLY 2.9 21.8 + - - -
147B PHE* 4.1 12.3 - - + -
214B ALA* 3.4 36.1 - - + +
215B VAL* 4.5 10.2 - - - +
218B ALA* 3.2 15.7 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 3.3 39.9 - - + +
72B ILE* 3.1 26.7 + - + +
73B THR 3.7 3.8 - - - +
75B ALA* 1.3 73.5 - - - +
77B LEU* 1.3 55.8 + - - +
79B GLY* 3.3 1.4 + - - +
80B ASN 2.7 30.3 + - - -
81B GLN* 2.9 39.8 + - + +
82B ILE* 4.3 8.5 - - + -
146B ILE* 5.9 2.0 - - + -
147B PHE* 3.4 31.6 - - + -
150B THR* 6.1 0.4 - - - +
218B ALA* 5.3 0.4 - - - -
222B PHE* 4.3 3.4 - - + -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B THR 3.2 14.8 + - - +
74B LEU* 3.8 17.0 - - + +
75B ALA 3.4 0.2 - - - -
76B LEU* 1.3 77.4 - - - +
78B VAL* 1.3 62.5 - - + +
80B ASN* 3.6 12.7 + - - +
82B ILE* 3.4 34.2 - - + +
83B SER 3.6 17.3 - - - +
84B LEU* 3.9 26.0 - - + +
87B ALA* 3.7 20.9 - - + -
239B ILE* 5.1 11.8 - - + +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 3.2 18.7 + - + +
75B ALA 3.7 5.2 - - - +
77B LEU* 1.3 77.9 - - + +
79B GLY* 1.3 52.3 + - - +
80B ASN* 3.3 1.4 + - - +
215B VAL* 4.1 26.2 - - + +
218B ALA* 5.6 0.2 - - + -
219B ILE* 4.1 26.5 - - + -
223B TYR* 2.5 30.4 + - + -
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA 2.9 16.7 + - - -
76B LEU 3.3 4.0 + - - -
78B VAL* 1.3 75.2 - - - +
80B ASN* 1.3 65.9 + - - +
81B GLN* 3.4 15.3 + - - -
218B ALA* 4.4 6.3 - - - +
222B PHE* 3.7 22.3 - - - +
223B TYR* 3.5 22.8 - - - -
235B ARG* 5.7 0.2 + - - -
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU 2.7 11.6 + - - -
77B LEU 3.8 8.7 - - - +
78B VAL 3.1 2.9 - - - +
79B GLY* 1.3 76.9 - - - +
81B GLN* 1.3 70.4 + - - +
82B ILE 3.9 1.8 - - - +
223B TYR* 3.8 14.4 - - + +
228B ASN* 5.0 4.9 + - - +
235B ARG* 3.5 52.9 - - - +
238B ILE* 3.8 24.3 - - - +
239B ILE* 3.6 27.9 - - - +
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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
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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