Contacts of the helix formed by residues 296 - 307 (chain B) in PDB entry 1CK4
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 THR 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B LEU* 4.0 29.3 - - + +
289B TYR* 3.3 40.4 - - + -
290B ASN* 4.0 11.9 + - - +
294B LEU 3.3 6.2 + - - +
295B SER* 1.3 71.0 + - - +
297B GLU* 1.3 67.9 + - - +
298B LYS 3.5 1.8 - - - -
299B PHE* 3.9 7.2 - - + -
300B VAL* 2.8 35.3 + - - +
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Residues in contact with GLU 297 (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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295B SER* 2.3 37.6 + - - +
296B THR* 1.3 83.2 + - - +
298B LYS* 1.3 66.5 + - - +
300B VAL* 4.2 3.0 - - - +
301B GLU* 3.3 24.4 + - - +
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Residues in contact with LYS 298 (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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259B GLU* 3.3 27.4 + - + +
263B ASN* 3.3 28.2 - - - +
295B SER* 4.8 3.7 + - - +
296B THR 3.5 0.2 - - - -
297B GLU* 1.3 78.1 - - - +
299B PHE* 1.3 63.4 + - - +
301B GLU* 3.3 15.5 - - - +
302B GLU* 3.0 24.4 + - + +
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Residues in contact with PHE 299 (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 THR 4.2 0.9 - - - -
257B ASP* 3.4 13.2 - - - -
258B GLY* 3.1 37.7 - - - -
259B GLU* 3.6 15.5 + - + +
284B ALA* 3.9 13.2 - - + -
285B ILE 3.6 18.2 - - - -
286B LEU* 3.7 15.0 - - + -
289B TYR* 3.6 42.0 - + + -
296B THR* 3.6 14.7 - - + +
298B LYS* 1.3 79.0 - - - +
300B VAL* 1.3 64.6 + - - +
302B GLU* 3.0 13.6 + - - +
303B ILE* 3.1 40.9 + - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ALA* 5.2 0.7 - - + -
286B LEU* 3.8 24.5 - - + -
296B THR* 2.8 24.7 + - - +
297B GLU* 4.2 3.1 - - - +
299B PHE* 1.3 75.1 - - + +
301B GLU* 1.3 66.6 + - - +
302B GLU 3.2 0.2 + - - -
303B ILE* 3.3 5.5 + - - -
304B LYS* 3.0 24.1 + - + +
315B PHE* 4.0 22.5 - - + -
317B ASN* 3.6 25.6 - - - +
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Residues in contact with GLU 301 (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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297B GLU 3.3 17.6 + - - +
298B LYS* 3.3 14.0 - - - +
300B VAL* 1.3 82.6 - - + +
302B GLU* 1.3 68.0 + - - +
304B LYS* 3.5 7.0 + - - +
305B SER* 2.9 34.3 + - - -
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 5.2 0.7 + - - -
258B GLY 4.4 2.1 - - - +
259B GLU* 3.5 13.0 - - - +
260B SER* 2.7 36.8 + - - -
263B ASN* 2.4 34.9 + - - +
266B LEU* 3.4 21.4 - - + +
298B LYS* 3.0 15.2 + - + +
299B PHE 3.0 10.6 + - - +
301B GLU* 1.3 81.2 + - - +
303B ILE* 1.3 71.4 + - + +
305B SER* 3.1 17.3 + - - -
306B ILE* 3.0 21.0 - - + +
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Residues in contact with ILE 303 (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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226B THR* 6.0 2.2 - - + +
254B ILE* 5.9 1.1 - - + -
256B THR* 3.5 23.1 - - + -
258B GLY 4.1 5.4 - - - +
282B SER* 2.6 47.1 + - - +
283B ILE 4.1 9.9 - - - +
284B ALA* 3.5 14.1 - - + -
299B PHE* 3.1 46.4 + - + +
300B VAL 3.3 1.3 + - - +
302B GLU* 1.3 87.4 - - + +
304B LYS* 1.3 60.4 + - - +
306B ILE* 3.1 18.6 + - + +
307B ALA 3.4 0.2 + - - -
315B PHE* 3.6 16.4 - - + -
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Residues in contact with LYS 304 (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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282B SER* 4.5 0.2 - - - -
300B VAL* 3.0 19.7 + - + +
301B GLU* 3.7 7.9 - - - +
303B ILE* 1.3 77.1 - - - +
305B SER* 1.3 63.4 + - - +
306B ILE 3.1 1.2 + - - -
307B ALA* 3.1 15.9 + - - +
311B THR* 2.9 44.4 + - + +
312B GLU* 3.7 27.3 + - - +
315B PHE* 3.5 39.6 + - + -
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Residues in contact with SER 305 (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 LEU* 4.6 9.9 - - - +
270B ILE* 4.2 18.2 - - - +
280B ARG* 5.7 0.2 + - - -
301B GLU* 2.9 23.9 + - - -
302B GLU* 3.1 16.9 + - - -
304B LYS* 1.3 77.0 - - - +
306B ILE* 1.3 61.5 + - - +
307B ALA 4.3 3.4 - - - +
311B THR* 5.7 0.7 - - - -
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Residues in contact with ILE 306 (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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226B THR* 4.9 8.3 - - + -
230B ILE* 4.0 16.2 - - + -
254B ILE* 3.7 31.6 - - + -
266B LEU* 4.1 24.2 - - + -
270B ILE* 3.9 27.8 - - + -
280B ARG* 2.7 37.0 + - + +
282B SER* 4.2 7.4 - - - -
302B GLU* 3.0 28.0 + - + +
303B ILE* 3.1 19.7 + - + +
304B LYS 3.0 0.4 - - - -
305B SER* 1.3 79.9 + - - +
307B ALA* 1.3 58.3 + - - +
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Residues in contact with ALA 307 (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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280B ARG* 3.4 12.0 + - - -
282B SER* 3.6 16.7 + - - +
303B ILE 3.4 2.6 + - - -
304B LYS 3.1 17.0 + - - +
305B SER 4.3 3.6 - - - +
306B ILE* 1.3 82.1 - - - +
308B SER* 1.3 66.6 + - - +
309B GLU* 3.9 2.3 + - - +
311B THR* 4.1 10.3 - - - +
314B HIS* 3.8 18.6 - - + -
315B PHE* 3.9 17.3 - - + +
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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