Contacts of the helix formed by residues 295 - 303 (chain A) in PDB entry 6J8H
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 SER 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A LEU 4.1 0.2 - - - -
294A GLU* 1.3 85.3 + - - +
296A GLU* 1.3 56.0 + - - +
297A GLU* 3.3 15.6 + - - +
298A ASP* 3.6 19.1 + - - +
299A PHE* 2.6 40.4 + - - +
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Residues in contact with GLU 296 (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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294A GLU* 4.5 1.0 + - - -
295A SER* 1.3 73.0 + - - +
297A GLU* 1.3 65.6 + - - +
299A PHE* 3.6 4.2 - - - +
300A ARG* 2.9 53.2 + - - +
305A TYR* 3.7 19.4 + - - -
309A SER 3.8 5.7 - - - +
310A LYS* 3.4 37.8 + - - +
335A ARG* 5.6 1.4 + - - -
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Residues in contact with GLU 297 (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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295A SER* 3.2 8.1 + - - +
296A GLU* 1.3 92.6 - - + +
298A ASP* 1.3 61.7 + - - +
300A ARG* 3.4 17.7 + - - +
301A LYS* 3.4 19.9 + - - +
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Residues in contact with ASP 298 (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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293A LEU* 2.6 44.9 - - + +
294A GLU 4.9 0.7 + - - +
295A SER* 3.2 21.8 + - - +
297A GLU* 1.3 81.0 - - - +
299A PHE* 1.3 62.2 + - - +
300A ARG 3.4 0.2 + - - -
301A LYS* 3.6 18.5 + - - +
302A TYR* 3.8 12.7 - - - -
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Residues in contact with PHE 299 (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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274A LYS* 5.6 10.1 - - + -
290A MET* 4.1 26.5 - - + -
293A LEU* 3.3 41.9 - - + +
294A GLU* 4.0 17.5 - - - -
295A SER 2.6 30.2 + - - +
296A GLU* 3.6 6.3 - - - +
298A ASP* 1.3 72.2 - - - +
300A ARG* 1.3 64.4 + - - +
302A TYR* 3.2 6.1 + - - +
303A PHE* 3.1 42.0 + + - -
305A TYR* 3.5 28.6 - + - +
312A ALA* 6.2 0.4 - - + -
334A GLY* 5.9 2.5 - - - -
335A ARG* 6.1 5.6 - - + -
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Residues in contact with ARG 300 (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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296A GLU* 2.9 43.9 + - - +
297A GLU* 3.7 18.6 - - - +
298A ASP 3.3 0.2 - - - -
299A PHE* 1.3 74.4 - - - +
301A LYS* 1.3 67.6 + - - +
303A PHE 2.8 17.0 - - - +
305A TYR* 3.5 38.3 + - + +
307A GLU* 3.9 3.2 - - - +
308A GLY* 2.8 41.0 - - - +
309A SER 3.7 11.1 + - - +
328A TYR* 4.9 0.5 + - - -
130B GLU* 2.4 55.1 + - + +
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Residues in contact with LYS 301 (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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277A ARG* 3.7 18.4 + - - +
297A GLU 3.4 16.8 - - - +
298A ASP* 3.8 15.0 - - - +
299A PHE 3.3 0.6 - - - -
300A ARG* 1.3 77.7 - - + +
302A TYR* 1.3 70.9 + - + +
328A TYR* 4.0 12.6 + - - -
130B GLU* 4.6 7.3 - - + +
131B ASN* 2.4 58.1 + - + +
132B TYR* 5.4 0.3 - - - +
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A PHE* 4.0 15.8 - + + -
277A ARG* 3.6 49.8 + - + +
280A LEU* 4.5 12.1 - - + -
284A GLU* 2.6 26.3 + - - -
289A ILE* 3.4 39.5 - - + +
293A LEU* 4.3 12.6 - - + -
298A ASP* 3.8 15.5 - - - +
299A PHE* 3.2 8.1 + - - +
300A ARG 3.2 0.6 - - - -
301A LYS* 1.3 90.0 - - + +
303A PHE* 1.3 75.0 + - + +
328A TYR* 4.2 0.8 - - - -
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Residues in contact with PHE 303 (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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274A LYS* 3.5 41.1 - - + -
275A CYS 3.4 14.4 - - - +
276A PHE* 4.1 25.6 - + + -
286A LEU* 4.9 3.4 - - + -
289A ILE* 5.7 1.8 - - + -
290A MET* 4.2 28.7 - - + -
293A LEU* 5.5 3.6 - - + -
299A PHE* 3.1 32.1 + + - +
300A ARG 2.8 18.9 - - - +
302A TYR* 1.3 89.8 - - + +
304A TYR* 1.3 64.5 - - - +
305A TYR* 3.8 13.3 - + + -
312A ALA* 4.3 7.9 - - + -
328A TYR* 3.8 7.6 + - - -
331A VAL* 5.1 4.0 - - + -
333A ILE* 4.9 13.2 - - + -
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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