Contacts of the helix formed by residues 300 - 307 (chain A) in PDB entry 4BM9
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 GLU 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A VAL* 4.5 8.5 - - - +
225A ALA 4.3 11.6 - - - +
226A LEU* 5.0 0.2 - - + -
227A HIS* 3.8 22.0 + - + +
228A LEU* 6.0 0.6 - - - +
298A ILE* 3.6 8.3 - - - +
299A LYS* 1.3 75.1 - - - +
301A LEU* 1.3 63.7 + - - +
302A HIS* 2.5 50.1 + - + +
303A HIS* 2.8 49.4 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.7 32.8 - - + +
284A GLY* 4.9 2.7 - - - -
285A TYR 3.8 12.3 - - - +
286A SER* 4.1 3.6 - - - -
298A ILE 3.9 17.9 - - - +
299A LYS* 3.3 10.2 + - - +
300A GLU* 1.3 69.5 + - - +
302A HIS* 1.3 58.3 + - + +
303A HIS 3.0 5.8 - - - -
304A PHE* 2.9 42.1 + - + +
305A ARG 4.4 0.3 + - - -
312A TYR* 4.4 8.3 - - - +
315A TYR* 3.8 27.7 + - + +
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 5.0 1.5 - - + +
224A VAL* 3.9 36.5 - - + +
226A LEU* 3.5 14.2 - - + +
300A GLU* 2.5 30.5 + - - +
301A LEU* 1.3 76.5 + - + +
303A HIS* 1.3 63.4 + - - +
304A PHE 3.0 0.7 - - - -
305A ARG* 3.0 26.8 + - + +
312A TYR* 4.3 7.2 + - - -
1476A SO4 3.1 45.8 + - - -
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.3 29.5 - - + +
227A HIS* 3.7 15.3 - + - -
228A LEU* 3.3 54.1 + - + +
229A ILE* 4.2 6.7 - - + -
249A LEU* 4.1 10.5 - - + -
264A PHE* 3.6 16.0 - - + -
298A ILE* 4.3 10.5 - - + -
300A GLU* 2.8 44.8 + - + +
301A LEU 3.0 1.0 - - - -
302A HIS* 1.3 78.1 - - - +
304A PHE* 1.3 61.6 + - + +
305A ARG 3.1 1.5 + - - -
306A ILE* 3.4 25.3 + - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 4.2 10.1 - + - -
268A CYS* 3.7 29.8 - - + -
277A PHE* 3.9 18.4 - + - -
285A TYR 4.0 0.2 - - - -
286A SER* 3.6 35.0 - - - -
287A LEU* 3.6 19.3 - - + -
298A ILE* 4.2 16.6 - - + -
301A LEU* 2.9 33.5 + - + +
303A HIS* 1.3 74.0 - - - +
305A ARG* 1.3 55.7 + - - +
306A ILE* 2.9 6.1 - - - -
307A LEU* 2.9 42.3 + - + +
312A TYR* 3.5 5.5 - - + -
315A TYR* 3.5 30.5 - + + -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 3.3 58.0 + - + -
151A LYS* 3.3 31.1 - - - +
226A LEU* 5.8 0.2 - - + -
302A HIS* 3.0 21.6 + - + +
304A PHE* 1.3 78.1 - - - +
306A ILE* 1.3 56.3 + - - +
307A LEU 3.0 5.6 + - - -
308A GLY* 3.1 14.3 + - - -
309A GLU* 4.9 13.9 + - - +
312A TYR* 3.3 47.3 - - - +
1476A SO4 2.4 43.1 + - - -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 4.5 5.6 - - + -
157A VAL* 3.8 22.2 - - + -
226A LEU* 4.6 4.5 - - + -
229A ILE* 4.0 26.5 - - + -
249A LEU* 4.9 1.8 - - + -
261A LEU* 4.4 16.4 - - + +
264A PHE* 3.7 24.7 - - + -
265A HIS* 2.6 58.1 + - + +
268A CYS* 5.8 1.1 - - - -
303A HIS* 3.5 19.1 - - - +
304A PHE* 2.9 0.6 - - - -
305A ARG* 1.3 73.8 - - - +
307A LEU* 1.3 56.8 + - - +
308A GLY* 3.2 1.3 + - - -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A HIS* 3.2 21.3 - - - -
268A CYS* 3.6 44.8 - - + +
269A VAL* 3.7 15.8 - - + +
272A LEU* 4.1 13.7 - - + -
277A PHE* 5.0 2.9 - - + -
304A PHE* 2.9 28.5 + - + +
306A ILE* 1.3 78.4 - - - +
308A GLY* 1.3 57.2 + - - +
311A GLN* 3.8 29.9 - - + +
312A TYR* 4.0 7.9 - - - +
315A TYR* 3.6 37.9 - - + -
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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