Contacts of the strand formed by residues 87 - 92 (chain D) in PDB entry 4JRX
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 SER 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D CYS 3.3 10.8 - - - -
24D VAL* 4.6 8.3 - - - -
25D TYR* 3.9 2.2 - - - -
79D ASN* 3.4 5.4 + - - +
80D PHE* 3.6 1.7 - - - -
81D GLN* 3.0 37.6 + - - +
85D THR* 3.2 22.2 + - - -
86D SER* 1.3 77.4 - - - +
88D PHE* 1.3 60.8 + - - +
89D ASN* 3.9 20.7 + - - -
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Residues in contact with PHE 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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23D CYS* 3.0 26.6 + - - +
25D TYR* 4.7 2.1 - - + -
39D LEU* 3.6 47.1 - - + -
40D PHE 4.6 0.4 - - - -
41D TRP* 2.9 44.6 + + - -
54D ILE* 3.7 22.4 - - + -
56D ARG* 3.6 27.6 - - + -
78D TRP* 3.7 23.6 - + + -
79D ASN 3.6 1.8 - - - -
80D PHE* 3.7 36.1 - + + -
87D SER* 1.3 71.5 - - - +
89D ASN* 1.3 60.8 + - - +
105D CYS* 4.4 4.7 - - - -
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Residues in contact with ASN 89 (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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20D THR* 4.1 10.5 - - + +
21D LEU 3.4 7.4 - - - +
22D ASP* 3.2 25.3 + - - +
23D CYS 2.9 31.4 + - - +
24D VAL* 5.2 0.7 - - - +
41D TRP* 4.5 1.1 - - - -
77D SER 4.1 0.2 - - - +
78D TRP* 3.5 4.5 - - - -
79D ASN* 3.0 44.0 + - + +
87D SER* 3.9 18.4 + - - -
88D PHE* 1.3 71.7 + - - +
90D PHE* 1.3 60.7 + - - +
91D THR* 4.0 2.9 + - - -
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D VAL 4.1 0.5 - - - +
20D THR* 3.4 0.7 - - - -
21D LEU* 2.7 49.8 + - + +
41D TRP* 3.5 41.3 - + + -
53D LEU* 3.8 14.1 - - + -
76D TYR* 3.5 50.9 - + + -
77D SER 4.0 2.0 - - - -
78D TRP* 3.2 28.3 - + + -
88D PHE 4.0 0.6 + - - -
89D ASN* 1.3 70.3 - - - +
91D THR* 1.3 70.6 + - - +
92D ILE* 3.6 14.2 + - + +
103D TYR* 3.5 30.1 - + - -
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Residues in contact with THR 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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18D ASP* 4.8 4.7 - - + +
19D VAL 3.3 17.5 - - - +
20D THR* 3.0 27.8 + - - +
75D ARG 3.7 1.0 - - - +
76D TYR* 3.6 5.0 - - - -
77D SER* 2.9 47.0 + - - +
89D ASN 4.6 2.6 + - - -
90D PHE* 1.3 72.9 - - - +
92D ILE* 1.3 62.6 + - - +
93D THR* 4.3 19.5 - - + +
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Residues in contact with ILE 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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17D GLU 4.1 1.2 - - - +
18D ASP* 3.3 2.8 - - - +
19D VAL* 2.8 46.7 + - + +
21D LEU* 4.6 6.3 - - + -
75D ARG* 3.4 21.5 - - - +
76D TYR* 4.3 7.2 - - + -
90D PHE* 3.6 32.3 - - + +
91D THR* 1.3 70.8 - - - +
93D THR* 1.3 61.3 + - - +
95D SER* 4.2 4.2 + - - +
99D ASP* 3.4 28.3 - - + +
103D TYR* 3.7 33.7 - - + +
127D LEU* 3.8 19.5 - - + -
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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