Contacts of the strand formed by residues 48 - 54 (chain D) in PDB entry 4QZU
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 ASN 48 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASP* 3.5 2.3 - - - +
44D GLN* 3.3 4.3 - - - -
45D ASP* 2.9 53.4 + - + +
46D GLY 3.2 0.2 - - - -
47D ASP* 1.3 78.0 - - - +
49D PHE* 1.3 60.9 + - - +
50D LYS* 5.5 5.4 - - + -
64D PHE 3.9 3.1 - - - -
65D THR* 3.4 24.7 + - - +
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Residues in contact with PHE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 4.0 8.1 - - - -
42D ILE* 3.8 24.2 - - + -
43D ASP 3.5 2.7 - - - -
44D GLN* 3.2 43.5 - - + -
46D GLY 4.1 3.4 - - - -
47D ASP 3.5 12.3 - - - -
48D ASN* 1.3 75.0 - - - +
50D LYS* 1.3 63.8 + - - +
51D THR* 4.1 6.7 - - + -
63D ASP* 3.3 4.4 - - - +
64D PHE* 2.9 69.1 + + + +
66D VAL* 3.6 19.5 - - + -
88D TRP* 4.1 12.1 - + - -
93D LEU* 3.8 22.2 - - + -
108D GLN* 5.1 1.6 - - - -
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Residues in contact with LYS 50 (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 VAL* 3.8 1.4 - - - +
42D ILE* 3.8 0.2 - - - -
43D ASP* 2.8 57.7 + - + +
48D ASN* 5.5 5.4 - - + -
49D PHE* 1.3 77.9 - - - +
51D THR* 1.3 60.3 + - - +
63D ASP* 3.3 25.4 - - + +
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Residues in contact with THR 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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40D LYS* 5.3 5.6 + - - -
41D VAL 3.2 7.2 - - - -
42D ILE* 3.9 30.7 - - + -
49D PHE* 4.2 17.5 - - + -
50D LYS* 1.3 78.7 - - - +
52D LYS* 1.3 61.7 + - - +
53D THR* 4.3 3.1 + - - -
60D TYR 5.3 0.2 - - - -
61D ASP* 2.8 25.6 - - - +
62D VAL* 2.7 50.5 + - - +
63D ASP* 3.4 1.0 + - - -
64D PHE* 4.6 7.1 - - + -
108D GLN* 5.7 2.2 - - - +
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D THR 3.6 1.6 - - - +
40D LYS* 3.3 3.6 - - - +
41D VAL* 2.8 54.5 + - + +
50D LYS 5.9 0.4 - - - -
51D THR* 1.3 74.3 - - - +
53D THR* 1.3 62.5 + - - +
54D THR* 4.1 14.1 - - + +
61D ASP* 3.3 31.4 - - + +
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLN* 3.7 24.9 - - + +
39D THR 3.5 7.4 - - - +
40D LYS* 2.8 37.3 + - + +
51D THR* 5.2 4.0 + - - -
52D LYS* 1.3 75.5 + - - +
54D THR* 1.3 65.2 + - - +
58D ARG 4.3 0.6 - - - +
59D ASN* 3.4 6.9 - - - +
60D TYR* 3.2 46.7 + - + +
62D VAL* 5.7 0.9 - - - +
130D PHE* 5.5 1.1 - - + -
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Residues in contact with THR 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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38D GLN* 3.3 6.1 - - - -
39D THR* 2.8 56.3 + - - +
41D VAL* 5.9 2.1 - - + +
52D LYS* 4.6 14.4 - - + -
53D THR* 1.3 84.0 - - - +
55D SER* 1.3 60.3 + - - +
59D ASN* 3.3 25.4 - - + +
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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