Contacts of the helix formed by residues 282 - 290 (chain A) in PDB entry 3DGR
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 ASP 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A GLU* 5.0 3.5 + - - +
278A SER 3.9 2.2 + - - +
279A ASP 4.3 0.8 + - - -
281A TYR* 1.3 83.4 - - + +
283A ILE* 1.3 58.0 + - - +
284A TYR* 3.1 13.5 + - - +
285A ASN* 3.1 36.0 + - + +
286A ALA* 3.0 26.3 + - - +
418B VAL* 3.9 26.5 - - + +
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Residues in contact with ILE 283 (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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278A SER* 3.3 26.2 + - - +
279A ASP* 3.7 22.8 - - + +
282A ASP* 1.3 74.5 + - - +
284A TYR* 1.3 88.4 + - + +
286A ALA* 3.4 1.1 + - - +
287A CYS* 3.1 35.2 + - - -
310A ILE* 5.5 0.2 - - + -
312A PRO* 3.9 19.1 - - + -
314A SER* 5.5 3.8 - - - +
320A THR* 4.4 6.5 - - + -
324A VAL* 2.9 39.0 - - + -
418B VAL* 4.4 6.7 - - + +
419B ALA* 5.9 2.5 - - + -
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Residues in contact with TYR 284 (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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282A ASP* 3.1 11.0 + - - +
283A ILE* 1.3 100.8 - - + +
285A ASN* 1.3 59.0 + - - +
288A GLU* 3.0 31.8 + - - +
319A ASP* 4.8 1.2 + - - +
320A THR* 3.3 38.3 + - + +
323A LYS* 3.6 58.7 - - + +
324A VAL* 4.4 2.0 - - + -
327A ILE* 3.8 21.0 - - + +
418B VAL* 4.2 13.5 - - + -
419B ALA* 4.8 12.2 - - + +
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Residues in contact with ASN 285 (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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258A GLU* 4.9 3.4 + - - -
282A ASP* 3.1 33.2 + - + +
284A TYR* 1.3 74.1 - - - +
286A ALA* 1.3 61.9 + - - +
288A GLU* 4.5 2.5 - - - +
289A LYS* 2.7 61.9 + - - +
290A ILE* 3.3 24.6 + - - +
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Residues in contact with ALA 286 (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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258A GLU* 4.6 2.7 - - - +
262A PHE* 3.9 20.9 - - + -
278A SER* 3.3 32.8 - - - +
282A ASP 3.0 12.5 + - - +
283A ILE 3.7 3.1 - - - +
284A TYR 3.4 0.4 - - - -
285A ASN* 1.3 74.8 - - - +
287A CYS* 1.3 54.2 + - - +
290A ILE* 3.0 22.4 + - + +
291A TRP* 2.7 34.9 + - - -
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Residues in contact with CYS 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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278A SER* 5.1 0.4 - - - -
283A ILE* 3.1 32.2 + - - +
284A TYR 4.0 2.0 - - - +
286A ALA* 1.3 80.1 - - - +
288A GLU* 1.3 59.2 + - - +
291A TRP* 3.8 11.1 - - - +
292A GLY* 2.9 26.9 + - - -
310A ILE* 3.9 28.7 - - - -
324A VAL* 4.1 16.2 - - - -
327A ILE* 3.8 21.5 - - + +
328A LEU* 4.0 16.5 - - + +
331A LYS* 4.7 0.5 - - - +
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Residues in contact with GLU 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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284A TYR 3.0 19.2 + - - +
285A ASN* 4.3 1.3 - - - +
287A CYS* 1.3 78.9 - - - +
289A LYS* 1.3 67.8 + - + +
292A GLY* 3.1 23.7 - - - -
293A GLU* 3.7 6.3 - - - +
327A ILE* 3.5 31.3 - - + +
331A LYS* 3.6 26.9 - - + +
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Residues in contact with LYS 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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285A ASN* 2.7 40.3 + - - +
288A GLU* 1.3 87.3 - - + +
290A ILE* 1.3 60.3 - - + +
293A GLU* 3.4 21.4 + - - +
294A ASP* 3.0 32.7 + - - +
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Residues in contact with ILE 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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258A GLU* 3.6 37.5 - - + +
259A LYS* 3.6 35.0 - - + +
262A PHE* 3.6 23.6 - - + -
285A ASN* 3.3 18.4 + - - +
286A ALA* 3.0 20.1 + - - +
289A LYS* 1.3 78.7 - - + +
291A TRP* 1.3 60.4 + - - +
294A ASP* 4.2 8.3 - - + +
295A LEU* 2.7 41.5 + - + +
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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