Contacts of the strand formed by residues 85 - 92 (chain D) in PDB entry 4MJI
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 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D GLN* 3.4 36.1 - - + +
38D ASN 3.3 13.2 - - - +
39D SER* 3.7 13.0 - - - +
83D ASP 3.3 2.0 + - - -
84D THR* 1.3 76.1 - - - +
86D SER* 1.3 59.8 + - - +
87D TYR* 3.2 17.4 - - + -
106D GLN* 5.1 1.1 - - - -
107D LEU 3.1 22.3 + - - +
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Residues in contact with SER 86 (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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36D ARG 3.8 0.3 - - - +
37D GLN* 3.7 2.6 - - - -
38D ASN* 2.8 47.5 + - - +
39D SER* 4.8 0.4 - - - +
85D ALA* 1.3 72.9 - - - +
87D TYR* 1.3 60.7 + - - +
88D PHE* 4.2 19.1 - - - -
105D THR 3.2 11.7 - - - -
106D GLN* 3.6 31.2 + - - +
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Residues in contact with TYR 87 (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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21D MET* 3.6 22.7 - - + -
35D TYR* 4.9 11.9 - + + -
36D ARG 3.3 8.7 - - - -
37D GLN* 4.1 23.3 + - + -
61D LEU* 5.4 1.6 - - + -
74D LEU* 3.8 21.5 - - + -
76D ILE* 3.7 22.9 - - + +
83D ASP* 2.7 40.4 + - - +
85D ALA* 3.2 28.3 - - + -
86D SER* 1.3 73.9 - - - +
88D PHE* 1.3 64.7 + - - +
104D GLY* 3.2 5.4 - - - -
105D THR* 2.8 31.9 + - - +
107D LEU* 3.6 21.3 - - + -
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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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35D TYR* 3.5 7.1 - - - -
36D ARG* 2.6 49.9 + - + +
38D ASN* 3.2 44.2 - - + -
44D VAL* 3.9 11.4 - - + -
86D SER* 4.7 13.9 - - - -
87D TYR* 1.3 79.1 - - - +
89D CYS* 1.3 66.4 + - - +
101D PHE* 4.3 6.7 - - + -
102D GLY 3.6 10.5 - - - -
103D SER 2.8 31.4 - - - -
104D GLY* 4.5 1.8 - - - -
40E GLN* 3.3 22.4 - - - -
43E GLY* 6.3 0.7 - - - -
44E GLN* 3.7 6.3 - - - -
45E GLY* 3.9 11.9 - - - -
46E PRO* 4.3 8.1 - - + -
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Residues in contact with CYS 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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23D CYS* 2.1 53.4 - - + +
33D GLN* 3.7 16.6 - - - +
34D TRP 3.4 3.4 - - - -
35D TYR* 3.2 27.1 - - - -
87D TYR 4.2 0.6 + - - -
88D PHE* 1.3 72.8 - - - +
90D ALA* 1.3 60.9 + - - +
91D THR* 5.5 2.2 - - + +
101D PHE* 3.1 11.6 - - - +
102D GLY* 3.1 33.1 + - - +
104D GLY* 5.1 4.0 - - - +
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Residues in contact with ALA 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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32D LEU* 4.7 0.9 - - - +
33D GLN* 3.2 4.9 - - - +
34D TRP* 2.5 43.7 + - + +
36D ARG* 3.6 16.6 - - + +
88D PHE 3.9 0.4 + - - -
89D CYS* 1.3 74.3 - - - +
91D THR* 1.3 61.7 + - - +
99D LEU* 3.9 15.0 - - + -
100D THR 3.3 7.4 - - - +
101D PHE* 3.4 29.2 - - + -
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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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25D TYR* 3.1 44.6 - - + -
27D THR* 3.8 2.3 - - - +
30D ASN* 4.2 11.0 - - - +
32D LEU 3.6 5.2 - - - -
33D GLN* 4.1 8.5 - - + +
89D CYS* 5.9 2.5 - - + -
90D ALA* 1.3 74.7 - - - +
92D ASP* 1.3 59.0 + - - +
93D ASP* 2.6 31.2 + - - +
99D LEU* 3.5 4.7 - - - -
100D THR* 2.7 45.6 + - + +
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Residues in contact with ASP 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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155A GLN* 3.6 24.8 + - - +
30D ASN* 3.3 3.5 - - - -
31D ASN* 3.1 22.7 + - + -
32D LEU* 3.2 34.0 + - + +
91D THR* 1.3 67.0 - - - +
93D ASP* 1.3 69.7 + - - +
94D ASP 3.4 0.7 + - - -
95D SER* 3.4 7.0 + - - -
96D ALA 3.3 4.3 + - - -
97D ARG* 2.6 46.5 + - - +
98D GLN 4.1 0.9 - - - -
99D LEU* 3.8 15.7 - - + +
102E GLY* 4.6 3.4 - - - -
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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