Contacts of the strand formed by residues 43 - 50 (chain C) in PDB entry 1ZDJ
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 LYS 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C GLU* 3.8 14.6 + - + -
32C TRP 3.3 5.8 - - - +
33C ILE* 3.6 16.6 - - + -
38C ARG* 4.0 25.5 - - - +
42C TYR* 1.3 77.2 - - - +
44C VAL* 1.3 66.2 + - - +
45C THR* 3.6 27.6 - - + +
61C LYS* 5.6 1.3 - - - +
62C VAL* 3.2 5.9 - - - +
63C GLU* 3.0 59.4 + - + +
83C ARG* 4.9 0.9 - - - +
12S A 2.7 31.1 + - - -
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.4 11.4 - - + -
9C LEU* 4.1 30.7 - - + -
20C VAL* 4.2 15.5 - - + -
31C GLU* 3.3 2.8 - - - -
32C TRP* 2.8 52.9 + - + +
43C LYS* 1.3 78.5 - - - +
45C THR* 1.3 71.5 + - - +
46C CYS* 5.6 0.9 - - + -
60C ILE* 4.7 8.3 - - + -
61C LYS 3.2 9.6 - - - +
62C VAL* 4.2 15.9 - - + -
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.2 5.8 - - + -
30C ALA 2.9 13.0 - - - +
31C GLU* 4.1 12.8 - - + +
32C TRP* 4.7 0.4 - - - -
43C LYS* 3.6 30.1 - - + -
44C VAL* 1.3 81.1 - - - +
46C CYS* 1.3 63.5 + - - +
60C ILE* 3.4 7.1 - - - +
61C LYS* 3.0 37.8 + - + +
12S A 2.6 44.5 + - + +
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Residues in contact with CYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 5.5 0.2 - - - -
28C GLY 4.0 0.5 - - - +
29C VAL* 3.6 0.7 - - - -
30C ALA* 2.8 32.8 + - + +
32C TRP* 4.1 20.4 - - + -
44C VAL* 5.6 1.1 - - + -
45C THR* 1.3 77.9 - - - +
47C SER* 1.3 68.6 + - - +
48C VAL* 5.2 3.1 - - - -
58C TYR* 4.6 11.0 - - - -
59C THR 3.3 7.2 - - - -
60C ILE* 3.6 27.6 - - + -
12S A 3.8 2.0 - - - -
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY 3.0 26.0 - - - -
29C VAL* 4.0 8.7 - - - +
46C CYS* 1.3 76.6 - - - +
48C VAL* 1.3 66.5 + - - +
49C ARG* 5.1 4.2 + - - +
57C LYS 3.9 0.8 - - - +
58C TYR* 3.4 4.5 - - - +
59C THR* 3.0 33.9 + - - -
12S A 2.9 29.8 + - - -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 5.1 18.7 + - - +
28C GLY 4.5 2.0 + - - +
46C CYS* 5.2 3.8 - - - -
47C SER* 1.3 81.5 - - - +
49C ARG* 1.3 71.4 + - - +
56C ARG* 3.5 30.1 - - + +
57C LYS 3.5 10.1 - - - +
58C TYR* 3.6 37.0 - - + +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C SER* 5.1 5.8 + - - +
48C VAL* 1.3 78.9 - - - +
50C GLN* 1.3 62.2 + - - +
51C SER* 3.3 13.4 + - - +
56C ARG* 3.2 5.5 - - - +
57C LYS* 2.6 73.9 + - + +
59C THR* 3.4 23.2 + - - -
89C GLU* 4.8 3.0 + - - -
12S A 6.1 0.8 - - - -
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 5.7 1.4 - - - +
49C ARG* 1.3 76.1 - - - +
51C SER* 1.3 64.2 + - - +
52C SER* 3.0 26.7 + - - +
53C ALA* 3.3 17.1 + - - +
55C ASN 3.3 12.5 + - - -
56C ARG* 3.4 20.3 - - + +
94C ILE* 3.5 19.9 - - - +
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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