Contacts of the strand formed by residues 186 - 191 (chain 1) in PDB entry 1W58
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 THR 186 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1541 THR 3.5 0.8 + - - -
1551 VAL* 3.4 26.5 - - + +
1561 ALA 3.2 21.8 + - - -
1841 THR* 3.4 5.4 + - - -
1851 ASP* 1.3 76.7 - - + +
1871 LEU* 1.3 60.2 + - - +
1881 VAL* 4.1 8.7 - - - +
2431 MET* 3.2 45.1 - - + +
2461 GLY* 3.7 16.9 - - - -
2471 GLY 3.6 4.7 - - - -
2491 ALA* 4.1 17.5 - - - +
3361 VAL* 5.6 0.7 - - - +
3381 THR* 4.6 4.6 - - + +
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Residues in contact with LEU 187 (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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1561 ALA* 3.8 13.2 - - + -
1581 VAL* 4.2 9.4 - - + -
1771 LEU* 3.7 47.8 - - + +
1801 LEU* 3.7 26.0 - - + -
1811 LYS* 3.8 26.0 - - + +
1841 THR* 3.5 14.8 - - + +
1861 THR* 1.3 71.3 + - - +
1881 VAL* 1.3 60.0 + - - +
2471 GLY 2.8 14.4 + - - +
2481 LEU* 3.3 15.3 - - + +
2491 ALA 2.8 28.6 + - - -
3461 PHE* 5.9 0.4 - - + -
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Residues in contact with VAL 188 (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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1551 VAL* 4.4 11.0 - - + -
1561 ALA 2.8 18.8 + - - +
1571 VAL* 3.4 22.6 - - + +
1581 VAL* 3.0 27.7 + - - +
1861 THR* 4.1 9.0 - - - +
1871 LEU* 1.3 72.8 - - - +
1891 VAL* 1.3 60.3 + - - +
1901 ILE* 4.6 4.0 - - + -
2181 ALA* 5.7 0.9 - - + -
2221 LEU* 4.6 7.9 - - + -
2491 ALA* 3.5 21.5 - - + +
2511 ILE* 3.5 32.1 - - + -
3361 VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 189 (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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1581 VAL* 3.5 11.0 - - + +
1601 LEU* 4.3 18.2 - - + -
1771 LEU* 3.2 39.3 - - + -
1871 LEU 4.3 0.4 - - - +
1881 VAL* 1.3 71.9 - - - +
1901 ILE* 1.3 65.6 + - - +
1911 PRO* 3.8 7.3 - - - +
2481 LEU* 3.0 34.8 - - + -
2491 ALA 3.1 9.7 + - - +
2501 MET* 4.2 18.2 - - + +
2511 ILE* 4.8 1.4 + - - +
2741 LEU 5.1 0.3 - - - +
3511 LEU* 4.2 18.8 - - + -
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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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1571 VAL* 4.7 9.0 - - + -
1581 VAL 2.9 15.9 + - - +
1591 THR* 3.1 22.1 - - + -
1601 LEU* 3.0 20.5 + - - -
1881 VAL* 4.6 4.7 - - + -
1891 VAL* 1.3 74.3 - - - +
1911 PRO* 1.3 67.8 - - + +
1921 ASN* 3.2 8.3 + - - +
1951 LEU* 5.0 2.5 - - + -
2141 VAL* 3.9 25.8 - - + -
2151 LEU* 5.1 3.8 - - + -
2181 ALA* 4.4 16.6 - - + -
2511 ILE* 3.3 37.2 - - + -
2741 LEU* 4.3 16.4 - - + -
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Residues in contact with PRO 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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1601 LEU* 4.0 21.5 - - + -
1891 VAL 3.8 7.4 - - - +
1901 ILE* 1.3 84.6 - - + +
1921 ASN* 1.3 64.3 + - - +
1931 GLU* 2.9 7.8 + - + +
1941 LYS* 3.0 35.6 + - + +
1951 LEU* 4.2 3.3 + - - +
2501 MET* 5.3 5.6 - - - -
2741 LEU* 4.3 19.2 - - + +
2761 ASP* 5.6 3.8 - - + -
3511 LEU* 4.4 21.3 - - + -
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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