Contacts of the strand formed by residues 44 - 49 (chain B) in PDB entry 1IZO
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 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 3.4 15.2 - - - +
41B LEU 2.9 33.4 + - - +
42B LEU 4.0 6.5 - - - +
43B GLY* 1.3 84.5 - - - +
45B ASN* 1.3 63.4 + - - +
46B PHE* 3.4 7.8 + - + -
68B ASN 6.0 2.0 - - - -
296B LEU* 6.5 0.9 - - - -
313B SER* 3.9 22.2 - - - +
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Residues in contact with ASN 45 (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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39B ALA 4.0 4.2 - - - -
40B ARG* 3.3 27.6 + - - +
44B LYS* 1.3 72.6 - - - +
46B PHE* 1.3 59.7 + - - +
312B THR* 3.6 12.1 - - + +
313B SER* 3.1 27.0 + - - +
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Residues in contact with PHE 46 (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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37B PHE 3.8 0.3 - - - +
38B GLN* 3.4 5.9 - - - +
39B ALA* 2.8 42.2 + - - +
41B LEU* 3.2 47.1 - - + -
42B LEU* 3.9 22.9 - - + -
44B LYS* 3.4 10.5 + - + -
45B ASN* 1.3 72.9 - - - +
47B ILE* 1.3 63.1 + - - +
48B CYS* 4.0 5.4 - - - -
69B ALA 4.4 12.8 - - - -
70B LEU* 4.8 4.3 - - + -
71B PRO* 6.0 0.2 - - + -
294B GLY* 5.3 1.1 - - - -
295B ALA 5.0 1.1 - - - -
312B THR* 4.9 0.7 - - - -
313B SER* 3.0 40.8 - - - -
314B VAL* 3.6 15.0 - - - -
315B LEU* 3.5 33.9 - - + -
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Residues in contact with ILE 47 (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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36B LEU* 3.8 30.3 - - + -
37B PHE 3.5 6.7 - - - +
38B GLN* 4.5 19.1 - - + -
46B PHE* 1.3 76.1 - - - +
48B CYS* 1.3 61.4 + - - +
49B MET* 3.7 3.1 + - + -
306B CYS* 4.1 23.6 - - - -
307B GLU 4.7 6.7 - - - +
308B PHE* 3.9 27.1 - - + -
312B THR* 4.4 16.4 - - + -
313B SER 2.7 8.1 + - - -
314B VAL* 3.1 15.0 - - + +
315B LEU 3.0 19.9 + - - -
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Residues in contact with CYS 48 (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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24B PHE* 5.0 0.9 - - - -
25B ILE* 4.1 17.5 - - + -
29B THR* 5.2 0.3 - - - +
35B ASP 3.8 0.2 - - - +
36B LEU* 3.3 5.4 - - - -
37B PHE* 3.1 67.5 + - + -
39B ALA* 5.5 2.0 - - - -
41B LEU* 4.0 26.7 - - - -
46B PHE* 4.7 7.2 - - - -
47B ILE* 1.3 73.8 - - - +
49B MET* 1.3 59.9 + - - +
315B LEU* 3.5 22.9 - - - +
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Residues in contact with MET 49 (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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25B ILE* 4.8 2.0 - - - -
35B ASP 3.2 5.4 - - - +
36B LEU* 3.3 27.1 - - + -
47B ILE* 3.9 11.7 - - + +
48B CYS* 1.3 75.0 - - - +
50B THR* 1.3 61.7 + - - +
54B ALA* 3.0 39.9 - - + +
57B VAL* 5.0 2.7 - - + -
58B PHE* 3.5 37.2 - - + +
64B PHE* 4.6 7.2 - - + -
303B TRP* 4.7 4.3 - - - -
308B PHE* 4.0 19.3 - - - -
314B VAL* 4.7 2.7 - - + -
315B LEU 3.0 9.4 + - - +
316B LEU* 3.7 6.3 - - + -
317B ASP* 2.9 30.4 + - - +
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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