Contacts of the strand formed by residues 153 - 160 (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 LEU 153 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231 ASP 3.0 12.5 + - - +
1241 MET* 3.3 45.5 - - + +
1251 VAL 2.8 31.0 + - - +
1511 GLY 4.0 0.8 + - - -
1521 ALA* 1.3 69.9 - - - +
1541 THR* 1.3 55.3 + - - +
1551 VAL* 4.0 3.1 - - + -
1851 ASP* 3.3 31.9 - - + +
2361 PHE* 4.6 7.9 - - + -
2391 VAL* 4.3 3.1 - - + -
2401 LYS* 4.1 34.1 - - + +
2431 MET* 3.9 32.8 - - + -
2441 ASN* 4.2 7.6 - - - +
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Residues in contact with THR 154 (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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1251 VAL 3.6 3.1 - - - +
1271 ILE* 4.6 9.0 - - + -
1441 ALA* 3.8 21.8 - - + +
1471 SER* 2.9 28.5 + - - +
1481 LYS* 3.5 18.8 + - - +
1521 ALA 3.1 10.2 + - - -
1531 LEU* 1.3 69.3 - - - +
1551 VAL* 1.3 62.3 + - - +
1831 HIS 3.8 19.3 - - - +
1841 THR* 3.5 5.8 + - - +
1851 ASP* 2.8 43.4 + - - +
1861 THR 3.5 1.4 + - - -
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Residues in contact with VAL 155 (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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1241 MET* 3.8 25.1 - - + -
1251 VAL 2.9 11.7 + - - +
1261 PHE* 3.0 33.4 - - + +
1271 ILE* 2.7 33.3 + - - +
1531 LEU* 4.6 7.9 - - + -
1541 THR* 1.3 77.9 - - - +
1561 ALA* 1.3 65.8 - - - +
1571 VAL* 4.5 0.9 - - + -
1841 THR* 4.5 0.4 - - - -
1861 THR* 3.4 34.8 - - + +
1881 VAL* 4.4 11.9 - - + -
2221 LEU* 4.9 3.8 - - + -
2431 MET* 4.0 6.3 - - - -
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Residues in contact with ALA 156 (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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1271 ILE* 3.2 17.9 - - + +
1551 VAL* 1.3 75.1 - - - +
1571 VAL* 1.3 60.4 + - - +
1581 VAL* 4.1 2.5 - - + -
1801 LEU* 4.2 19.5 - - + -
1841 THR* 3.9 12.1 + - - +
1861 THR 3.2 4.6 + - - -
1871 LEU* 3.8 21.8 - - + -
1881 VAL* 2.8 36.9 + - - +
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Residues in contact with VAL 157 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 PHE* 4.1 29.6 - - + -
1271 ILE 3.0 8.2 + - - +
1281 THR* 2.7 35.5 + - - +
1551 VAL* 4.5 0.7 - - + -
1561 ALA* 1.3 77.3 - - - +
1581 VAL* 1.3 60.9 + - - +
1881 VAL* 3.4 25.4 - - + +
1901 ILE* 4.7 5.8 - - + -
2151 LEU* 4.1 9.7 - - + +
2181 ALA* 4.1 19.7 - - + -
2191 VAL* 3.8 28.3 - - + -
2221 LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 158 (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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1271 ILE 4.2 8.7 - - - +
1291 CYS* 3.3 33.7 - - - +
1311 LEU* 3.8 26.0 - - + -
1401 ALA* 5.6 1.6 - - + -
1561 ALA* 4.5 1.1 - - + -
1571 VAL* 1.3 81.9 - - - +
1591 THR* 1.3 64.4 + - - +
1771 LEU* 4.2 0.2 - - + -
1801 LEU* 4.1 16.8 - - + -
1871 LEU* 4.2 12.6 - - + -
1881 VAL 3.0 11.0 + - - +
1891 VAL* 3.5 15.5 - - + -
1901 ILE* 2.9 27.5 + - - +
2151 LEU* 5.0 1.3 - - - -
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Residues in contact with THR 159 (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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1291 CYS 3.4 4.4 + - - -
1301 GLY* 3.4 18.4 - - - -
1311 LEU* 3.0 32.1 + - - +
1581 VAL* 1.3 78.6 - - - +
1601 LEU* 1.3 64.6 + - - +
1901 ILE* 3.1 22.7 - - + +
1921 ASN* 3.5 34.0 + - - +
2111 ALA* 5.4 2.7 - - + +
2141 VAL* 6.3 0.4 - - + -
2151 LEU* 4.0 29.8 - - + +
13621 G2P 4.9 7.2 + - - +
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Residues in contact with LEU 160 (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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1311 LEU* 4.2 18.4 - - + -
1591 THR* 1.3 82.4 - - - +
1611 PRO* 1.4 66.5 - - + +
1701 MET* 3.4 24.9 - - + -
1731 ALA* 4.3 8.1 - - + +
1741 MET* 4.1 14.1 - - - -
1771 LEU* 4.6 4.3 - - + -
1891 VAL* 4.3 15.5 - - + -
1901 ILE 3.0 5.7 + - - +
1911 PRO* 4.0 20.6 - - + -
1921 ASN* 3.2 24.1 + - - +
3501 GLY* 5.3 0.2 - - - -
3511 LEU* 3.6 40.6 - - + +
13621 G2P 4.8 0.2 - - - -
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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
------------------------------------------------------------
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