Contacts of the strand formed by residues 87 - 95 (chain D) in PDB entry 5BRZ
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 ALA 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.5 31.4 - - + +
39D GLN 3.6 11.9 - - - +
40D ASP* 3.9 6.5 - - - +
41D PRO* 5.5 4.0 - - - -
85D ASP 3.9 1.8 + - - -
86D SER* 1.3 76.2 - - - +
88D THR* 1.3 63.9 + - - +
89D TYR* 3.4 19.8 - - + -
110D LYS* 3.9 3.1 - - - -
111D LEU 2.9 29.4 + - - +
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Residues in contact with THR 88 (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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38D ARG* 3.6 2.4 - - - -
39D GLN* 2.9 54.4 + - - +
41D PRO* 5.6 3.2 - - - +
87D ALA* 1.3 72.8 + - - +
89D TYR* 1.3 66.5 + - - +
90D LEU* 4.1 8.3 + - + +
107D LYS 4.9 3.6 - - - +
108D GLY* 4.5 6.7 - - - -
109D THR 3.8 21.5 - - - +
110D LYS* 3.4 29.7 + - + +
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN* 2.9 9.0 + - - -
22D LEU* 3.5 28.7 - - + -
36D TRP* 4.4 7.2 - + + -
37D PHE 3.5 4.0 - - - +
38D ARG* 4.3 10.8 + - + -
48D LEU* 3.7 31.0 - - + -
63D LEU* 5.6 2.2 - - + -
76D LEU* 4.1 11.9 - - + -
78D ILE* 5.3 5.5 - - + +
85D ASP* 2.8 34.1 + - - +
87D ALA* 3.4 33.4 - - + -
88D THR* 1.3 76.3 - - - +
90D LEU* 1.3 61.0 + - - +
108D GLY* 2.9 2.3 - - - -
109D THR* 2.9 41.6 + - - +
111D LEU* 3.9 24.7 - - + +
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Residues in contact with LEU 90 (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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7D GLN* 3.5 1.3 - - - -
35D GLN 3.9 0.2 - - - +
36D TRP* 3.4 7.9 - - - -
37D PHE* 2.8 49.4 + - + +
39D GLN* 4.2 23.8 - - + +
45D LEU* 3.7 29.2 - - + -
88D THR* 4.8 7.9 - - + +
89D TYR* 1.3 75.6 - - - +
91D CYS* 1.3 57.5 + - - +
105D PHE* 4.4 12.1 - - + -
106D GLY 3.5 19.3 - - - +
107D LYS 3.7 4.9 - - - +
108D GLY* 3.5 24.2 - - - +
38E GLN* 5.3 2.2 - - - +
44E LEU* 4.7 14.1 - - + -
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Residues in contact with CYS 91 (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 VAL* 3.5 13.3 - - - +
7D GLN* 3.0 23.4 + - - -
24D CYS* 2.1 52.9 - - + -
34D LEU* 4.8 2.7 - - + -
35D GLN 3.4 8.1 - - - +
36D TRP* 3.9 17.0 - - + +
90D LEU* 1.3 74.2 - - - +
92D ALA* 1.3 62.4 + - - +
105D PHE* 3.4 2.6 - - - +
106D GLY 2.8 27.2 + - - -
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Residues in contact with ALA 92 (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 VAL* 5.1 1.1 - - - -
24D CYS* 6.1 0.4 - - - -
33D ASN* 5.4 0.7 - - - -
34D LEU* 3.4 7.5 - - - +
35D GLN* 2.9 36.6 + - + +
37D PHE* 4.3 6.5 - - + -
90D LEU 4.3 0.2 + - - -
91D CYS* 1.3 75.6 - - - +
93D VAL* 1.3 63.7 + - - +
103D VAL* 3.5 20.4 - - + -
104D VAL 2.9 14.1 - - - +
105D PHE* 3.7 23.3 - - + -
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Residues in contact with VAL 93 (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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3D GLN* 3.7 30.1 - - + +
5D VAL* 4.8 6.3 - - + -
24D CYS* 5.9 1.6 - - - -
26D PHE* 4.0 16.6 - - + -
31D ILE* 3.5 29.4 - - + -
33D ASN* 3.4 15.7 - - - +
34D LEU* 3.8 23.6 - - + +
92D ALA* 1.3 79.3 - - - +
94D ARG* 1.3 59.9 + - - +
95D PRO* 3.2 2.6 - - - +
103D VAL* 3.5 4.6 - - - -
104D VAL* 3.0 32.4 + - + +
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Residues in contact with ARG 94 (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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31D ILE* 3.2 3.6 - - - -
32D TYR* 2.6 50.8 + - + -
33D ASN* 3.1 36.0 + - - +
93D VAL* 1.3 71.7 - - - +
95D PRO* 1.3 61.2 - - - +
101D PHE* 2.8 41.7 + - - -
102D PHE* 3.9 2.6 - - - +
103D VAL* 3.5 27.8 - - + +
49E GLU* 2.9 41.4 + - - -
95E SER* 4.3 9.3 + - - -
98E MET* 3.0 41.7 + - - +
100E THR 5.0 2.4 + - - -
102E GLN* 4.2 8.7 - - - +
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Residues in contact with PRO 95 (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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3D GLN* 4.0 25.6 - - + +
28D ASP* 6.0 0.9 - - + -
30D ALA 3.9 4.5 - - - +
31D ILE* 4.2 5.4 - - + -
32D TYR* 3.7 7.9 - - - -
93D VAL* 3.2 12.1 - - + +
94D ARG* 1.3 86.7 - - - +
96D GLY* 1.3 58.0 + - - +
97D GLY 3.7 3.8 - - - +
100D PRO 4.0 8.7 - - - +
101D PHE* 3.6 35.8 - - - +
102D PHE 3.3 25.8 - - - +
104D VAL* 4.3 10.3 - - + -
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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