Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 1BQD
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 PRO 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B LEU* 6.3 0.2 - - + -
75B GLY 3.2 11.0 - - - +
76B ILE* 1.3 88.8 - - + +
78B GLU* 1.3 73.4 + - + +
80B GLY* 3.1 11.9 + - - +
81B ARG* 3.1 15.9 + - - +
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Residues in contact with GLU 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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76B ILE* 2.8 25.7 - - + +
77B PRO* 1.3 89.8 - - + +
79B PHE* 1.3 65.1 + - - +
81B ARG* 3.4 21.2 - - - +
82B CYS* 3.0 32.0 + - - +
307B ALA* 4.5 12.7 - - + +
311B SER* 5.9 4.5 - - - -
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Residues in contact with PHE 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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76B ILE* 3.1 26.2 + - + +
78B GLU* 1.3 78.4 - - - +
80B GLY* 1.3 61.8 + - - +
82B CYS* 3.9 4.0 - - - +
83B THR* 2.9 42.9 + - - -
102B THR* 5.3 0.9 - - + -
104B GLN* 3.9 25.4 - - + +
256B TYR* 3.3 35.2 - + - -
267B VAL* 3.7 22.4 - - + -
268B GLY 3.7 22.2 - - - -
269B ALA* 3.9 10.1 - - + -
303B ALA* 3.5 24.2 - - + +
306B VAL* 3.8 16.8 - - + -
307B ALA* 4.2 12.0 - - + +
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Residues in contact with GLY 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 ILE 3.2 4.7 + - - -
77B PRO* 3.1 8.2 + - - -
79B PHE* 1.3 79.4 - - - +
81B ARG* 1.3 59.1 + - - +
83B THR* 3.2 2.9 + - - -
84B GLN* 3.0 36.7 + - - +
102B THR* 4.1 26.8 + - - -
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Residues in contact with ARG 81 (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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77B PRO 3.1 13.7 + - - +
78B GLU* 3.4 27.3 + - - +
80B GLY* 1.3 74.1 - - - +
82B CYS* 1.3 83.3 + - - +
84B GLN* 3.5 9.4 + - - +
85B GLU* 3.0 55.0 + - - +
90B LYS* 4.4 7.7 - - - +
95B ILE* 5.6 0.3 - - - +
311B SER* 4.8 11.1 - - - +
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Residues in contact with CYS 82 (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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78B GLU* 3.0 23.4 + - - +
79B PHE* 3.9 4.5 - - - +
81B ARG* 1.3 103.1 - - - +
83B THR* 1.3 62.2 + - - +
85B GLU* 3.5 8.1 + - - +
86B LEU* 3.2 23.4 + - - +
307B ALA* 4.9 5.6 - - - -
310B LEU* 4.1 47.6 - - + +
311B SER* 4.5 7.0 - - - -
316B ARG* 6.1 1.6 - - - +
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Residues in contact with THR 83 (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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79B PHE* 2.9 31.0 + - - -
80B GLY* 3.5 5.8 - - - -
82B CYS* 1.3 77.4 - - - +
84B GLN* 1.3 62.6 + - - +
86B LEU* 3.2 5.1 + - - +
87B LEU* 3.0 42.2 + - + +
102B THR* 4.4 4.9 - - + -
254B SER* 4.1 13.0 - - - +
256B TYR* 2.5 35.2 + - - +
269B ALA* 4.1 12.8 - - + -
271B THR* 4.4 6.1 - - - +
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Residues in contact with GLN 84 (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 GLY 3.0 17.4 + - - +
81B ARG* 3.9 8.1 - - - +
82B CYS 3.3 0.2 - - - -
83B THR* 1.3 77.3 - - - +
85B GLU* 1.3 57.0 + - - +
87B LEU* 4.4 5.4 - - - -
88B PHE* 2.8 40.4 + - + +
95B ILE* 3.9 28.2 - - + +
100B ALA* 3.3 37.5 + - - +
101B ARG* 3.8 0.4 - - - +
102B THR* 2.9 41.3 + - - +
271B THR* 4.4 8.3 - - + +
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Residues in contact with GLU 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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81B ARG* 3.0 46.2 + - - +
82B CYS* 3.7 7.9 - - - +
83B THR 3.3 0.4 - - - -
84B GLN* 1.3 76.7 - - - +
86B LEU* 1.3 57.5 + - - +
89B GLY* 2.7 32.4 + - - +
90B LYS* 3.2 53.1 + - + +
95B ILE* 4.1 14.8 - - + +
234B GLU* 4.7 2.1 - - - +
316B ARG* 5.5 4.7 + - - -
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Residues in contact with LEU 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 CYS 3.2 9.4 + - - +
83B THR* 3.4 9.6 - - - +
85B GLU* 1.3 80.1 - - - +
87B LEU* 1.3 60.1 + - + +
226B GLN* 3.0 41.1 + - - +
233B LEU* 4.4 20.6 - - + -
234B GLU* 4.4 8.1 - - - +
241B ARG* 3.3 13.2 + - - -
256B TYR* 4.0 30.7 - - + +
259B ASN* 5.5 3.8 - - - +
310B LEU* 4.2 16.4 - - + -
316B ARG* 3.9 28.5 - - - +
319B TRP* 4.8 10.5 - - + -
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Residues in contact with LEU 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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83B THR* 3.0 36.3 + - + +
84B GLN* 3.6 5.4 - - - +
86B LEU* 1.3 81.5 - - + +
88B PHE* 1.3 76.3 + - + +
89B GLY 3.4 0.2 - - - -
223B PHE* 3.8 23.1 - - + -
226B GLN* 3.8 12.3 - - - +
237B ALA* 3.8 4.5 - - - +
240B LEU* 3.9 21.5 - - + +
241B ARG* 2.9 26.3 + - - +
252B VAL* 4.1 19.5 - - + -
254B SER* 4.2 13.7 - - - +
256B TYR* 5.8 0.9 - - - +
271B THR* 3.9 16.8 - - - +
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Residues in contact with PHE 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 GLN* 2.8 31.4 + - + +
87B LEU* 1.3 83.8 - - + +
89B GLY* 1.3 62.9 + - - +
92B SER* 3.2 27.3 - - - +
94B LEU* 4.0 29.8 - - + -
95B ILE* 4.5 5.8 - - + -
100B ALA* 4.2 18.8 - - + -
240B LEU* 4.1 30.1 - - + -
241B ARG* 3.8 19.2 + - + +
244B ALA* 4.3 11.7 - - + -
250B LEU* 4.7 1.3 - - + -
252B VAL* 4.4 9.6 - - + -
271B THR* 4.2 14.4 - - + -
273B VAL* 3.9 19.3 - - + -
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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