Contacts of the helix formed by residues 260 - 268 (chain C) in PDB entry 1K4R
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 GLN 260 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLY* 4.0 8.9 + - - -
266B LYS* 3.4 30.4 + - - +
61C LEU* 2.8 29.6 + - + +
225C LEU* 4.0 19.8 - - + +
241C LEU* 3.6 24.7 - - + +
257C LEU* 3.1 24.6 + - - +
258C GLY 3.0 19.0 + - - +
259C ASP* 1.3 70.2 - - - +
261C THR* 1.3 64.9 + - - +
262C GLY 3.3 2.7 - - - -
263C VAL* 3.0 17.4 + - + +
264C LEU* 2.9 21.7 + - - +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B GLY* 5.1 5.6 - - - -
259B ASP 5.4 2.9 - - - +
61C LEU* 3.6 23.3 - - - +
125C LYS* 3.5 15.3 + - - +
202C LEU* 4.5 15.3 - - + -
209C LEU* 5.4 4.0 - - + -
259C ASP* 2.6 28.7 + - - -
260C GLN* 1.3 75.6 - - - +
262C GLY* 1.3 58.0 - - - +
264C LEU* 3.1 5.1 + - - +
265C LEU* 2.8 54.5 + - + +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B LEU 4.0 18.5 - - - +
259B ASP 3.4 26.3 + - - +
260B GLN* 4.0 6.3 + - - -
263B VAL* 4.1 7.4 - - - -
259C ASP 4.5 0.4 + - - -
260C GLN 3.3 0.8 - - - -
261C THR* 1.3 78.7 - - - +
263C VAL* 1.3 62.3 + - - +
265C LEU* 3.5 2.5 + - - +
266C LYS* 3.3 27.4 + - - +
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Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLY* 4.1 3.4 - - - -
263B VAL* 3.7 35.4 - - + +
266B LYS* 3.9 26.5 - - + +
260C GLN* 3.0 31.6 + - + +
262C GLY* 1.3 76.8 - - - +
264C LEU* 1.3 64.0 + - - +
266C LYS* 3.3 16.6 + - - +
267C ALA* 3.4 10.6 + - - +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 3.9 23.6 - - + -
127C ALA* 4.3 5.6 - - + -
200C LEU* 4.3 11.0 - - + -
202C LEU* 3.8 30.5 - - + -
219C TRP* 3.8 30.5 - - + -
223C LEU* 4.3 17.7 - - + -
225C LEU* 5.3 4.0 - - + -
260C GLN 2.9 12.0 + - - +
261C THR* 3.5 7.4 - - - +
263C VAL* 1.3 78.5 - - - +
265C LEU* 1.3 57.5 + - + +
267C ALA* 2.9 24.0 + - + +
268C LEU* 2.9 25.7 + - + +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ASN 4.2 0.4 - - - +
257B LEU* 3.6 40.1 - - + +
258B GLY* 4.1 3.1 - - - +
202C LEU* 4.3 6.5 - - + -
209C LEU* 4.1 27.4 - - + -
213C TRP* 3.9 33.4 - - + -
261C THR* 2.8 40.5 + - + +
262C GLY 3.8 4.7 - - - +
264C LEU* 1.3 72.4 - - - +
266C LYS* 1.3 62.0 + - + +
268C LEU* 3.3 13.2 + - + +
269C ALA* 3.3 19.9 + - - +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B LEU* 6.1 4.5 - - + +
260B GLN* 3.4 27.6 + - - +
263B VAL* 3.9 25.8 - - + +
262C GLY 3.3 14.0 + - - +
263C VAL* 3.6 8.3 - - - +
264C LEU 3.2 0.4 - - - -
265C LEU* 1.3 75.4 - - + +
267C ALA* 1.3 63.6 + - - +
268C LEU 3.4 0.2 + - - -
269C ALA* 3.4 18.4 + - - +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C TRP* 4.0 27.8 + - + +
263C VAL* 3.4 8.5 + - + +
264C LEU* 2.9 14.9 + - + +
266C LYS* 1.3 81.6 - - - +
268C LEU* 1.3 58.3 + - - +
269C ALA 3.5 6.2 + - - +
271C VAL* 4.0 8.8 - - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 3.9 21.5 - - + -
202C LEU* 5.0 1.1 - - + -
213C TRP* 3.7 50.8 + - + +
215C VAL* 3.9 15.0 - - + -
219C TRP* 3.6 27.4 - - + -
264C LEU* 2.9 31.3 + - + +
265C LEU* 3.3 17.2 + - + +
266C LYS 3.2 0.4 - - - -
267C ALA* 1.3 75.2 - - - +
269C ALA* 1.3 65.2 + - - +
270C GLY 3.4 0.2 + - - -
271C VAL* 3.2 27.2 + - + +
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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