Contacts of the helix formed by residues 296 - 304 (chain B) in PDB entry 7CN9
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 LEU 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ASP* 2.4 31.4 + - + +
295B PRO* 1.3 69.9 - - - +
297B SER* 1.3 63.1 + - - +
298B GLU 3.3 0.9 - - - -
299B THR* 3.1 21.3 + - + -
300B LYS* 3.0 26.1 + - + +
308B VAL* 4.4 17.7 - - + -
597B VAL* 5.7 0.2 - - + -
599B THR* 5.7 2.0 - - + -
605B SER* 3.5 36.1 - - - +
606B ASN* 5.6 0.4 - - - -
608B VAL* 3.4 18.4 - - + +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 3.8 17.8 - - - +
290B ASP 3.2 21.1 - - - +
291B CYS 3.1 5.6 + - - +
293B LEU* 3.0 20.4 + - - -
294B ASP* 2.2 36.9 + - - +
296B LEU* 1.3 70.2 - - - +
298B GLU* 1.3 78.1 + - - -
300B LYS* 3.4 5.5 + - - +
301B CYS* 2.8 28.4 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B CYS* 3.1 16.6 - - - +
292B ALA* 3.0 27.1 - - + +
293B LEU 4.7 0.2 - - - -
294B ASP 2.6 16.6 - - - +
295B PRO* 3.8 7.8 - - + +
297B SER* 1.3 81.3 + - - +
299B THR* 1.3 66.2 + - - +
301B CYS* 4.0 3.4 - - - -
302B THR* 2.8 35.2 + - + +
315B THR* 4.0 23.1 - - + +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO 2.9 23.9 + - - -
296B LEU* 3.2 16.3 - - + +
298B GLU* 1.3 77.7 - - - +
300B LYS* 1.3 62.8 + - - +
302B THR* 3.1 5.3 + - - -
303B LEU* 3.0 30.8 + - + +
308B VAL* 3.9 28.9 - - + -
313B TYR* 4.3 19.1 - - + +
315B THR* 5.4 5.4 - - - +
597B VAL* 3.3 21.7 - - + +
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.6 31.4 + - + +
289B VAL* 3.4 33.4 - - + +
296B LEU* 3.0 16.7 + - + +
297B SER* 3.6 8.3 - - - +
299B THR* 1.3 77.2 - - - +
301B CYS* 1.3 63.7 + - - +
302B THR 2.9 1.6 + - - -
303B LEU* 5.3 1.1 - - - -
304B LYS* 3.2 19.9 + - - -
305B SER 3.6 18.4 + - - +
306B PHE* 3.2 64.9 - - - +
307B THR 6.4 0.4 - - - -
308B VAL* 5.9 3.3 - - - +
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Residues in contact with CYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 6.4 2.7 - - - -
274B THR* 6.0 0.2 - - - -
275B PHE 5.6 0.4 - - - -
276B LEU* 3.7 24.8 - - + +
290B ASP 4.9 0.4 - - - +
291B CYS* 2.0 55.2 - - - +
297B SER 2.8 21.2 + - - +
298B GLU 3.0 5.1 + - - +
300B LYS* 1.3 73.3 - - - +
302B THR* 1.3 59.2 + - + +
304B LYS* 3.4 26.5 + - - +
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Residues in contact with THR 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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291B CYS* 5.3 2.9 - - - -
298B GLU* 2.8 22.5 + - + +
299B THR* 3.1 6.8 + - - -
301B CYS* 1.3 86.1 - - + +
303B LEU* 1.3 66.3 + - - +
304B LYS* 3.0 24.6 + - - +
313B TYR* 6.1 0.3 - - - +
315B THR* 4.6 20.2 - - - +
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Residues in contact with LEU 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 THR* 3.0 23.9 + - + +
300B LYS* 4.6 0.9 - - - +
302B THR* 1.3 80.2 + - - +
304B LYS* 1.3 70.1 + - - +
305B SER* 3.4 10.3 + - - +
307B THR 5.4 3.8 - - - +
308B VAL* 4.9 5.6 - - + -
309B GLU* 5.3 7.6 - - - +
313B TYR* 3.3 55.9 - - + -
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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
----------------------------------------------------------
48B LEU* 4.2 18.0 + - + +
49B HIS* 6.1 0.2 - - - +
50B SER* 5.4 10.7 - - - +
276B LEU* 4.7 17.9 - - + +
300B LYS 3.2 7.2 + - - -
301B CYS* 3.4 21.9 + - - +
302B THR* 3.0 19.1 - - - +
303B LEU* 1.3 79.6 - - - +
305B SER* 1.3 61.8 + - - +
964B LYS* 5.9 4.9 - - - +
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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