Contacts of the helix formed by residues 282 - 289 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A VAL* 3.8 26.7 - - + +
258B GLU* 5.0 4.1 + - - +
278B SER 4.1 2.6 + - - -
281B TYR* 1.3 84.2 - - + +
283B ILE* 1.3 63.6 + - - +
284B TYR* 3.1 13.3 + - - +
285B ASN* 3.1 36.3 + - + +
286B ALA* 3.0 21.3 + - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A VAL* 4.4 7.0 - - + +
419A ALA* 5.8 2.2 - - + -
278B SER* 3.3 40.3 + - - +
279B ASP* 3.8 17.6 + - + +
282B ASP* 1.3 73.4 + - - +
284B TYR* 1.3 91.5 + - + +
286B ALA* 3.3 0.5 + - - +
287B CYS* 3.1 38.4 + - - -
310B ILE* 4.4 1.8 - - + -
312B PRO* 4.0 25.4 - - + -
314B SER* 5.5 4.7 - - - +
320B THR* 4.5 5.6 - - + -
324B VAL* 3.7 22.2 - - + -
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A VAL* 4.1 15.0 - - + -
419A ALA* 4.6 13.6 - - + +
282B ASP* 3.1 11.5 + - - +
283B ILE* 1.3 99.5 - - + +
285B ASN* 1.3 58.5 + - - +
287B CYS* 3.5 1.1 + - - -
288B GLU* 2.9 32.7 + - - +
319B ASP* 5.0 1.0 + - - +
320B THR* 3.4 37.2 + - + +
323B LYS* 3.5 51.7 - - + +
324B VAL* 4.6 3.8 - - + -
327B ILE* 3.8 25.7 - - + +
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B GLU* 5.0 3.4 + - - -
282B ASP* 3.1 33.9 + - + +
284B TYR* 1.3 74.9 - - - +
286B ALA* 1.3 59.3 + - - +
288B GLU* 4.9 1.1 - - - -
289B LYS* 2.9 53.1 + - - +
290B ILE* 3.4 24.1 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B GLU* 4.5 5.2 - - - +
262B PHE* 3.8 24.5 - - + -
278B SER* 3.4 30.5 - - - +
282B ASP 3.0 11.5 + - - +
283B ILE 3.3 2.6 + - - +
285B ASN* 1.3 76.7 - - - +
287B CYS* 1.3 56.2 + - - +
290B ILE* 3.3 15.7 + - + +
291B TRP* 2.7 37.3 + - - -
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Residues in contact with CYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B SER* 5.1 0.2 - - - -
283B ILE* 3.1 31.6 + - - +
284B TYR 3.9 1.3 - - - +
286B ALA* 1.3 79.7 - - - +
288B GLU* 1.3 57.6 + - - +
291B TRP* 3.8 10.4 - - - +
292B GLY* 2.9 26.2 + - - -
310B ILE* 3.8 33.0 - - - -
324B VAL* 4.1 19.7 - - - -
327B ILE* 3.7 22.8 - - + +
328B LEU* 4.0 13.2 - - + +
331B LYS* 4.7 0.9 - - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B TYR 2.9 18.5 + - - +
285B ASN* 4.5 1.1 - - - +
287B CYS* 1.3 77.4 - - - +
289B LYS* 1.3 68.6 + - + +
292B GLY* 3.3 18.9 - - - -
293B GLU* 3.5 4.8 - - - +
327B ILE* 3.6 30.5 - - + +
330B LYS* 6.0 1.7 - - - +
331B LYS* 3.5 31.1 - - + -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ASN* 2.9 35.4 + - - +
288B GLU* 1.3 86.1 - - + +
290B ILE* 1.3 64.8 + - + +
293B GLU* 3.1 35.6 + - - +
294B ASP* 2.8 34.8 + - - +
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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