Contacts of the strand formed by residues 88 - 96 (chain D) in PDB entry 43C9
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 88 (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* 3.8 36.1 - - + -
39D GLN 3.4 16.8 - - - +
40D SER* 4.1 7.4 - - - +
43D LYS* 4.6 0.9 - - - -
86D ASP 3.3 2.0 + - - -
87D SER* 1.3 77.2 - - - +
89D MET* 1.3 61.5 + - - +
90D TYR* 3.3 10.9 - - + -
108D LEU* 3.9 8.1 - - - -
109D VAL 3.1 27.6 + - - -
11F LEU* 4.7 2.0 - - - -
110F THR* 4.9 0.6 - - - +
112F SER* 4.5 1.6 - - - -
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Residues in contact with MET 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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38D ARG* 3.1 4.5 - - - -
39D GLN* 2.9 38.4 + - + +
88D ALA* 1.3 72.4 - - - +
90D TYR* 1.3 59.6 + - - +
91D TYR* 3.7 33.6 - - + +
105D GLN 5.1 3.8 - - - +
106D GLY* 3.8 10.1 - - - -
107D THR 3.5 31.2 - - - -
108D LEU* 3.6 23.9 - - + +
11F LEU* 4.5 12.5 - - + +
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Residues in contact with TYR 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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6D GLU* 4.2 2.1 - - - +
18D LEU* 3.8 15.4 - - + +
20D ILE* 3.4 30.7 - - + -
36D TRP* 5.0 4.5 - + + -
37D VAL 3.6 2.2 - - - -
38D ARG* 3.1 16.5 + - + -
48D LEU* 3.6 31.6 - - + -
80D LEU* 4.1 6.5 - - + -
82D MET* 3.0 24.4 - - + +
86D ASP 2.9 27.6 + - - -
88D ALA* 3.3 23.6 - - + -
89D MET* 1.3 74.3 - - - +
91D TYR* 1.3 59.8 + - - +
106D GLY* 3.3 5.0 - - - -
107D THR* 2.9 40.1 + - + +
109D VAL* 3.7 21.1 - - + -
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Residues in contact with TYR 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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38C GLN* 4.0 1.7 + - - -
42C GLN 4.5 0.7 + - - -
43C SER* 3.3 40.8 + - - -
44C PRO* 4.4 2.2 - - + -
6D GLU* 3.4 4.3 - - - +
35D HIS 3.7 0.2 - - - +
36D TRP* 3.2 12.2 - - - -
37D VAL* 2.8 50.5 + - + +
39D GLN* 3.8 30.2 + - + -
89D MET* 3.7 32.9 - - + +
90D TYR* 1.3 73.3 - - - +
92D CYS* 1.3 60.4 + - - +
93D VAL* 4.8 0.2 - - - -
103D TRP* 3.3 31.6 - + + +
104D GLY 3.6 9.0 - - - -
105D GLN 3.6 17.2 + - - -
106D GLY* 3.5 17.3 - - - -
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Residues in contact with CYS 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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4D LEU* 3.4 13.7 - - - +
6D GLU* 3.1 26.0 + - - +
22D CYS* 2.0 54.7 - - + -
34D VAL* 3.8 10.5 - - + -
35D HIS 3.0 9.9 - - - +
36D TRP* 3.9 9.0 - - + -
91D TYR* 1.3 75.2 - - - +
93D VAL* 1.3 60.9 + - - +
104D GLY 2.9 24.6 + - - -
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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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4D LEU* 4.1 0.7 - - - -
33D ASN 3.6 1.0 - - - +
34D VAL* 3.3 2.6 - - - -
35D HIS* 2.7 43.6 + - + +
37D VAL* 4.5 14.8 - - + -
91D TYR* 4.6 0.7 - - + -
92D CYS* 1.3 80.3 - - - +
94D SER* 1.3 63.6 + - - +
95D TYR* 3.7 28.7 - - + +
101D SER* 4.8 2.2 - - - +
102D TYR 3.4 12.8 - - - +
103D TRP* 3.4 56.8 - - + +
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Residues in contact with SER 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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4D LEU* 3.7 19.4 - - - +
27D ILE* 3.8 12.0 - - - +
29D LEU* 6.4 0.4 - - - -
32D TYR* 4.3 11.7 - - - -
33D ASN 3.0 12.1 - - - -
34D VAL* 4.4 10.5 - - - -
93D VAL* 1.3 75.0 - - - +
95D TYR* 1.3 61.4 + - - +
101D SER* 3.0 10.4 - - - -
102D TYR* 2.8 51.5 + - - +
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Residues in contact with TYR 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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36C TYR* 2.6 39.8 + + - -
46C LEU* 4.4 8.5 - - + -
49C TYR* 6.3 0.2 - - + -
89C GLN* 3.7 6.2 + - - -
91C HIS* 3.9 10.5 - + - -
32D TYR* 3.2 4.9 - - - -
33D ASN* 2.8 48.1 + - + +
35D HIS* 3.5 41.5 - + - +
93D VAL* 3.7 24.6 - - + +
94D SER* 1.3 74.4 - - - +
96D GLY* 1.3 57.5 + - - +
100D PHE* 3.4 31.4 - - + +
101D SER* 3.2 30.3 - - - -
103D TRP* 4.2 1.6 - - - -
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Residues in contact with GLY 96 (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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31D ARG 3.6 10.8 - - - -
32D TYR* 3.1 21.7 + - - -
33D ASN* 5.8 0.4 - - - -
95D TYR* 1.3 75.9 - - - +
97D TYR* 1.3 67.4 + - - -
100D PHE* 3.0 37.2 + - - +
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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