Contacts of the strand formed by residues 155 - 160 (chain 1) in PDB entry 1KZB
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 ALA 155 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511 ALA* 4.1 5.8 - - + -
1531 ASP 3.2 8.0 + - - +
1541 VAL* 1.3 77.0 - - - +
1561 PHE* 1.3 63.5 + - - +
1571 LEU* 6.1 0.2 - - + -
1971 VAL* 3.1 5.3 - - - -
1981 LEU* 2.7 42.4 + - + +
2131 PHE* 4.4 0.4 - - - -
2141 LEU* 3.3 23.6 - - + +
2161 VAL* 3.8 28.3 - - + -
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Residues in contact with PHE 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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1191 MET 3.2 27.1 - - - -
1211 LEU* 3.5 45.1 - - + -
1241 ALA* 4.4 6.3 - - + -
1351 VAL* 3.8 14.6 - - + +
1551 ALA* 1.3 76.2 - - - +
1571 LEU* 1.3 64.2 + - - +
1951 CYS* 3.9 23.8 - - + -
1961 VAL 3.4 15.3 - - - -
1971 VAL* 3.7 4.5 - - + +
2071 VAL* 4.0 7.9 - - + -
2081 PRO 4.4 1.8 - - - -
2091 CYS 4.2 2.7 - - - -
2111 ASP 3.3 20.2 - - - -
2131 PHE* 3.5 24.4 - + + +
2141 LEU 2.9 22.7 + - - +
2151 VAL* 4.6 5.2 - - + -
2161 VAL* 3.9 15.1 + - - +
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Residues in contact with LEU 157 (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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1211 LEU* 4.4 8.0 - - - +
1351 VAL* 3.5 6.5 - - - +
1361 ALA* 3.2 15.3 - - + +
1381 PRO* 4.0 17.0 - - + -
1471 ILE* 4.1 19.3 - - + -
1551 ALA 4.6 0.7 - - - +
1561 PHE* 1.3 84.4 - - - +
1581 GLY* 1.3 58.2 + - - +
1591 ILE* 2.9 24.2 + - + +
1961 VAL* 2.9 25.6 + - + +
1981 LEU* 4.0 30.3 - - + +
2041 TRP* 3.7 45.3 - - + +
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Residues in contact with GLY 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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1211 LEU* 5.7 0.2 - - - -
1351 VAL* 3.4 21.5 - - - +
1361 ALA 2.7 14.8 + - - -
1371 THR* 3.1 20.2 + - - -
1571 LEU* 1.3 67.8 - - - +
1591 ILE* 1.3 61.0 + - - +
1701 ASP* 3.1 19.9 - - - -
1711 LEU* 3.4 21.5 + - - -
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Residues in contact with ILE 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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1211 LEU* 5.9 0.2 - - - +
1371 THR* 4.0 18.8 - - + -
1381 PRO* 4.5 3.1 - - + +
1571 LEU* 2.9 20.8 + - + +
1581 GLY* 1.3 82.6 - - - +
1601 THR* 1.3 74.4 + - - +
1681 PHE* 3.8 31.4 - - + -
1691 GLU 3.4 11.4 - - - +
1701 ASP 5.0 0.2 - - - -
1761 VAL* 4.1 18.2 - - + -
1951 CYS* 4.0 0.5 - - - +
1961 VAL* 3.5 32.6 + - + +
2041 TRP* 3.5 42.0 - - + -
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Residues in contact with THR 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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1211 LEU* 4.1 8.7 - - + -
1591 ILE* 1.3 83.7 - - - +
1611 ASP* 1.3 61.7 + - - +
1621 GLN* 3.6 19.1 + - + +
1631 ARG 5.1 0.3 + - - -
1671 VAL 3.6 0.9 - - - +
1681 PHE* 3.5 7.6 - - - -
1691 GLU* 3.0 38.7 + - - +
1701 ASP 5.4 1.0 + - - -
1711 LEU* 4.0 22.2 - - + +
1941 ASN 3.1 15.5 - - - +
1951 CYS* 4.0 17.5 - - - +
2091 CYS* 5.0 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
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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