Contacts of the strand formed by residues 160 - 169 (chain 2) in PDB entry 1KZC
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 160 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1562 ALA* 4.1 7.4 - - + -
1582 ASP 3.2 8.6 + - - +
1592 VAL* 1.3 77.1 - - - +
1612 PHE* 1.3 63.1 + - - +
1622 LEU* 6.2 0.2 - - + -
2022 VAL* 3.1 6.3 - - - -
2032 LEU* 2.6 42.5 + - + +
2182 PHE* 4.4 0.4 - - - -
2192 LEU* 3.2 22.2 - - + +
2212 VAL* 3.9 26.9 - - + -
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Residues in contact with PHE 161 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242 MET 3.2 27.6 - - - -
1252 PRO 4.3 0.2 - - - -
1262 LEU* 3.3 47.6 - - + -
1292 ALA* 4.4 4.9 - - + -
1402 VAL* 3.7 7.8 - - + +
1602 ALA* 1.3 75.4 - - - +
1622 LEU* 1.3 65.6 + - - +
2002 CYS* 3.8 23.6 - - + -
2012 VAL 3.5 14.8 - - - -
2022 VAL* 3.6 16.3 - - + +
2122 VAL* 3.8 4.5 - - + -
2132 PRO 4.3 2.7 - - - -
2142 CYS 4.1 4.5 - - - -
2162 ASP 3.3 19.3 - - - -
2182 PHE* 3.5 14.8 - + + +
2192 LEU 2.8 20.7 + - - +
2202 VAL* 4.5 6.3 - - + -
2212 VAL* 3.7 19.6 + - - +
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Residues in contact with LEU 162 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262 LEU* 4.3 11.1 - - - +
1402 VAL* 3.4 6.9 - - - +
1412 ALA* 3.2 15.7 - - + +
1432 PRO* 4.0 17.3 - - + -
1522 ILE* 4.1 21.3 - - + -
1602 ALA* 4.6 0.7 - - + +
1612 PHE* 1.3 81.9 - - - +
1632 GLY* 1.3 59.8 + - - +
1642 ILE* 3.0 22.4 + - + +
2012 VAL* 2.9 25.7 + - + +
2032 LEU* 4.1 28.3 - - + +
2092 TRP* 3.6 44.6 - - + +
2212 VAL* 5.8 0.2 - - + -
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Residues in contact with GLY 163 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262 LEU* 5.5 0.2 - - - -
1402 VAL* 3.4 14.8 - - - +
1412 ALA 2.7 14.8 + - - -
1422 THR* 3.2 15.0 + - - -
1622 LEU* 1.3 68.4 - - - +
1642 ILE* 1.3 60.4 - - - +
1752 ASP* 3.1 23.4 - - - -
1762 LEU* 3.1 29.2 + - - -
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Residues in contact with ILE 164 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262 LEU* 5.4 0.2 - - - +
1422 THR* 4.0 20.4 - - + -
1432 PRO* 4.6 2.9 - - + +
1622 LEU* 3.0 17.9 + - + +
1632 GLY* 1.3 85.1 - - - +
1652 THR* 1.3 74.0 + - - +
1732 PHE* 3.7 30.7 - - + -
1742 GLU 3.4 12.1 - - - +
1762 LEU* 4.1 0.6 - - - +
1812 VAL* 4.3 14.6 - - + -
2002 CYS* 3.9 0.5 - - - +
2012 VAL* 3.5 34.4 + - + -
2092 TRP* 3.5 41.7 - - + -
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Residues in contact with THR 165 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262 LEU* 4.0 18.6 - - + -
1642 ILE* 1.3 82.5 - - - +
1662 ASP* 1.3 60.9 + - - +
1672 GLN* 3.3 21.6 + - + +
1682 ARG 5.0 0.5 + - - -
1722 VAL 3.7 0.7 - - - +
1732 PHE* 3.4 7.4 - - - -
1742 GLU* 2.9 36.2 + - - +
1752 ASP 5.6 0.7 + - - -
1762 LEU* 3.7 24.2 - - + -
1992 ASN 3.1 16.6 - - - +
2002 CYS* 4.2 3.6 - - - -
2142 CYS* 5.2 0.4 - - - -
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Residues in contact with ASP 166 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652 THR* 1.3 74.0 - - - +
1672 GLN* 1.3 63.8 + - - +
1682 ARG 3.3 2.9 - - - +
1692 THR 3.3 18.6 - - - +
1702 GLU* 3.1 6.2 + - - +
1712 ASN 2.8 23.9 + - - +
1722 VAL 3.3 20.6 - - - +
1732 PHE* 3.5 25.1 - - + -
1742 GLU* 5.8 0.2 - - - -
1982 GLU 3.7 0.2 - - - +
1992 ASN* 3.0 24.6 + - - +
6012 CA 2.5 30.4 - - - -
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Residues in contact with GLN 167 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652 THR* 3.3 19.1 + - - +
1662 ASP* 1.3 77.1 - - - +
1682 ARG* 1.3 67.3 + - - +
1702 GLU 5.4 0.2 + - - -
1992 ASN* 3.3 35.1 + - - +
2142 CYS* 4.4 9.0 - - - -
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Residues in contact with ARG 168 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652 THR* 5.0 0.8 + - - -
1662 ASP* 3.3 1.0 - - - +
1672 GLN* 1.3 82.3 - - - +
1692 THR* 1.3 79.3 + - - +
1722 VAL* 4.0 17.3 - - - +
1742 GLU* 2.7 43.9 + - - +
1802 ARG* 5.8 1.4 - - - +
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Residues in contact with THR 169 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662 ASP 3.3 10.2 - - - +
1682 ARG* 1.3 109.3 + - - +
1702 GLU* 1.3 74.6 + - - +
1722 VAL* 3.1 39.9 + - + +
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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