Contacts of the strand formed by residues 189 - 195 (chain 1) in PDB entry 3EXG
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 CYS 189 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1451 GLY 4.1 2.0 - - - -
1461 ALA* 3.9 15.3 - - - -
1491 ALA* 3.6 12.8 - - + -
1611 CYS 3.5 4.3 - - - -
1631 THR* 3.4 25.1 - - - -
1821 ALA* 5.0 0.7 - - + -
1871 LEU* 2.6 18.6 + - + +
1881 PRO* 1.3 71.4 - - - +
1901 ILE* 1.3 62.6 + - - +
1911 PHE* 3.4 43.1 + - + -
2441 CYS* 3.9 3.4 - - - -
2501 PRO* 3.4 6.3 - - + +
2511 ILE 3.3 20.6 + - - -
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Residues in contact with ILE 190 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791 ILE* 5.5 0.7 - - + -
1601 VAL* 4.8 4.9 - - + -
1611 CYS 3.0 11.0 + - - +
1621 LEU* 3.4 28.1 - - + -
1631 THR 2.9 25.3 + - - -
1891 CYS* 1.3 69.7 - - - +
1911 PHE* 1.3 62.5 + - - +
1921 ILE* 3.4 21.9 + - + +
2371 THR* 4.7 3.6 - - + +
2401 ALA* 3.9 11.7 - - + -
2411 ALA* 3.7 35.9 - - + +
2441 CYS* 4.0 16.8 - - + -
2511 ILE* 3.6 20.0 - - + +
2531 MET* 4.5 9.6 - - + -
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Residues in contact with PHE 191 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1421 VAL* 3.6 38.6 - - + -
1461 ALA* 4.4 2.7 - - + -
1631 THR* 3.7 9.2 - - + -
1651 TYR* 4.5 7.0 - + + -
1781 ALA* 4.0 17.0 - - + -
1791 TYR* 4.0 26.5 - + + -
1821 ALA* 3.7 30.1 - - + -
1891 CYS* 3.4 32.5 + - - -
1901 ILE* 1.3 72.4 - - - +
1921 ILE* 1.3 59.1 + - - +
1931 CYS 4.2 0.2 - - - -
2201 ILE* 4.5 1.8 - - + -
2501 PRO* 4.2 9.9 - - + -
2511 ILE 2.9 13.9 + - - +
2521 LEU* 3.3 21.3 - - + +
2531 MET* 3.0 24.4 + - - +
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Residues in contact with ILE 192 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751 LEU* 3.7 26.0 - - + -
1621 LEU* 3.8 27.1 - - + -
1631 THR 3.0 8.9 + - - +
1641 LEU* 3.0 20.4 - - + +
1651 TYR* 2.9 28.3 + - - -
1901 ILE* 3.7 19.5 - - + +
1911 PHE* 1.3 75.6 - - - +
1931 CYS* 1.3 66.1 + - - +
1941 GLU 3.6 1.6 + - - +
2531 MET* 3.3 27.1 - - + +
2551 LEU* 4.1 26.9 - - + -
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Residues in contact with CYS 193 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651 TYR* 3.3 35.8 + - + +
1671 ASP* 4.0 20.2 - - - -
1701 ALA* 4.9 0.2 - - - -
1911 PHE 4.1 1.0 + - - -
1921 ILE* 1.3 72.2 - - - +
1941 GLU* 1.3 60.9 + - - +
1951 ASN* 2.8 18.2 + - - -
2131 TYR* 3.8 38.1 - - + -
2521 LEU* 5.6 4.0 - - + +
2531 MET 2.9 11.8 + - - +
2541 GLU* 3.5 4.1 - - + -
2551 LEU 3.1 20.3 + - - -
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Residues in contact with GLU 194 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651 CYS* 5.9 1.7 - - - +
681 GLN* 3.2 24.3 - - - +
711 CYS* 4.7 14.5 - - + +
871 THR* 4.3 7.3 + - - -
901 ARG* 5.3 11.5 - - - +
941 PHE* 3.8 16.9 - - - -
1641 LEU* 3.6 35.2 - - + +
1651 TYR* 2.8 17.7 + - - +
1661 GLY* 3.9 3.9 - - - -
1671 ASP* 3.4 16.8 + - - +
1921 ILE* 3.6 3.1 + - + -
1931 CYS* 1.3 70.7 - - - +
1951 ASN* 1.3 61.5 + - - +
1961 ASN* 3.3 8.4 + - - +
2551 LEU* 3.8 12.6 - - + -
2571 THR* 4.4 8.5 - - + -
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Residues in contact with ASN 195 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1671 ASP* 3.6 12.4 - - - +
1931 CYS* 2.8 9.2 + - - +
1941 GLU* 1.3 69.4 - - - +
1961 ASN* 1.3 60.6 + - - +
1971 ARG* 2.9 28.7 + - - +
2111 THR* 5.0 1.8 + - - -
2131 TYR* 3.5 35.9 + - + -
2541 GLU* 3.1 29.8 + - + -
2551 LEU 3.1 5.3 + - - +
2561 GLN* 3.3 18.3 - - - +
2571 THR 2.8 22.7 + - - -
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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