Contacts of the helix formed by residues 268 - 276 (chain B) in PDB entry 4KSL
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 ASP 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B TYR* 4.4 14.6 - - + +
261B PHE* 4.0 5.4 - - - -
266B SER 4.3 0.5 - - - -
267B ASN* 1.3 80.6 + - + +
269B PRO* 1.3 76.8 - - + +
270B GLY* 3.1 7.8 + - - +
271B GLN* 2.7 50.8 + - - +
272B LEU* 3.0 11.1 + - - +
274B ARG* 4.2 3.6 + - - -
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Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TRP* 3.6 24.2 - - + -
237B LEU* 4.1 5.5 - - + +
240B ALA* 5.3 1.1 - - + -
241B ILE* 3.8 27.6 - - + +
244B TYR* 3.7 39.9 - - + -
261B PHE* 3.8 9.6 - - + -
268B ASP* 1.3 88.8 - - + +
270B GLY* 1.3 56.3 + - - +
272B LEU* 3.3 12.6 + - + +
273B LEU* 2.9 29.8 + - - +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TRP* 3.6 29.6 - - - -
268B ASP* 3.1 8.6 + - - -
269B PRO* 1.3 80.0 - - - +
271B GLN* 1.3 55.7 + - - +
273B LEU* 3.2 3.6 + - - +
274B ARG* 2.9 48.0 + - - +
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Residues in contact with GLN 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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264B ASP 3.7 6.9 + - - +
265B THR 3.1 21.0 + - - +
266B SER* 3.7 3.1 - - - -
267B ASN* 2.9 39.8 + - - +
268B ASP* 2.7 25.6 + - - +
270B GLY* 1.3 70.0 - - - +
272B LEU* 1.3 60.5 + - - +
274B ARG* 3.5 20.8 - - - +
275B ASN* 2.9 44.7 + - - +
276B HIS* 4.3 0.2 - - - -
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Residues in contact with LEU 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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237B LEU* 4.8 2.9 - - + -
240B ALA* 3.6 31.4 - - + -
260B LEU* 4.5 13.7 - - + -
261B PHE* 4.9 4.0 - - + -
263B ARG* 3.5 28.5 - - - +
266B SER* 3.6 13.3 - - - +
268B ASP 3.0 11.6 + - - +
269B PRO* 3.4 13.2 - - + +
271B GLN* 1.3 76.3 - - - +
273B LEU* 1.3 57.9 + - - +
276B HIS* 3.0 36.9 + - + +
277B LEU* 3.0 28.2 + - + -
290B GLU* 4.4 7.2 - - + +
293B LEU* 4.1 13.2 - - + -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TRP* 3.8 30.5 - - + +
168B ILE* 3.8 26.0 - - - +
170B GLN* 4.5 3.6 - - + +
171B TRP* 3.6 33.2 - - + +
237B LEU* 4.4 7.6 - - + -
269B PRO 2.9 13.2 + - - +
270B GLY 3.2 7.2 + - - +
272B LEU* 1.3 79.0 - - - +
274B ARG* 1.3 63.7 + - + +
277B LEU* 4.1 17.7 - - + +
278B ASN* 3.1 58.6 + - - +
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Residues in contact with ARG 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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167B TRP* 4.6 7.5 - - - +
170B GLN* 3.0 49.1 + - + +
268B ASP* 4.2 4.6 + - - -
270B GLY* 2.9 28.4 + - - +
271B GLN* 3.5 34.6 - - - +
273B LEU* 1.3 80.8 - - + +
275B ASN* 1.3 63.8 + - - +
278B ASN* 4.0 10.9 + - - +
279B GLN* 2.3 26.2 + - - -
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Residues in contact with ASN 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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265B THR* 2.9 38.4 + - + +
271B GLN* 2.9 24.8 + - - +
274B ARG* 1.3 85.6 + - - +
276B HIS* 1.3 74.6 + - + +
279B GLN* 3.2 19.5 + - - +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG* 3.4 31.8 + - - -
265B THR* 2.8 30.6 + - - -
266B SER* 4.0 13.9 + - - -
271B GLN 4.3 0.2 - - - -
272B LEU* 3.0 19.6 + - + +
274B ARG 3.5 0.2 - - - -
275B ASN* 1.3 93.8 + - + +
277B LEU* 1.3 66.0 + - + +
278B ASN 3.3 1.1 - - - -
279B GLN* 3.2 16.3 + - - +
280B VAL* 3.2 16.5 + - - +
285B GLY 5.3 0.9 - - - +
287B GLU* 3.9 14.4 + - - +
290B GLU* 2.9 25.7 + - - +
42C ARG* 5.0 1.8 - - - -
74C ARG* 6.3 1.8 - - - +
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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