Contacts of the helix formed by residues 276 - 284 (chain A) in PDB entry 3DL2
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 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 4.0 4.3 - - + -
215A LEU* 3.7 33.2 - - + -
240A LEU* 3.8 27.8 - - + -
251A PHE* 4.6 4.5 - - + -
253A VAL* 3.9 25.1 - - + -
272A MET* 3.5 23.8 - - + +
273A PHE* 3.0 6.0 + - + +
274A ARG 3.3 1.0 - - - -
275A ALA* 1.3 82.7 - - - +
277A VAL* 1.3 69.2 + - + +
278A PRO* 3.3 2.9 - - - -
279A ALA* 3.1 6.9 + - - +
280A LEU* 3.1 39.0 + - + +
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Residues in contact with VAL 277 (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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251A PHE* 3.7 23.3 - - + -
273A PHE* 2.8 51.5 + - + +
276A LEU* 1.3 73.5 - - - +
278A PRO* 1.4 60.3 - - + +
280A LEU* 3.8 0.7 - - - +
281A GLY* 2.8 28.6 + - - -
289A LEU* 4.5 3.4 - - + -
303A THR* 3.5 40.2 - - + +
306A LEU* 3.8 11.4 - - + -
307A SER* 3.8 15.1 - - - -
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Residues in contact with PRO 278 (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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273A PHE 3.7 1.6 - - - +
274A ARG 3.4 25.4 - - - +
275A ALA 4.5 0.7 - - - -
276A LEU 3.4 5.2 - - - +
277A VAL* 1.4 94.3 - - + +
279A ALA* 1.3 56.6 + - - +
281A GLY* 4.0 0.7 - - - -
282A HIS* 3.1 26.5 + - - +
306A LEU* 3.8 32.8 - - + +
307A SER* 5.0 2.0 - - - -
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Residues in contact with ALA 279 (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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240A LEU* 3.7 24.5 - - + -
275A ALA 5.0 4.3 - - - +
276A LEU 3.1 10.1 + - - +
278A PRO* 1.3 78.4 - - - +
280A LEU* 1.3 60.4 + - - +
282A HIS* 3.3 7.4 + - - +
283A TYR* 3.0 45.2 + - + -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 3.6 21.8 - - + -
213A LEU* 3.6 19.7 - - + -
240A LEU* 4.1 15.5 - - + +
243A SER* 3.3 25.4 + - - +
249A VAL* 4.2 12.3 - - + +
251A PHE* 3.4 37.5 - - + -
276A LEU* 3.1 32.7 + - + +
277A VAL 4.0 2.9 - - - +
279A ALA* 1.3 76.1 - - - +
281A GLY* 1.3 57.6 + - - +
283A TYR* 3.3 4.0 + - - +
284A SER* 3.1 31.5 + - - +
289A LEU* 5.6 1.8 - - + -
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Residues in contact with GLY 281 (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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251A PHE* 6.0 0.2 - - - -
277A VAL 2.8 16.5 + - - -
278A PRO 4.0 1.3 - - - -
280A LEU* 1.3 73.0 - - - +
282A HIS* 1.3 63.2 + - - +
285A GLN* 3.3 29.3 + - - +
289A LEU* 5.2 4.8 - - - +
307A SER* 4.9 9.0 - - - -
309A PHE* 3.7 28.0 - - - -
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Residues in contact with HIS 282 (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 PRO 3.1 16.0 + - - +
279A ALA* 3.3 11.9 + - - +
281A GLY* 1.3 75.8 - - - +
283A TYR* 1.3 81.9 + + - +
285A GLN* 2.9 48.1 + - - +
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Residues in contact with TYR 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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240A LEU* 4.1 14.1 - - + -
241A SER* 3.5 42.5 - - - -
243A SER* 4.0 15.0 - - - +
244A ALA* 3.3 19.5 - - + +
245A HIS* 3.0 25.5 + - - -
279A ALA* 3.0 35.2 + - + +
280A LEU 3.3 4.0 + - - +
281A GLY 3.3 0.2 - - - -
282A HIS* 1.3 96.9 - + - +
284A SER* 1.3 58.2 + - - +
285A GLN 3.8 0.9 - - - -
502A PO4 4.7 1.6 + - - -
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Residues in contact with SER 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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243A SER* 2.8 27.5 + - - -
245A HIS* 3.2 6.3 + - - +
246A SER* 2.9 24.9 + - - +
249A VAL* 4.2 5.0 - - - +
280A LEU 3.1 12.1 + - - +
281A GLY 3.4 3.1 - - - +
283A TYR* 1.3 74.0 - - - +
285A GLN* 1.3 62.1 + - - +
286A HIS 3.1 3.4 + - - -
287A SER* 2.7 41.8 + - - -
309A PHE* 3.3 6.6 - - - -
502A PO4 4.6 2.0 - - - -
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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