Contacts of the helix formed by residues 64 - 75 (chain D) in PDB entry 3BRW
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B ILE* 4.5 3.1 - - + -
313B PHE* 4.3 10.8 - + - -
377B TYR* 4.1 17.7 - + - -
382B PHE* 3.9 36.8 - + + -
385B LEU* 5.3 4.5 - - + -
36D ILE* 4.9 5.8 - - + -
61D THR* 5.4 1.8 - - + +
62D GLU 4.0 0.6 - - - -
63D GLN* 1.3 111.6 - - + +
65D THR* 1.3 63.8 + - - +
66D ALA 3.3 2.0 - - - -
67D MET* 2.9 40.9 + - + +
68D ARG* 2.8 24.5 + - + +
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Residues in contact with THR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B SER* 6.1 0.5 - - - -
62D GLU 5.2 3.7 + - - +
63D GLN 2.9 12.7 + - - -
64D PHE* 1.3 67.9 - - - +
66D ALA* 1.3 63.8 + - - +
68D ARG* 3.7 6.4 - - - +
69D ASP* 2.9 32.4 + - + +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B HIS* 3.8 45.8 + - + +
389B THR* 4.3 4.9 - - + -
393B LEU* 4.4 7.6 - - + -
64D PHE 3.0 2.6 + - - +
65D THR* 1.3 78.4 - - - +
67D MET* 1.3 63.8 + - - +
69D ASP* 3.1 11.8 + - - +
70D LEU* 3.1 20.9 + - - +
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Residues in contact with MET 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LEU* 3.6 38.8 - - + +
388B ARG* 4.3 8.3 - - - +
389B THR* 3.4 29.3 - - + +
36D ILE* 5.7 5.4 - - + +
59D ALA* 6.4 2.0 - - + -
64D PHE* 2.9 42.5 + - + +
66D ALA* 1.3 73.1 - - - +
68D ARG* 1.3 77.7 + - + +
70D LEU* 2.9 21.2 + - + +
71D TYR* 3.2 45.4 + - + +
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Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 5.6 8.4 - - - +
10D GLY 5.2 3.2 + - - +
58D THR* 5.1 4.0 + - - -
59D ALA* 3.4 22.1 + - - +
60D GLY 4.6 2.8 + - - -
61D THR* 2.7 30.0 + - - +
62D GLU* 3.7 24.3 - - - +
63D GLN 4.6 0.4 - - - +
64D PHE* 2.8 36.8 + - - +
65D THR* 3.7 7.0 - - - +
67D MET* 1.3 78.4 - - + +
69D ASP* 1.3 59.2 + - - +
71D TYR* 3.3 41.2 + - - +
72D MET* 2.9 27.2 - - + +
96D LEU* 4.5 23.6 - - - +
99D GLN* 4.7 9.0 + - - +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 2.9 25.2 + - + +
66D ALA* 3.3 7.4 - - - +
68D ARG* 1.3 73.6 - - - +
70D LEU* 1.3 60.7 + - + +
72D MET* 3.0 31.2 + - - +
73D LYS* 3.4 8.1 + - - +
99D GLN* 3.4 16.6 + - - +
102D ARG* 5.6 2.1 + - - -
103D VAL* 3.5 27.4 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ARG* 5.8 4.3 - - - +
389B THR* 4.4 12.1 - - + +
392B ALA* 5.2 14.1 - - + -
393B LEU* 4.0 30.1 - - + -
66D ALA 3.1 26.1 + - - +
67D MET* 2.9 11.7 + - + +
69D ASP* 1.3 73.8 - - + +
71D TYR* 1.3 67.5 + - + +
72D MET 3.1 1.7 + - - -
73D LYS* 3.4 17.7 + - + +
74D ASN* 3.3 48.5 + - - +
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Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ARG* 4.4 10.1 - - - -
7D VAL* 4.1 10.1 - - + +
9D LEU* 5.4 3.1 - - + -
36D ILE 4.8 1.7 + - - -
37D GLU* 2.5 36.8 + - + +
56D LEU* 3.6 24.0 - - + -
58D THR* 3.8 33.2 - - + -
59D ALA 5.2 1.3 - - - -
67D MET* 3.2 41.3 - - + +
68D ARG* 3.3 37.0 - - - +
69D ASP 3.3 0.4 - - - -
70D LEU* 1.3 76.6 - - + +
72D MET* 1.3 67.7 + - + +
74D ASN* 4.8 1.3 - - - +
75D GLY* 3.1 24.1 + - - -
78D PHE* 3.8 5.4 - - - -
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Residues in contact with MET 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.1 17.5 - - + -
68D ARG* 2.9 41.1 - - + +
69D ASP* 3.0 15.5 + - - +
71D TYR* 1.3 79.5 - - + +
73D LYS* 1.3 64.4 + - - +
78D PHE* 3.5 9.9 - - - -
96D LEU* 5.7 1.3 - - + -
99D GLN* 3.3 38.8 - - - +
100D ILE* 3.6 47.3 - - + +
103D VAL* 3.7 18.2 - - + -
104D LYS* 3.2 23.7 + - - +
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Residues in contact with LYS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B THR* 5.3 12.1 + - - +
69D ASP* 3.4 7.0 + - - +
70D LEU* 3.4 19.9 + - + +
72D MET* 1.3 76.9 - - - +
74D ASN* 1.3 68.9 + - - +
75D GLY 3.1 0.8 + - - -
103D VAL* 3.8 22.4 - - + +
104D LYS* 2.6 29.8 + - - +
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Residues in contact with ASN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 3.9 36.8 - - - +
70D LEU* 3.3 33.9 + - - +
71D TYR* 4.8 1.1 - - - +
73D LYS* 1.3 86.4 - - - +
75D GLY* 1.3 61.2 + - - +
76D GLN* 3.7 4.9 + - - +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 4.0 4.3 - - - -
7D VAL* 4.0 14.4 - - - -
71D TYR 3.1 20.0 + - - -
73D LYS 3.1 1.7 + - - +
74D ASN* 1.3 78.2 - - - +
76D GLN* 1.3 59.9 + - - +
78D PHE* 3.6 13.0 - - - -
104D LYS* 2.5 34.5 + - - -
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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