Contacts of the helix formed by residues 299 - 308 (chain B) in PDB entry 6CNC
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B TYR 3.4 3.0 + - - -
297B THR 2.7 6.4 + - - +
298B GLN* 1.3 87.6 + - + +
300B GLN* 1.3 66.0 + - - +
302B LEU* 3.8 1.2 - - - +
303B GLU* 2.8 40.1 + - - +
322B GLU* 3.5 30.7 + - - +
187M ASP* 3.5 39.0 + - + +
190M ASN* 3.1 33.0 + - + +
194M LYS* 5.7 2.6 - - - +
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Residues in contact with GLN 300 (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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294B ASP* 3.5 28.7 - - + -
295B ILE* 2.7 24.4 - - + +
296B TYR* 2.8 10.9 + - - +
297B THR 3.4 0.8 + - - -
299B GLN* 1.3 82.6 - - + +
301B ALA* 1.3 55.8 + - - +
303B GLU* 2.8 8.0 + - - +
304B TYR* 2.4 38.1 + - - +
186M ILE* 3.2 35.4 + - - +
190M ASN* 4.8 7.4 - - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ILE* 3.7 30.3 - - + +
258B LYS* 4.3 6.1 - - + -
259B ALA* 4.3 0.4 - - + -
294B ASP* 3.2 19.6 + - - +
295B ILE 5.6 1.6 - - - +
297B THR* 3.1 25.0 - - - +
300B GLN* 1.3 76.2 - - - +
302B LEU* 1.3 65.2 + - - +
304B TYR* 3.0 1.8 + - - +
305B ILE* 2.9 31.6 + - - +
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Residues in contact with LEU 302 (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 ALA* 3.5 33.7 - - + +
297B THR* 2.6 42.6 + - + +
298B GLN* 3.6 30.3 - - - +
299B GLN 4.0 1.6 - - - +
301B ALA* 1.3 72.1 - - - +
303B GLU* 1.3 62.5 + - - +
305B ILE* 3.6 6.1 - - - +
306B GLY 3.5 10.9 + - - -
322B GLU* 3.7 22.2 - - + +
323B GLY* 5.7 2.7 - - - -
324B ILE* 4.3 2.4 - - - +
325B GLU* 4.5 4.3 + - - +
326B ALA* 4.9 15.7 - - + +
329B THR* 5.1 6.1 - - - +
342B PHE* 4.5 15.3 - - + -
234M HIS* 6.4 0.7 - - + +
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Residues in contact with GLU 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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299B GLN* 2.8 26.4 + - - +
300B GLN* 2.8 8.3 + - - +
302B LEU* 1.3 67.9 - - - +
304B TYR* 1.3 58.4 + - - +
305B ILE 3.0 2.2 - - - -
306B GLY* 2.6 25.7 + - - +
307B ALA* 2.8 23.0 + - + +
321B GLN 2.6 29.1 - - - +
322B GLU* 3.3 11.5 + - + +
324B ILE* 3.3 12.6 - - - +
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Residues in contact with TYR 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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250B GLU 5.0 4.3 + - - -
251B ILE* 4.4 13.4 - - + +
252B PRO* 4.4 14.4 - - + +
255B ILE* 3.9 32.5 - - + -
293B LEU* 4.1 25.0 - - + +
294B ASP* 4.2 6.5 - - + +
300B GLN* 2.4 29.2 + - + +
301B ALA* 3.0 9.2 + - - +
303B GLU* 1.3 68.2 - - - +
305B ILE* 1.3 64.6 + - - +
307B ALA* 3.5 19.5 + - + +
308B LYS* 3.7 22.4 + - + +
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Residues in contact with ILE 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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247B ILE* 4.1 15.3 - - + +
251B ILE* 3.6 23.8 - - + -
255B ILE* 4.1 7.2 - - + -
256B VAL* 3.6 31.6 - - + -
259B ALA* 4.4 13.0 - - + -
301B ALA 2.9 17.6 + - - +
302B LEU* 3.6 8.3 - - - +
303B GLU 2.9 0.2 + - - -
304B TYR* 1.3 75.9 - - - +
306B GLY* 1.3 57.8 + - - +
307B ALA 3.0 5.9 + - - -
308B LYS* 3.0 16.0 + - - +
309B VAL 3.5 6.8 + - - -
325B GLU* 3.5 24.2 - - + -
328B ALA* 5.7 0.7 - - + -
329B THR* 4.4 13.2 - - - +
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Residues in contact with GLY 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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302B LEU 3.5 4.0 + - - -
303B GLU* 2.6 13.8 + - - -
305B ILE* 1.3 73.6 - - - +
307B ALA* 1.3 56.6 + - - -
308B LYS 3.4 0.2 - - - -
309B VAL* 3.1 21.6 - - - +
324B ILE* 3.3 30.1 - - - +
325B GLU* 3.4 25.9 - - - +
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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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303B GLU* 2.8 19.7 + - + +
304B TYR* 3.7 20.9 - - + +
305B ILE 3.0 0.4 + - - -
306B GLY* 1.3 79.9 - - - +
308B LYS* 1.3 59.5 + - + +
309B VAL* 3.4 4.7 + - - +
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Residues in contact with LYS 308 (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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247B ILE* 4.2 5.8 - - + -
248B ALA* 3.0 29.4 + - + +
249B GLU* 2.7 48.9 + - - +
250B GLU* 3.1 29.2 + - - +
251B ILE* 5.3 7.0 - - + -
304B TYR* 3.7 23.3 + - + +
305B ILE 3.0 8.8 + - - +
307B ALA* 1.3 76.1 - - + +
309B VAL* 1.3 67.2 + - - +
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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