Contacts of the strand formed by residues 219 - 224 (chain 1) 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 LEU 219 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191 SER* 4.3 5.8 - - - +
1201 SER* 3.6 21.5 - - - +
1211 VAL* 3.5 24.9 - - - +
1221 ARG 3.6 15.5 - - - +
1231 ARG* 3.4 20.9 - - + +
1561 ALA 5.2 0.2 - - - -
1571 LYS* 4.3 11.7 - - + +
1581 ASP* 3.6 39.0 - - + +
1591 VAL 3.3 10.3 + - - +
1601 ALA* 3.7 8.5 - - + -
1611 PHE* 2.9 22.5 + - - +
2181 PHE* 1.3 81.0 - - - +
2201 VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 220 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 MET 4.0 0.5 - - - +
1191 SER* 3.4 2.9 + - - -
1201 SER* 2.8 53.3 + - - +
1241 MET* 4.1 11.2 - - + -
1291 ALA* 3.6 29.6 - - + -
1321 LEU* 3.9 18.6 - - + -
1331 CYS* 3.8 23.1 - - - -
1401 VAL* 4.0 11.0 - - + -
1601 ALA* 4.4 0.4 - - - -
1611 PHE* 4.3 4.9 - - + +
2181 PHE 5.0 1.1 - - - +
2191 LEU* 1.3 75.4 - - - +
2211 VAL* 1.3 68.9 + - - +
2221 CYS* 4.1 3.5 + - - -
1362 LEU* 4.9 0.2 - - - +
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Residues in contact with VAL 221 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 PHE* 4.0 7.2 - - + -
1181 MET 3.3 10.3 - - - +
1191 SER* 4.3 4.5 - - - -
1401 VAL* 3.7 8.8 - - - +
1411 ALA* 2.8 37.9 + - + +
1521 ILE* 3.8 25.8 - - + -
1551 VAL* 3.7 22.4 - - + -
1561 ALA* 3.9 25.1 - - + -
1601 ALA* 3.9 9.9 - - + -
1611 PHE 3.8 8.9 + - - +
2201 VAL* 1.3 79.4 - - - +
2221 CYS* 1.3 67.0 + - - +
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Residues in contact with CYS 222 (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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1161 TYR 3.7 0.5 - - - +
1171 PHE* 3.4 5.9 - - - -
1181 MET 2.7 35.1 + - - +
1321 LEU* 4.5 3.4 - - - -
1331 CYS* 2.0 53.2 - - + -
1391 THR 3.4 4.7 - - - -
1411 ALA* 4.2 1.1 - - - -
2201 VAL* 4.4 4.9 - - - -
2211 VAL* 1.3 76.7 - - - +
2231 GLU* 1.3 60.1 + - - +
2241 PHE* 3.6 23.9 - - + -
1362 LEU* 3.9 25.1 - - + -
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Residues in contact with GLU 223 (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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1151 LYS* 4.0 31.5 + - + +
1161 TYR 3.4 4.0 - - - -
1171 PHE* 3.6 17.8 - - + -
1381 GLY* 3.3 6.1 - - - -
1391 THR* 2.7 53.4 + - + +
1411 ALA* 3.5 8.9 - - - -
1421 THR* 2.9 37.1 + - - +
1441 ARG* 5.2 5.2 + - - -
2221 CYS* 1.3 74.2 - - - +
2241 PHE* 1.3 70.1 + - - +
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Residues in contact with PHE 224 (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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1151 LYS* 3.1 8.1 - - - +
1161 TYR* 2.7 42.2 + - + +
1181 MET* 3.4 33.9 - - + -
1331 CYS 4.0 3.4 - - - -
1361 LEU* 3.5 20.4 - - + -
1371 GLN 4.4 2.2 - - - -
1381 GLY* 3.4 31.0 - - - -
2221 CYS* 3.6 31.9 - - + -
2231 GLU* 1.3 74.3 - - - +
2251 SER* 1.3 66.2 + - - +
1182 MET* 3.2 44.0 - - + -
1362 LEU* 4.1 11.2 - - + -
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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