Contacts of the strand formed by residues 50 - 58 (chain D) in PDB entry 5IXG
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 THR 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.8 2.1 - - - +
45D ASP* 2.9 41.2 + - - +
48D ALA* 3.5 19.4 - - + +
49D LYS* 1.3 84.0 - - - +
51D GLY* 1.3 60.5 + - - +
92D THR* 6.0 1.8 - - - -
93D ILE 4.3 4.5 - - - -
95D PHE* 3.6 14.5 - - - -
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Residues in contact with GLY 51 (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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43D THR* 3.0 18.2 - - - -
44D LEU* 4.2 0.7 - - - -
45D ASP 4.7 0.2 - - - -
50D THR* 1.3 80.0 - - - +
52D THR* 1.3 69.6 + - - +
92D THR* 3.4 9.3 - - - +
93D ILE* 2.9 35.5 + - - -
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Residues in contact with THR 52 (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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41D THR 4.8 0.2 - - - -
42D VAL* 3.3 9.2 - - - +
43D THR* 2.5 57.6 + - - +
51D GLY* 1.3 80.5 - - - +
53D VAL* 1.3 66.2 + - - +
91D GLY 3.2 11.2 - - - +
92D THR* 4.4 7.4 - - - +
93D ILE* 3.9 0.4 - - - +
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Residues in contact with VAL 53 (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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11D PHE* 4.2 12.8 - - + -
41D THR 3.7 3.8 - - - -
42D VAL* 4.2 5.6 - - + -
52D THR* 1.3 80.5 - - - +
54D ASP* 1.4 65.6 + - - +
55D VAL* 4.3 10.8 - - + -
89D TYR* 4.4 7.4 - - + -
90D LYS* 3.3 5.1 - - - +
91D GLY 2.8 32.7 + - - +
93D ILE* 4.0 14.8 - - + -
103D VAL* 4.1 20.0 - - + -
201D OTP 3.8 47.1 - - + -
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Residues in contact with ASP 54 (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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11D PHE* 4.0 0.5 - - - -
40D GLY* 3.2 4.8 - - - -
41D THR* 2.9 45.2 + - - +
53D VAL* 1.4 73.8 - - - +
55D VAL* 1.3 68.4 + - - +
56D THR* 4.6 4.9 + - - -
88D ASN* 5.7 0.9 - - - +
89D TYR 3.5 3.5 - - - +
90D LYS* 3.5 36.7 + - + +
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Residues in contact with VAL 55 (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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11D PHE* 4.1 14.6 - - + -
16D THR* 5.2 0.2 - - + -
38D SER* 4.4 6.7 - - - -
39D SER 3.4 15.3 - - - +
40D GLY* 4.4 0.2 - - - -
53D VAL* 4.3 3.4 - - + -
54D ASP* 1.3 77.6 + - - +
56D THR* 1.3 75.4 + - - +
57D THR* 4.5 2.9 - - - +
88D ASN* 3.4 2.8 - - - +
89D TYR* 2.8 62.8 + - + +
201D OTP 3.6 45.7 - - + +
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Residues in contact with THR 56 (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 SER* 3.2 4.7 - - - -
39D SER* 2.9 40.2 + - - -
54D ASP* 4.6 5.5 + - - -
55D VAL* 1.3 76.6 + - - +
57D THR* 1.3 64.2 + - - +
58D ASP* 5.0 0.8 - - - +
86D GLN* 3.4 35.7 - - + +
87D ALA 3.4 5.8 - - - +
88D ASN* 3.0 29.6 + - - +
201D OTP 5.3 0.2 - - - -
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Residues in contact with THR 57 (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 PRO* 3.9 10.5 - - + +
35D PHE* 3.3 42.8 - - + -
37D LYS 3.4 5.4 - - - +
38D SER* 2.9 22.1 + - - +
55D VAL* 4.5 0.5 - - - +
56D THR* 1.3 72.2 - - - +
58D ASP* 1.3 63.1 + - - +
59D ILE* 3.5 0.6 + - + -
86D GLN* 3.1 9.6 - - - +
87D ALA* 2.9 34.4 + - + +
201D OTP 3.4 31.1 - - + +
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Residues in contact with ASP 58 (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 PHE* 3.6 5.9 - - - -
37D LYS* 2.9 52.7 + - + +
56D THR* 5.0 1.4 - - - +
57D THR* 1.3 73.7 - - - +
59D ILE* 1.3 62.0 + - - +
60D ALA* 4.5 4.7 - - + +
61D SER* 2.7 34.1 + - - +
85D PRO 3.8 2.5 - - - +
86D GLN* 2.5 35.6 + - - +
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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