Contacts of the helix formed by residues 125 - 136 (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 PRO 125 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241 MET* 1.3 92.2 - - + +
1261 LEU* 1.3 59.8 + - - +
1271 ASN* 3.3 6.7 - - + +
1281 ARG* 3.2 23.5 + - + +
1291 ALA* 2.9 23.6 + - - +
1611 PHE* 3.6 0.9 - - - -
2141 CYS 3.8 9.6 - - - +
2151 SER* 3.9 16.4 - - - +
2161 ASP 3.3 12.6 - - - +
2171 SER* 3.3 15.3 - - - +
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Residues in contact with LEU 126 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 PRO* 1.3 69.9 - - - +
1271 ASN* 1.3 64.4 + - - +
1291 ALA* 3.9 5.4 - - + -
1301 LYS* 2.8 58.0 + - + +
1401 VAL* 4.7 6.3 - - + -
1611 PHE* 3.4 38.1 - - + -
1621 LEU 4.3 11.4 - - - +
1651 THR* 4.1 15.5 - - + -
1761 LEU* 4.9 4.3 - - + -
2001 CYS* 3.2 29.6 - - - -
2141 CYS* 3.3 20.8 + - + +
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Residues in contact with ASN 127 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 PRO* 3.3 5.6 - - + +
1261 LEU* 1.3 80.7 - - - +
1281 ARG* 1.3 59.9 + - - +
1301 LYS* 3.5 28.6 + - - +
1311 ALA* 3.1 25.5 + - - +
2141 CYS* 4.9 3.2 + - - +
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Residues in contact with ARG 128 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 ARG* 5.9 2.4 - - - +
1231 ARG 3.8 10.9 + - - -
1241 MET* 3.4 44.2 - - + +
1251 PRO* 3.2 24.0 + - + +
1261 LEU 3.2 0.2 - - - -
1271 ASN* 1.3 76.4 - - - +
1291 ALA* 1.3 61.2 + - - +
1311 ALA* 3.2 8.2 + - + +
1321 LEU* 2.9 28.0 + - + +
2171 SER* 5.3 0.6 + - - -
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Residues in contact with ALA 129 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 MET* 3.8 15.2 - - + -
1251 PRO 2.9 13.9 + - - +
1261 LEU* 3.0 18.1 + - + +
1281 ARG* 1.3 76.9 - - - +
1301 LYS* 1.3 61.7 + - - +
1321 LEU* 3.2 4.0 + - - +
1331 CYS* 3.1 27.4 + - - -
1401 VAL* 4.2 3.4 - - + -
1611 PHE* 4.3 9.4 - - + -
2201 VAL* 3.6 29.1 - - + +
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Residues in contact with LYS 130 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 LEU* 2.8 34.2 + - + +
1271 ASN* 3.6 33.7 - - - +
1291 ALA* 1.3 73.3 - - - +
1311 ALA* 1.3 58.6 + - - +
1331 CYS* 4.0 1.3 - - - +
1341 SER* 3.0 38.1 + - - +
1401 VAL* 3.9 11.7 - - + -
1761 LEU* 3.8 34.5 - - + -
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Residues in contact with ALA 131 (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 ASN 3.1 14.5 + - - +
1281 ARG* 3.5 13.7 - - + +
1291 ALA 3.2 0.2 - - - -
1301 LYS* 1.3 77.4 - - - +
1321 LEU* 1.3 56.9 + - - +
1341 SER* 3.8 5.3 - - - -
1351 GLU* 2.9 30.3 + - - +
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Residues in contact with LEU 132 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201 SER* 4.1 0.7 - - - -
1241 MET* 3.9 21.5 - - + -
1281 ARG* 2.9 13.6 + - + +
1291 ALA 3.2 8.5 + - - +
1311 ALA* 1.3 73.9 - - - +
1331 CYS* 1.3 66.3 + - - +
1351 GLU* 3.2 18.2 + - - +
1361 LEU* 3.7 6.8 + - - +
2201 VAL* 3.9 17.0 - - + -
2221 CYS* 4.5 0.7 - - - -
1322 LEU* 3.9 26.0 - - + -
1352 GLU* 3.6 34.5 - - + -
1362 LEU* 4.0 25.7 - - + +
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Residues in contact with CYS 133 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291 ALA 3.1 16.4 + - - +
1301 LYS 4.1 2.5 - - - +
1321 LEU* 1.3 79.0 - - - +
1341 SER* 1.3 60.9 + - - +
1361 LEU* 3.2 9.5 + - - +
1381 GLY* 2.9 23.5 + - - -
1391 THR* 3.6 26.9 - - - +
1401 VAL* 3.8 8.5 - - + +
2201 VAL* 3.8 13.2 - - - -
2221 CYS* 2.0 56.5 - - + -
2241 PHE* 4.0 4.4 - - - -
1362 LEU* 5.3 0.4 - - - -
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Residues in contact with SER 134 (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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1301 LYS* 3.0 25.6 + - - +
1311 ALA* 3.8 5.8 - - - -
1331 CYS* 1.3 74.5 - - - +
1351 GLU* 1.3 62.6 + - - +
1371 GLN* 2.9 19.2 + - - +
1381 GLY 3.5 12.1 + - - -
1391 THR* 5.4 1.2 - - - -
1212 VAL* 4.0 10.2 - - - +
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Residues in contact with GLU 135 (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 ALA 2.9 15.0 + - - +
1321 LEU* 3.2 15.4 + - + +
1341 SER* 1.3 77.3 - - - +
1361 LEU* 1.3 56.9 + - - +
1371 GLN 3.6 1.0 + - - -
1202 SER* 3.1 8.3 - - - -
1212 VAL* 2.9 43.3 + - - +
1222 ARG* 2.9 70.4 + - - +
1242 MET* 5.0 0.2 - - + -
1322 LEU* 3.7 31.4 - - + -
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Residues in contact with LEU 136 (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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1321 LEU 3.7 3.3 + - - +
1331 CYS 3.2 3.5 + - - +
1341 SER 3.1 0.4 - - - -
1351 GLU* 1.3 76.1 - - - +
1371 GLN* 1.3 71.0 + - - +
1381 GLY 3.3 3.1 + - - -
2241 PHE* 3.5 14.8 - - + -
1182 MET* 3.7 43.0 - - + +
1192 SER 3.5 19.0 + - - +
1202 SER* 3.9 15.9 - - - +
1322 LEU* 4.1 25.1 - - + +
1362 LEU* 3.8 22.4 - - + -
2222 CYS* 3.9 32.1 - - - -
2242 PHE* 4.1 4.7 - - + -
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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