Contacts of the helix formed by residues 84 - 96 (chain B) in PDB entry 5DSG
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 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.1 33.3 + - + +
83B ALA* 1.3 92.4 - - + +
85B SER* 1.3 67.6 + - - +
86B MET 3.4 0.6 + - - -
87B ASN* 3.5 2.3 + - - +
88B LEU* 3.1 40.4 + - + +
111B LEU* 4.0 22.9 - - + -
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Residues in contact with SER 85 (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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80B ILE* 3.7 2.5 + - - +
81B ILE* 3.2 26.6 + - - +
84B PHE* 1.3 77.8 - - - +
86B MET* 1.3 64.8 + - - +
89B TYR* 2.9 26.7 + - - +
108B TRP* 3.8 8.3 + - - +
111B LEU* 4.9 5.2 - - - +
112B ASP* 2.4 35.6 + - - -
115B VAL* 6.1 0.3 - - - +
443B TYR* 3.6 22.9 + - - -
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Residues in contact with MET 86 (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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42B LEU* 4.1 3.6 - - + +
43B SER* 3.6 35.0 - - - -
46B THR* 3.4 22.2 - - + +
81B ILE* 3.1 15.9 + - + +
82B GLY* 3.8 19.1 - - - +
84B PHE 3.4 0.2 - - - -
85B SER* 1.3 77.9 - - - +
87B ASN* 1.3 57.7 + - - +
89B TYR 3.3 0.2 + - - -
90B THR* 2.9 33.7 + - - +
440B TRP* 3.4 37.1 - - + -
443B TYR* 3.5 39.9 - - + +
444B VAL* 4.5 1.3 - - + +
447B THR* 3.4 11.0 - - - +
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Residues in contact with ASN 87 (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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40B GLY* 5.2 4.0 - - - -
43B SER* 3.2 29.9 + - - -
83B ALA* 2.5 30.1 + - - +
84B PHE* 3.5 2.6 + - - +
85B SER 3.4 0.4 - - - -
86B MET* 1.3 75.3 - - - +
88B LEU* 1.3 59.1 + - + +
90B THR* 2.4 27.0 + - - +
91B VAL* 2.9 20.1 + - + +
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Residues in contact with LEU 88 (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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84B PHE* 3.1 35.4 + - + +
85B SER 3.9 2.2 - - - +
87B ASN* 1.3 76.1 - - + +
89B TYR* 1.3 63.0 + - - +
91B VAL* 3.0 12.4 + - + +
92B TYR* 3.0 21.1 + - - +
98B TRP* 3.9 11.0 - - + -
100B LEU* 3.7 29.4 - - + -
104B VAL* 5.1 7.4 - - + -
108B TRP* 3.4 41.5 - - + +
111B LEU* 5.7 2.0 - - + -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 2.9 18.6 + - - +
86B MET 3.6 3.6 - - - +
88B LEU* 1.3 76.4 - - - +
90B THR* 1.3 57.4 - - - +
92B TYR* 3.2 12.2 + + + +
93B ILE* 2.9 54.3 + - + +
108B TRP* 3.6 26.4 - + + -
436B SER* 3.2 39.8 + - - -
439B TYR* 3.6 18.6 - + - +
440B TRP* 3.7 25.8 - + + -
443B TYR* 3.8 15.0 - + + -
1205B P6G 3.3 36.8 - - - -
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Residues in contact with THR 90 (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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35B ILE* 5.6 2.0 - - + -
36B ALA* 5.9 0.9 - - - -
39B THR* 3.3 40.6 - - + +
86B MET 2.9 18.6 + - - +
87B ASN* 2.4 34.7 + - - +
89B TYR* 1.3 73.5 - - - +
91B VAL* 1.3 59.2 + - - +
93B ILE* 4.2 9.0 - - + -
94B ILE* 2.9 43.0 + - - +
440B TRP* 3.6 12.1 - - + -
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Residues in contact with VAL 91 (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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87B ASN* 2.9 22.9 + - + +
88B LEU* 3.2 16.2 - - + +
90B THR* 1.3 75.9 + - - +
92B TYR* 1.3 63.8 + - - +
94B ILE* 4.9 2.5 - - - -
95B LYS* 2.9 42.2 + - + +
98B TRP* 5.4 0.7 - - + -
99B PRO* 3.9 28.9 - - + -
100B LEU* 4.7 14.8 - - + -
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Residues in contact with TYR 92 (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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88B LEU 3.0 11.8 + - - +
89B TYR* 3.3 22.9 - + + +
91B VAL* 1.3 78.8 - - - +
93B ILE* 1.3 61.3 + - + +
96B GLY* 3.1 20.7 + - - -
97B TYR* 3.4 33.3 + - - -
98B TRP* 3.6 20.6 - + + -
108B TRP* 4.1 16.4 - + - -
184B GLN* 2.5 28.1 + - - +
185B CYS* 2.9 46.8 + - + -
186B PHE* 5.3 1.4 - - - -
1205B P6G 5.3 9.2 - - - -
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Residues in contact with ILE 93 (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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32B MET* 4.2 13.0 - - + +
35B ILE* 4.4 35.4 - - + -
39B THR* 5.8 1.6 - - + -
89B TYR* 2.9 57.1 + - + +
90B THR* 3.8 9.9 - - + +
91B VAL 3.3 0.2 - - - -
92B TYR* 1.3 77.5 - - + +
94B ILE* 1.3 65.7 + - + +
96B GLY* 3.3 12.1 + - - -
436B SER* 4.8 16.2 - - - +
440B TRP* 5.1 9.0 - - + -
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Residues in contact with ILE 94 (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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28B GLU* 5.6 0.5 - - - +
32B MET* 3.3 63.6 - - + +
35B ILE* 4.1 16.6 - - + -
36B ALA* 4.3 12.8 - - + +
90B THR* 2.9 29.2 + - - +
91B VAL* 4.2 2.9 - - - +
93B ILE* 1.3 74.7 - - + +
95B LYS* 1.3 67.0 + - + +
96B GLY* 3.4 0.5 + - - -
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Residues in contact with LYS 95 (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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91B VAL* 2.9 29.2 + - + +
94B ILE* 1.3 81.7 - - + +
96B GLY* 1.3 56.2 + - - +
97B TYR* 3.1 52.7 + - + +
99B PRO* 3.7 31.5 - - + +
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Residues in contact with GLY 96 (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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92B TYR* 3.1 16.1 + - - -
93B ILE* 3.3 7.4 + - - -
94B ILE 3.2 4.0 - - - -
95B LYS* 1.3 76.7 - - - +
97B TYR* 1.3 62.1 + - - +
184B GLN* 4.5 6.8 + - - +
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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
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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