Contacts of the helix formed by residues 85 - 97 (chain B) in PDB entry 3DRB
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.7 42.4 - - + -
45B LYS* 3.9 15.7 - - + -
47B THR* 4.2 8.3 - - + -
51B PHE 3.8 16.8 - - - -
52B THR* 3.6 13.2 - - - -
53B LEU* 3.4 35.7 - - + -
56B VAL* 3.9 17.7 - - + -
81B SER* 3.0 22.5 + - - +
84B VAL* 1.3 97.0 - - + +
86B LYS* 1.3 56.8 + - - -
87B ASP 3.2 3.6 - - - -
88B LEU* 2.9 24.8 + - + +
89B PHE* 3.1 24.5 + - + -
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Residues in contact with LYS 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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82B TYR 3.3 20.4 + - - +
83B GLU* 3.2 35.0 + - - +
84B VAL 3.5 1.3 - - - +
85B PHE* 1.3 76.6 - - - +
87B ASP* 1.3 71.8 + - - +
88B LEU 3.0 0.2 - - - -
89B PHE* 4.3 4.5 - - - +
90B ASP* 2.7 69.5 + - - +
102B PRO* 5.2 6.3 - - - +
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Residues in contact with ASP 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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38B LEU* 3.4 34.1 - - + +
41B GLU* 3.7 18.0 - - - +
42B LEU* 4.5 9.3 - - + +
85B PHE 3.1 1.6 + - - -
86B LYS* 1.3 93.5 + - - +
88B LEU* 1.3 55.4 + - - +
90B ASP* 4.9 1.9 - - - +
91B PRO* 3.6 18.8 - - - +
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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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30B MET* 4.7 4.3 - - + -
33B VAL* 4.1 10.4 - - + +
34B LEU* 4.3 20.9 - - + +
38B LEU* 4.1 15.5 - - + -
42B LEU* 4.3 13.6 - - + +
53B LEU* 3.5 26.7 - - + -
56B VAL* 3.9 16.4 - - + -
57B ILE* 3.8 16.8 - - + -
74B CYS* 5.1 1.3 - - + -
85B PHE* 2.9 11.0 + - + +
87B ASP* 1.3 79.3 - - - +
89B PHE* 1.3 67.8 + - + +
90B ASP 3.5 0.2 - - - -
91B PRO* 3.2 11.3 - - - +
92B ILE* 3.3 36.3 - - + +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.6 22.4 - - + -
74B CYS* 3.7 21.3 - - - -
75B VAL 3.7 16.4 - - - -
76B ALA* 4.3 4.7 - - - -
81B SER* 3.4 32.5 - - - -
82B TYR* 3.7 29.8 - + + +
85B PHE* 3.1 28.8 + - + +
86B LYS* 4.2 5.2 - - - +
88B LEU* 1.3 82.0 - - + +
90B ASP* 1.3 56.5 + - - +
92B ILE* 3.2 4.9 + - + +
93B ILE* 2.7 45.4 + - + +
284B PRO* 3.7 32.5 - - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR 5.2 1.0 - - - +
86B LYS* 2.7 66.7 + - - +
87B ASP* 4.9 2.5 - - - +
89B PHE* 1.3 73.0 - - - +
91B PRO* 1.3 61.5 - - + +
93B ILE* 3.4 12.1 + - - +
94B GLU* 2.9 28.9 + - - +
100B TYR 4.7 1.2 - - - +
102B PRO* 4.1 29.6 - - + +
276B HIS* 4.5 14.1 + - - -
277B LEU* 5.5 0.9 - - - +
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Residues in contact with PRO 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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33B VAL* 3.7 29.0 - - + +
87B ASP* 3.6 20.9 - - - +
88B LEU 3.2 12.3 - - - +
90B ASP* 1.3 96.1 - - + +
92B ILE* 1.3 61.6 + - - +
94B GLU* 3.2 12.3 + - + +
95B ASP* 2.9 23.6 + - - +
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Residues in contact with ILE 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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29B HIS* 3.8 27.3 + - + +
30B MET* 3.8 19.1 - - - -
33B VAL* 4.0 10.5 - - + -
72B VAL* 3.6 24.7 - - + -
74B CYS* 3.5 27.1 - - - -
88B LEU* 3.3 30.3 - - + +
89B PHE* 3.2 9.8 + - - +
91B PRO* 1.3 78.6 - - - +
93B ILE* 1.3 54.6 + - - +
95B ASP* 3.1 5.9 + - - +
96B ARG* 2.7 36.7 + - + +
284B PRO* 4.6 8.5 - - + -
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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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82B TYR* 4.5 4.3 - - + -
89B PHE* 2.7 38.3 + - + +
90B ASP* 3.7 11.4 - - - +
92B ILE* 1.3 72.2 - - - +
94B GLU* 1.3 57.9 + - - +
96B ARG* 4.7 1.1 - - - -
97B HIS* 2.9 38.3 + - - +
100B TYR* 4.1 15.7 - - + +
276B HIS* 5.7 1.3 - - - +
277B LEU* 4.0 18.2 - - + -
284B PRO* 4.5 14.1 - - + +
287B LEU* 3.6 28.3 - - + -
342B LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 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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90B ASP 2.9 14.8 + - - +
91B PRO* 3.2 13.4 + - - +
93B ILE* 1.3 78.7 - - - +
95B ASP* 1.3 58.8 + - - +
98B GLY 3.7 0.9 + - - -
99B GLY* 2.7 44.5 + - - -
100B TYR 3.2 20.3 + - - +
101B LYS* 3.3 33.4 - - - +
102B PRO* 3.9 7.5 - - + +
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Residues in contact with ASP 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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29B HIS* 3.3 24.4 + - + +
32B LYS* 2.6 36.3 + - - +
33B VAL* 5.8 4.5 - - + +
91B PRO 2.9 13.0 + - - +
92B ILE* 3.5 7.9 - - - +
94B GLU* 1.3 77.5 - - - +
96B ARG* 1.3 65.4 + - - +
97B HIS 3.3 0.7 + - - -
98B GLY* 3.6 7.8 + - - -
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Residues in contact with ARG 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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29B HIS* 3.6 33.1 - - + +
70B MET* 4.9 9.1 + - - -
72B VAL* 4.4 7.4 - - + +
92B ILE* 2.7 24.2 + - + +
93B ILE* 4.7 0.4 - - - -
95B ASP* 1.3 74.6 - - - +
97B HIS* 1.3 85.6 + - + +
98B GLY 3.7 1.7 + - - -
284B PRO* 5.8 0.9 - - + -
285B SER* 3.7 34.6 + - - +
318B GLN* 4.9 7.9 - - - +
320B ARG* 6.0 0.2 - - - +
339B ALA* 3.2 32.1 + - - +
340B ASP* 4.8 1.0 - - - +
341B ARG* 4.5 10.9 - - - +
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 30.6 + - + +
94B GLU 3.7 1.6 - - - -
96B ARG* 1.3 96.0 + - + +
98B GLY* 1.3 65.4 + - - +
99B GLY 3.4 2.0 - - - -
100B TYR* 3.1 24.4 + - + +
284B PRO 2.9 29.4 - - - -
285B SER* 3.2 27.4 + - - -
287B LEU 4.6 1.4 + - - -
316B ARG* 5.9 0.9 - - - -
340B ASP* 4.8 7.4 - - + -
341B ARG* 3.9 10.8 + - - +
342B LEU* 3.6 48.7 + - + +
344B PHE* 6.2 0.2 - - - -
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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