Contacts of the helix formed by residues 283 - 298 (chain A) in PDB entry 4DTZ
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 ASN 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A PHE* 2.8 29.0 + - - +
280A LEU 3.0 7.0 + - - +
282A LYS* 1.3 92.5 + - - +
284A PRO* 1.3 66.6 - - - +
285A HIS 3.2 2.9 - - - -
286A GLU* 3.0 32.0 + - + +
287A LEU 3.1 9.4 + - - -
374A PHE* 3.6 37.5 - - + +
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Residues in contact with PRO 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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280A LEU 4.1 1.6 - - - +
281A VAL 4.2 8.5 - - - +
282A LYS 3.6 8.1 - - - +
283A ASN* 1.3 88.5 - - - +
285A HIS* 1.3 61.7 + - + +
287A LEU* 3.5 12.2 - - + +
288A GLN* 2.9 30.2 + - - +
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Residues in contact with HIS 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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283A ASN 3.1 0.8 + - - -
284A PRO* 1.3 79.7 - - + +
286A GLU* 1.3 75.6 + - - +
288A GLN* 3.5 11.3 + - - +
289A LYS* 3.0 31.6 + - - +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.9 6.0 - - + +
283A ASN* 3.0 29.1 + - - +
285A HIS* 1.3 89.3 - - - +
287A LEU* 1.3 65.6 + - - +
289A LYS* 3.3 5.4 + - - +
290A ALA* 2.9 25.8 + - - +
313A TYR* 3.4 27.6 - - + +
374A PHE* 4.0 25.1 - - + -
376A PRO* 3.9 18.6 - - + -
377A GLU* 4.5 8.5 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 5.4 1.3 - - + -
280A LEU* 3.5 46.9 - - + +
281A VAL* 4.5 15.5 - - + -
283A ASN 3.1 5.5 + - - -
284A PRO* 3.5 11.9 - - + +
286A GLU* 1.3 76.9 - - - +
288A GLN* 1.4 58.6 + - - +
290A ALA* 3.2 0.9 + - - -
291A ALA* 2.8 32.5 + - + +
418A LEU* 3.2 35.4 - - + -
423A PHE* 4.6 23.1 - - + +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 2.9 17.1 + - - +
285A HIS* 3.8 11.4 + - - +
286A GLU 3.3 0.2 - - - -
287A LEU* 1.4 76.2 - - - +
289A LYS* 1.3 58.6 + - - +
291A ALA* 3.3 6.7 + - + +
292A GLU* 2.8 63.2 + - + +
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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 HIS* 3.0 22.2 + - - +
286A GLU* 3.8 10.1 + - - +
287A LEU 3.2 0.2 - - - -
288A GLN* 1.3 78.1 - - - +
290A ALA* 1.4 61.2 + - - +
292A GLU* 3.3 14.1 + - - +
293A GLU* 3.1 21.7 + - - +
296A ARG* 5.3 1.2 + - - -
313A TYR* 3.4 47.7 + - + -
377A GLU* 3.7 11.8 + - + +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 4.4 5.6 - - + -
286A GLU 2.9 17.4 + - - +
287A LEU 3.8 2.0 - - - +
289A LYS* 1.4 74.8 - - - +
291A ALA* 1.3 58.7 + - - +
293A GLU* 3.3 5.5 + - - +
294A ALA* 2.9 27.0 + - - +
313A TYR* 3.7 20.7 - - + -
314A VAL* 4.3 11.5 - - + +
317A VAL* 4.4 10.3 - - + -
414A LEU* 6.2 0.2 - - + -
418A LEU* 3.4 24.6 - - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 2.8 19.5 + - + +
288A GLN* 3.7 7.4 - - + +
290A ALA* 1.3 76.0 - - - +
292A GLU* 1.3 59.3 - - + +
294A ALA* 3.2 2.8 + - - +
295A ALA* 2.9 30.7 + - - +
418A LEU* 3.9 33.0 - - + +
451A LYS* 5.5 8.5 - - - +
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Residues in contact with GLU 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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288A GLN* 2.8 54.4 + - + +
289A LYS* 3.8 14.2 - - - +
291A ALA* 1.3 70.6 - - + +
293A GLU* 1.3 64.6 + - - +
295A ALA* 3.5 6.1 + - - +
296A ARG* 3.0 41.5 + - - +
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Residues in contact with GLU 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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289A LYS 3.1 12.0 + - - +
290A ALA* 3.6 7.4 - - - +
292A GLU* 1.3 75.9 - - - +
294A ALA* 1.3 64.1 + - - +
296A ARG* 3.1 25.6 + - - +
297A VAL* 2.9 38.1 + - + +
310A GLN 4.1 1.8 - - - +
311A LEU* 3.1 12.4 - - + -
312A LYS* 3.2 15.4 + - - +
313A TYR* 2.7 31.0 + - + +
314A VAL* 2.9 33.4 + - - +
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Residues in contact with ALA 294 (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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290A ALA 2.9 14.0 + - - +
291A ALA 3.2 7.2 + - - +
293A GLU* 1.3 75.8 + - - +
295A ALA* 1.3 56.3 + - - +
298A LEU* 2.9 38.1 + - + +
311A LEU* 4.1 12.3 - - + +
314A VAL* 5.4 0.7 - - + -
415A GLY* 3.5 30.1 - - - +
418A LEU* 4.0 6.1 - - + -
419A LYS* 3.9 15.4 - - - +
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Residues in contact with ALA 295 (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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291A ALA 2.9 19.2 + - - +
292A GLU* 3.8 7.0 - - - +
294A ALA* 1.3 74.8 - - - +
296A ARG* 1.3 60.6 + - - +
297A VAL 3.6 0.2 + - - -
298A LEU 4.3 5.5 + - - +
299A VAL* 4.2 11.3 - - - +
419A LYS* 5.1 11.6 - - - +
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Residues in contact with ARG 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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289A LYS 5.3 1.0 + - - -
292A GLU* 3.0 43.6 + - - +
293A GLU* 3.6 31.0 + - - +
295A ALA* 1.3 76.5 - - - +
297A VAL* 1.3 63.0 + - + +
299A VAL* 3.3 17.8 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 2.9 31.6 + - + +
296A ARG* 1.3 84.5 - - + +
298A LEU* 1.3 61.4 + - + +
299A VAL* 3.0 13.6 + - - +
307A GLN* 3.3 45.5 + - - +
310A GLN* 3.7 35.2 - - + +
311A LEU* 3.6 13.2 - - + -
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Residues in contact with LEU 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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294A ALA* 2.9 25.1 + - + +
295A ALA* 4.5 4.5 - - - +
297A VAL* 1.3 73.2 - - + +
299A VAL* 1.3 59.8 + - - +
300A ASP 3.3 3.8 - - - +
303A PRO* 3.8 33.4 - - + -
307A GLN* 4.0 22.9 - - + +
308A VAL* 4.9 0.9 - - + +
311A LEU* 4.2 19.1 - - + -
412A LEU* 5.2 0.9 - - + +
415A GLY* 3.5 40.2 - - - +
416A MET* 4.0 6.3 - - + +
419A LYS* 2.8 40.0 + - + +
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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