Contacts of the helix formed by residues 264 - 278 (chain B) in PDB entry 3KSA
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 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B MET 3.9 4.7 + - - -
109B ASP 3.6 1.7 + - - -
110B GLY* 3.5 29.1 - - - -
262B GLU 4.3 0.6 + - - -
263B ILE* 1.3 78.4 - - + +
265B LYS* 1.3 67.8 + - - +
266B ALA* 2.7 12.6 + - - +
267B ASN* 2.9 40.4 + - + +
268B LEU* 2.9 20.6 + - - +
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 3.4 27.2 + - + +
109B ASP* 3.3 17.5 - - - +
259B ILE* 3.9 19.1 - - + +
263B ILE 3.5 5.7 + - - -
264B ASN* 1.3 69.8 - - - +
266B ALA* 1.3 62.2 + - - +
268B LEU* 3.5 6.7 - - - +
269B VAL* 3.0 23.6 + - - +
289B ASP* 2.9 30.1 - - - +
291B SER* 3.4 28.9 - - - -
296B LEU* 4.0 24.7 - - + -
298B ILE* 4.5 15.5 - - + -
447C ARG* 5.1 0.7 - - - +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.1 34.7 - - + +
264B ASN* 2.7 15.4 + - - +
265B LYS* 1.3 79.3 - - - +
267B ASN* 1.3 68.3 + - - +
269B VAL* 3.1 13.6 + - - +
270B LYS* 3.2 11.8 + - - +
289B ASP* 5.9 1.1 - - - -
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Residues in contact with ASN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP 5.5 0.2 + - - -
264B ASN* 2.9 33.9 + - + +
266B ALA* 1.3 74.8 - - - +
268B LEU* 1.3 66.4 + - - +
270B LYS* 2.9 9.9 + - - +
271B LYS* 2.8 26.0 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 5.4 0.2 - - + -
259B ILE* 4.6 6.3 - - + -
263B ILE* 4.5 16.9 - - + +
264B ASN 2.9 17.9 + - - +
265B LYS* 3.5 8.5 - - - +
267B ASN* 1.3 76.7 - - - +
269B VAL* 1.3 63.2 + - - +
271B LYS* 3.5 5.3 + - + +
272B ILE* 3.2 29.5 + - + +
298B ILE* 4.0 24.9 - - + -
319B THR* 4.3 8.7 - - - +
320B ASP* 3.8 42.4 - - + +
321B LEU* 3.8 26.2 - - + +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS 3.0 14.3 + - - +
266B ALA* 3.1 10.7 + - - +
268B LEU* 1.3 75.2 - - + +
270B LYS* 1.3 69.2 + - - +
272B ILE* 3.1 9.1 + - - +
273B ASP* 3.1 21.9 + - + +
287B VAL* 5.0 10.0 - - + +
288B ARG 5.5 0.7 - - - -
289B ASP* 4.0 28.9 - - + +
298B ILE* 3.8 39.0 - - + -
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ALA 3.2 7.3 + - - +
267B ASN* 2.9 11.0 + - - +
269B VAL* 1.3 81.3 - - - +
271B LYS* 1.3 58.3 + - - +
273B ASP* 3.0 8.8 + - - +
274B ASP* 2.8 30.9 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ASN 2.8 19.6 + - - +
268B LEU* 3.7 8.3 - - + +
270B LYS* 1.3 73.6 - - - +
272B ILE* 1.3 61.0 + - - +
274B ASP* 3.6 9.9 - - - +
275B VAL* 3.4 20.1 + - - +
319B THR* 4.3 16.6 - - + +
320B ASP 6.0 0.2 - - - +
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 4.7 4.0 - - + -
268B LEU* 3.2 22.4 + - + +
269B VAL* 3.1 10.2 + - - +
270B LYS 3.1 0.8 - - - -
271B LYS* 1.3 74.1 - - - +
273B ASP* 1.3 62.3 + - - +
275B VAL* 2.9 32.3 + - + +
276B ARG* 3.4 3.5 + - - +
287B VAL* 3.7 21.1 - - + -
298B ILE* 5.4 5.2 - - + -
300B ILE* 3.5 33.0 - - + -
315B LEU* 4.1 16.8 - - + -
319B THR* 4.4 13.0 - - + +
321B LEU* 4.1 25.6 - - + -
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 3.1 9.8 + - + +
270B LYS* 3.0 10.2 + - - +
272B ILE* 1.3 80.2 - - - +
274B ASP* 1.3 65.7 + - - +
276B ARG* 3.0 44.0 + - - +
277B VAL* 3.0 24.4 + - - +
287B VAL* 3.7 30.2 + - + +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B LYS 2.8 16.4 + - - +
271B LYS* 3.6 11.7 - - - +
273B ASP* 1.3 75.7 - - - +
275B VAL* 1.3 57.1 + - - +
277B VAL* 4.1 6.4 - - - +
278B ASN* 3.0 34.3 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS 3.4 9.7 + - - +
272B ILE* 2.9 15.3 + - + +
274B ASP* 1.3 79.5 - - - +
276B ARG* 1.3 64.2 + - - +
278B ASN* 3.6 0.8 - - - -
279B ASN* 3.0 16.5 + - - -
280B LYS* 3.0 19.8 + - + -
281B VAL* 4.4 17.7 + - + +
284B ILE* 4.4 11.9 - - + -
314B TYR* 3.9 26.2 - - + +
315B LEU* 4.5 13.2 - - + -
318B TYR* 5.2 2.2 - - + -
319B THR* 4.4 15.5 - - + -
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ILE 3.4 2.5 + - - +
273B ASP* 3.0 45.6 + - - +
275B VAL* 1.3 80.4 - - - +
277B VAL* 1.3 88.6 + - - +
279B ASN* 2.6 28.9 + - - +
284B ILE* 3.5 30.3 - - + +
285B ALA 3.4 31.2 - - - +
287B VAL* 4.9 5.2 - - + +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 3.0 16.8 + - - +
274B ASP* 4.1 6.1 - - - +
276B ARG* 1.3 107.0 - - - +
278B ASN* 1.3 61.6 + - + +
279B ASN* 2.9 12.0 + - - +
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Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP 3.0 19.1 + - - +
275B VAL* 4.1 2.5 - - - +
277B VAL* 1.3 79.0 - - + +
279B ASN* 1.3 67.9 + - - +
280B LYS* 2.9 13.5 + - + +
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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