Contacts of the helix formed by residues 286 - 293 (chain A) in PDB entry 4G8O
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.9 20.9 - - + -
23A VAL* 5.4 0.2 - - + -
34A PHE* 4.0 14.1 - - + -
39A VAL* 3.8 32.1 - - + -
42A VAL* 5.5 3.8 - - + -
43A LEU* 5.3 0.7 - - + -
165A LEU* 5.1 7.6 - - + -
167A ASN* 6.3 0.2 - - + -
284A VAL* 4.3 8.1 - - + +
285A ASP* 1.3 70.4 - - - +
287A ARG* 1.3 64.2 + - - +
289A PRO* 3.6 10.5 - - + -
290A LEU* 3.3 37.0 + - + +
299A PHE* 3.4 5.5 - - - -
320A ALA* 3.0 24.8 + - + +
321A LEU 4.1 25.6 - - - +
322A GLN* 4.4 6.7 - - + +
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Residues in contact with ARG 287 (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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285A ASP* 3.2 19.3 + - - +
286A LEU* 1.3 79.2 - - - +
288A LYS* 1.4 62.7 - - - +
291A GLU* 2.9 42.3 + - - +
299A PHE* 3.5 64.8 + - + +
300A ARG* 4.0 20.6 - - - +
317A VAL 5.0 2.4 + - - -
318A ALA 5.9 0.6 + - - -
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Residues in contact with LYS 288 (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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285A ASP 4.7 0.6 + - - -
287A ARG* 1.4 78.5 - - - +
289A PRO* 1.4 66.5 - - + +
291A GLU* 3.3 10.3 + - - +
292A ASN* 3.0 33.2 + - - +
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Residues in contact with PRO 289 (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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19A VAL* 4.1 18.2 - - + -
22A GLN* 4.0 26.9 - - + +
23A VAL* 3.8 23.6 - - + +
284A VAL* 6.2 0.2 - - + -
285A ASP 3.6 20.6 - - - +
286A LEU* 3.6 10.3 - - + +
287A ARG 3.6 4.0 - - - -
288A LYS* 1.4 92.4 - - + +
290A LEU* 1.4 58.5 + - - +
292A ASN* 3.6 5.8 + - - +
293A LEU* 3.5 27.0 + - - +
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Residues in contact with LEU 290 (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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15A PHE* 4.1 15.7 - - + -
19A VAL* 4.3 19.1 - - + -
39A VAL* 4.9 0.7 - - + -
43A LEU* 4.0 26.7 - - + -
165A LEU* 5.5 0.4 - - + -
286A LEU* 3.3 39.8 + - + +
287A ARG 3.5 2.1 + - - +
289A PRO* 1.4 73.7 - - - +
291A GLU* 1.4 61.2 + - - +
293A LEU* 3.4 5.3 + - + +
294A GLY 3.4 5.0 + - - -
295A MET* 2.9 55.0 + - + +
298A MET* 4.3 11.7 - - + -
299A PHE* 4.1 18.4 - - + -
320A ALA* 5.2 2.2 - - + -
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Residues in contact with GLU 291 (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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287A ARG* 2.9 55.2 + - - +
288A LYS* 3.3 10.9 + - - +
290A LEU* 1.4 74.9 - - - +
292A ASN* 1.4 63.0 + - - +
293A LEU 3.2 0.4 - - - -
294A GLY* 3.3 10.0 + - - -
295A MET 3.5 15.7 - - - +
296A THR* 3.6 26.9 - - + +
299A PHE* 4.2 4.4 - - + -
300A ARG* 3.2 30.8 + - - +
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Residues in contact with ASN 292 (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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22A GLN* 3.3 32.5 + - - +
25A GLN* 5.5 2.6 + - - -
288A LYS* 3.0 23.9 + - - +
289A PRO* 3.8 7.6 - - - +
290A LEU 3.4 0.2 - - - -
291A GLU* 1.4 77.0 - - - +
293A LEU* 1.3 60.0 + - - +
294A GLY 3.3 0.6 + - - -
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Residues in contact with LEU 293 (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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15A PHE* 4.6 5.2 - - + -
18A ARG* 3.8 36.8 - - + +
19A VAL* 3.8 37.9 - - + +
22A GLN* 4.4 11.2 - - + +
57A GLN 5.3 0.3 - - - +
61A ALA* 4.1 18.4 - - + +
289A PRO 3.5 17.9 + - - +
290A LEU* 3.4 16.7 + - + +
291A GLU 3.2 0.6 - - - -
292A ASN* 1.3 77.5 - - - +
294A GLY* 1.3 55.8 - - - +
295A MET* 3.7 13.0 - - + -
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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