Contacts of the helix formed by residues 145 - 156 (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 ASN 145 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1432 PRO* 3.5 1.7 - - - +
1442 ARG* 1.3 82.7 + - - +
1462 ALA* 1.3 58.6 + - - +
1472 GLU* 2.9 13.8 + - - +
1482 GLU* 2.8 38.2 + - - +
1492 ASN* 3.0 23.2 + - - +
1832 TYR* 3.7 20.2 - - + -
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Residues in contact with ALA 146 (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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1452 ASN* 1.3 72.1 - - - +
1472 GLU* 1.3 65.2 + - - +
1492 ASN* 3.6 1.9 - - - +
1502 ARG* 3.0 45.7 + - + +
1832 TYR* 3.5 27.1 - - + +
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Residues in contact with GLU 147 (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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1452 ASN* 2.9 12.8 + - - +
1462 ALA* 1.3 77.8 - - - +
1482 GLU* 1.3 61.5 + - + +
1502 ARG* 3.2 32.6 + - - +
1512 ALA* 3.0 26.7 + - + +
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Residues in contact with GLU 148 (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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1152 LYS* 2.8 46.9 + - + +
1172 PHE* 4.2 13.0 - - + -
1422 THR 3.7 0.9 - - - +
1432 PRO* 3.6 12.4 - - + +
1442 ARG* 2.8 33.7 + - - +
1452 ASN* 2.8 27.0 + - - +
1472 GLU* 1.3 78.1 - - + +
1492 ASN* 1.3 62.8 + - - +
1512 ALA* 3.2 9.2 + - - +
1522 ILE* 3.0 29.1 + - - +
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Residues in contact with ASN 149 (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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1432 PRO* 3.5 17.7 - - + +
1452 ASN 3.0 10.5 + - - +
1462 ALA 3.6 8.7 - - - +
1472 GLU 3.2 0.4 - - - -
1482 GLU* 1.3 77.2 - - - +
1502 ARG* 1.3 57.0 + - + +
1522 ILE* 3.3 5.7 + - - +
1532 GLN* 3.0 32.1 + - - +
1832 TYR* 3.6 19.5 + - - +
1852 ASN* 3.4 9.1 - - - +
2032 LEU* 3.4 10.2 - - - +
2072 GLY* 3.0 26.5 + - - -
2092 TRP* 2.8 28.3 + - - -
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Residues in contact with ARG 150 (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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1462 ALA* 3.0 41.2 + - - +
1472 GLU* 3.2 39.5 + - - +
1492 ASN* 1.3 76.8 - - + +
1512 ALA* 1.3 59.3 + - - +
1532 GLN* 3.2 21.8 + - - +
1542 ASN* 3.0 37.5 + - - +
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Residues in contact with ALA 151 (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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1172 PHE* 4.0 22.7 - - + -
1472 GLU* 3.0 14.5 + - + +
1482 GLU* 3.2 10.7 + - - +
1502 ARG* 1.3 75.8 - - - +
1522 ILE* 1.3 63.1 + - - +
1542 ASN* 3.4 25.6 + - - +
1552 VAL* 3.6 13.3 + - - +
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Residues in contact with ILE 152 (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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1172 PHE* 3.9 28.0 - - + -
1412 ALA* 3.6 21.1 - - + -
1432 PRO* 3.7 33.0 - - + -
1482 GLU 3.0 14.6 + - - +
1492 ASN* 3.6 7.2 - - - +
1512 ALA* 1.3 73.6 - - - +
1532 GLN* 1.3 66.9 + - - +
1552 VAL* 3.2 8.7 + - - +
1562 ALA* 3.0 21.0 + - - +
1622 LEU* 4.1 14.1 - - + -
2032 LEU* 4.3 13.5 - - + -
2212 VAL* 3.9 27.6 - - + -
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Residues in contact with GLN 153 (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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1492 ASN* 3.0 18.1 + - - +
1502 ARG* 3.2 32.5 - - - +
1522 ILE* 1.3 77.6 - - - +
1542 ASN* 1.3 64.7 + - - +
1552 VAL 3.2 1.0 + - - -
1562 ALA* 3.3 19.9 - - - +
2032 LEU* 3.8 14.4 - - + -
2042 LEU 5.1 0.2 - - - +
2052 THR 4.3 6.3 + - - +
2062 ASN* 3.5 9.9 + - - +
2072 GLY* 3.4 41.4 - - - +
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Residues in contact with ASN 154 (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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1502 ARG* 3.0 24.0 + - - +
1512 ALA* 3.5 17.8 - - - +
1522 ILE 3.2 0.4 - - - -
1532 GLN* 1.3 79.2 - - - +
1552 VAL* 1.3 62.5 + - + +
1562 ALA 5.1 0.3 - - - +
1572 LYS* 5.4 5.5 + - - +
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Residues in contact with VAL 155 (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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1371 GLN* 4.7 4.6 + - - +
1172 PHE* 3.7 27.1 - - + +
1182 MET* 5.1 0.4 - - - -
1192 SER* 3.3 23.3 - - - +
1512 ALA 3.6 13.7 + - - +
1522 ILE* 3.2 15.3 - - - +
1542 ASN* 1.3 82.2 - - + +
1562 ALA* 1.3 62.5 + - - +
1572 LYS* 3.4 13.1 + - - +
2212 VAL* 4.0 26.7 - - + -
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Residues in contact with ALA 156 (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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1192 SER* 4.2 7.9 - - - -
1522 ILE 3.0 17.5 + - - +
1532 GLN* 3.3 13.1 - - - +
1542 ASN 5.2 0.4 - - - -
1552 VAL* 1.3 75.6 - - - +
1572 LYS* 1.3 59.6 + - - +
1582 ASP 3.2 18.1 + - - +
1602 ALA* 4.1 7.2 - - + -
2032 LEU* 4.7 12.3 - - + -
2052 THR* 5.7 2.3 - - - +
2192 LEU* 5.4 0.4 - - + -
2212 VAL* 3.9 19.1 - - + -
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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