Contacts of the strand formed by residues 18 - 24 (chain B) in PDB entry 1ZJD
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 ILE 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.3 2.0 - - - +
39A LEU* 3.9 14.8 - - + -
57A HIS 3.5 13.5 - - - +
58A CYS 4.2 5.4 - - - +
59A TYR* 3.4 49.4 - - + +
16B ALA* 4.1 9.4 - - + -
17B MET* 1.3 75.7 - - - +
19B SER* 1.3 65.8 + - - +
20B ARG* 3.3 20.0 + - + +
34B PHE* 3.5 4.9 - - - -
35B TYR* 2.8 47.1 + - + +
37B GLY* 3.5 19.1 - - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.1 53.6 + - - +
17B MET 3.8 0.6 + - - -
18B ILE* 1.3 73.4 - - - +
20B ARG* 1.3 66.5 + - - +
21B TRP* 5.1 2.6 + - - -
33B PHE 4.1 3.8 - - - -
34B PHE* 3.5 15.3 - - - -
46B ASP* 4.5 10.6 - - - +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.4 40.9 - - - +
18B ILE* 3.6 17.3 - - + +
19B SER* 1.3 79.7 + - - +
21B TRP* 1.3 70.9 + - - +
32B PRO* 3.2 7.8 - - - +
33B PHE* 3.0 47.4 + - + +
35B TYR* 3.8 14.8 - - + -
44B ASN* 2.6 56.8 + - - +
45B PHE 3.4 8.1 + - - +
46B ASP* 2.9 46.9 + - - +
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER* 5.1 2.8 + - - -
20B ARG* 1.3 84.2 + - - +
22B TYR* 1.3 61.6 + - - +
30B CYS* 4.0 4.3 - - + -
31B ALA* 3.3 29.6 - - - -
32B PRO* 3.7 31.0 - - + -
33B PHE* 3.6 2.5 - - - -
44B ASN* 3.4 5.5 - - - -
45B PHE* 2.6 44.6 + - - +
46B ASP 3.4 23.7 + - - -
47B THR* 3.6 16.7 - - - +
48B GLU* 3.6 55.8 - - + +
51B CYS* 4.1 9.0 - - + -
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU 4.7 1.3 - - - -
8B GLN* 5.7 1.3 - - - -
9B ALA* 3.7 29.4 - - + -
21B TRP* 1.3 73.4 - - - +
23B PHE* 1.3 69.4 + - - +
24B ASP* 2.8 42.1 + - + +
30B CYS* 3.2 1.2 - - - -
31B ALA* 2.8 59.3 + - + +
32B PRO 3.6 17.3 - - - -
33B PHE* 3.5 21.1 - + + -
43B ASN* 3.3 33.0 - - + +
51B CYS* 3.6 6.5 - - - -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 3.3 25.6 - - + +
6B SER* 5.4 0.3 - - - -
7B GLU 4.6 1.0 - - - +
22B TYR* 1.3 77.5 - - - +
24B ASP* 1.3 65.6 + - - +
25B VAL* 3.7 15.6 + - + +
28B GLY* 3.4 23.1 - - - -
29B LYS* 3.3 32.5 - - - -
30B CYS* 3.8 8.7 - - - +
43B ASN* 2.7 31.3 + - - +
51B CYS* 3.7 5.5 - - - -
55B CYS* 3.5 53.2 - - + -
56B GLY* 4.5 5.8 - - - -
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 2.8 35.6 + - + +
23B PHE* 1.3 74.1 - - - +
25B VAL* 1.3 61.2 + - - +
26B THR* 3.3 12.7 + - - -
27B GLU* 2.8 43.8 + - + +
28B GLY* 2.8 24.6 + - - -
29B LYS 3.0 21.9 + - - +
31B ALA* 4.9 5.2 - - + -
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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