Contacts of the helix formed by residues 295 - 307 (chain H) in PDB entry 6BCH
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 295 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H THR* 3.8 5.3 - - - +
291H LYS 4.5 7.6 - - - +
292H GLU* 3.1 13.1 + - - +
293H HIS 4.0 0.2 - - - +
294H LEU* 1.3 85.7 - - + +
296H SER* 1.3 59.1 + - - +
297H GLU* 3.9 5.1 + - - +
298H GLY* 3.1 17.3 + - - -
299H LEU* 2.9 30.1 + - - +
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Residues in contact with SER 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H THR* 4.2 7.5 - - - +
295H THR* 1.3 72.0 - - - +
297H GLU* 1.3 65.1 + - - +
299H LEU* 3.2 9.7 + - - +
300H GLU* 2.9 28.8 + - - +
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Residues in contact with GLU 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H THR* 3.4 5.3 + - - +
296H SER* 1.3 82.1 + - - +
298H GLY* 1.3 59.6 + - - +
300H GLU* 3.2 8.5 + - - +
301H LYS* 2.9 26.6 + - - +
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Residues in contact with GLY 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H LEU* 4.5 1.9 - - - +
292H GLU* 3.3 28.0 - - - -
295H THR* 3.1 10.8 + - - -
297H GLU* 1.3 77.7 - - - +
299H LEU* 1.3 57.2 + - - +
301H LYS* 3.1 11.1 - - - +
302H ILE* 2.9 33.2 + - - +
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Residues in contact with LEU 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H ILE* 4.9 8.3 - - + -
199H THR* 3.8 23.8 - - - +
201H TYR* 3.5 39.7 - - + -
203H VAL* 3.8 28.9 - - + -
292H GLU 4.1 1.0 + - - -
293H HIS 4.4 6.1 - - - +
295H THR 2.9 18.5 + - - +
296H SER* 3.5 8.3 - - - +
298H GLY* 1.3 73.0 - - - +
300H GLU* 1.3 59.1 - - - +
302H ILE* 3.3 10.5 + - + +
303H GLN* 2.9 30.3 + - + +
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Residues in contact with GLU 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H SER 2.9 13.3 + - - +
297H GLU* 3.4 12.3 - - - +
299H LEU* 1.3 73.5 - - - +
301H LYS* 1.3 66.6 + - - +
303H GLN* 3.3 8.1 + - - +
304H LYS* 2.9 24.3 + - - +
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Residues in contact with LYS 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H LEU* 5.2 4.5 - - + -
297H GLU 2.9 13.6 + - - +
298H GLY* 3.1 15.2 + - - +
300H GLU* 1.3 75.6 - - - +
302H ILE* 1.3 57.8 + - + +
304H LYS* 3.1 9.1 + - - +
305H ILE* 2.9 39.4 + - + +
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Residues in contact with ILE 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H ILE* 3.9 27.8 - - + -
191H ILE* 4.6 9.0 - - + -
203H VAL* 3.8 20.4 - - + -
284H VAL* 4.3 8.2 - - + +
287H LEU* 3.5 39.3 - - + -
288H ILE* 4.5 2.9 - - + -
293H HIS* 3.6 25.1 - - + -
298H GLY 2.9 16.0 + - - +
299H LEU* 3.6 9.6 - - + +
301H LYS* 1.3 73.0 - - - +
303H GLN* 1.3 62.7 + - - +
305H ILE* 3.1 10.6 + - - +
306H LYS* 2.8 28.8 + - + +
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Residues in contact with GLN 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H ILE* 4.1 27.8 - - + +
299H LEU* 2.9 20.9 + - + +
300H GLU* 3.6 8.1 - - - +
302H ILE* 1.3 77.0 - - - +
304H LYS* 1.3 58.4 + - - +
306H LYS* 3.4 8.0 + - - +
307H GLU* 2.9 38.6 + - + +
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Residues in contact with LYS 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H GLU 2.9 14.3 + - - +
301H LYS* 3.1 11.6 + - - +
303H GLN* 1.3 78.1 - - - +
305H ILE* 1.3 62.9 + - + +
307H GLU* 3.5 14.3 + - - +
308H GLY* 3.6 7.1 + - - -
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Residues in contact with ILE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280H ASP* 4.3 18.7 - - + +
283H LYS* 5.7 5.4 - - + -
284H VAL* 3.7 34.3 - - + +
287H LEU* 4.2 15.9 - - + -
301H LYS* 2.9 25.0 + - + +
302H ILE* 3.6 4.7 - - - +
304H LYS* 1.3 73.4 - - + +
306H LYS* 1.3 61.8 + - - +
308H GLY* 2.9 19.4 + - - -
309H MET* 3.3 21.0 + - - +
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Residues in contact with LYS 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 4.7 23.6 - - + +
191H ILE* 5.9 3.8 - - + -
284H VAL* 5.5 0.2 - - - +
302H ILE* 2.8 18.9 + - + +
303H GLN* 3.6 12.3 - - - +
305H ILE* 1.3 76.1 - - - +
307H GLU* 1.3 62.2 + - - +
309H MET* 3.0 33.3 + - - +
18J C 5.2 3.1 + - - -
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Residues in contact with GLU 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H GLN* 2.9 28.8 + - - +
304H LYS* 3.7 8.7 - - - +
305H ILE 3.2 0.2 - - - -
306H LYS* 1.3 75.6 - - - +
308H GLY* 1.3 57.4 + - - +
309H MET 3.4 0.7 - - - -
312H GLY* 3.7 22.1 - - - +
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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