Contacts of the helix formed by residues 288 - 301 (chain D) in PDB entry 4PS1
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 THR 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D LYS* 5.8 2.9 - - + -
287D CYS* 1.3 74.9 - - - +
289D VAL* 1.3 66.2 + - - +
290D GLU* 3.5 7.9 + - - +
291D GLN* 3.0 46.9 + - - +
292D ILE* 2.9 21.4 + - - +
325D GLY* 4.0 2.2 - - - -
326D THR* 3.3 13.4 + - - +
327D ASP* 3.4 34.5 - - + +
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Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D THR* 1.3 73.8 - - - +
290D GLU* 1.3 64.1 + - - +
292D ILE* 3.0 9.6 + - + +
293D TYR* 3.0 49.8 + - + -
325D GLY* 3.4 13.6 - - - +
327D ASP* 3.2 4.2 + - - +
329D GLN* 3.1 48.7 - - + +
330D GLU 3.8 17.5 - - - +
331D ALA* 4.1 10.1 - - + +
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Residues in contact with GLU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D THR* 3.3 8.1 + - - +
289D VAL* 1.3 79.5 - - - +
291D GLN* 1.3 59.1 + - + +
293D TYR* 3.3 8.7 + - - +
294D GLU* 3.0 47.8 + - + +
327D ASP* 5.0 2.5 + - - +
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Residues in contact with GLN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ASP 3.7 7.3 - - - +
287D CYS* 3.4 16.0 - - + -
288D THR* 3.0 46.2 + - - +
290D GLU* 1.3 76.7 - - + +
292D ILE* 1.3 59.2 + - - +
294D GLU* 3.3 18.4 + - - +
295D ILE* 2.9 39.5 + - + +
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ILE* 4.0 32.8 - - + -
241D ASN* 4.3 6.5 - - - +
287D CYS* 3.7 25.1 - - + +
288D THR 2.9 20.7 + - - +
289D VAL* 3.0 11.4 + - + +
291D GLN* 1.3 74.9 - - - +
293D TYR* 1.3 65.4 + - + +
295D ILE* 3.3 8.3 + - - +
296D LEU* 3.0 28.0 + - + +
314D ILE* 5.3 0.9 - - + -
323D ILE* 3.6 27.1 - - + -
325D GLY* 4.4 3.1 - - - -
331D ALA* 5.4 2.0 - - + -
336D LEU* 4.0 29.8 - - + -
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Residues in contact with TYR 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D VAL* 3.0 40.8 + - + -
290D GLU* 3.7 9.4 - - - +
292D ILE* 1.3 75.9 - - + +
294D GLU* 1.3 58.3 + - + +
296D LEU* 3.9 5.9 - - + +
297D LYS* 2.9 30.5 + - - +
330D GLU 4.7 0.8 + - - -
331D ALA* 3.8 8.4 - - + +
332D PRO* 3.5 27.2 - - - +
335D GLU* 3.6 25.6 - - + +
336D LEU* 3.5 25.6 - - + -
339D GLN* 5.4 7.9 - - + -
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D GLU* 3.0 39.2 + - + +
291D GLN* 3.5 24.0 - - - +
292D ILE 3.2 0.2 - - - -
293D TYR* 1.3 77.9 - - + +
295D ILE* 1.3 63.2 + - + +
297D LYS* 3.4 6.1 + - - +
298D ILE* 3.0 32.4 + - + +
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Residues in contact with ILE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 3.8 25.1 - - + -
239D ILE* 4.9 8.3 - - + -
284D HIS* 3.5 46.9 - - + +
287D CYS* 3.7 26.5 - - - -
291D GLN* 2.9 20.9 + - + +
292D ILE* 3.7 7.0 - - - +
294D GLU* 1.3 73.9 - - + +
296D LEU* 1.3 69.6 + - + +
298D ILE* 3.2 12.0 + - + +
299D TYR* 3.1 28.5 + - + -
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D LEU* 3.8 25.8 - - + -
239D ILE* 4.4 7.0 - - + -
292D ILE* 3.0 25.7 + - + +
293D TYR* 4.1 5.6 - - + +
295D ILE* 1.3 76.5 - - - +
297D LYS* 1.3 57.0 + - - +
299D TYR* 3.3 1.8 + - - -
300D GLN* 2.8 30.9 + - - +
312D CYS* 4.2 16.2 - - + -
314D ILE* 5.6 0.9 - - + -
336D LEU* 3.6 53.4 - - + +
339D GLN* 4.7 11.2 - - + -
340D PHE* 3.5 25.0 - - + -
355D PHE* 5.2 1.8 - - + -
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Residues in contact with LYS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D TYR 2.9 18.2 + - - +
294D GLU* 3.7 6.7 - - - +
295D ILE 3.2 0.2 - - - -
296D LEU* 1.3 75.3 - - - +
298D ILE* 1.3 66.7 + - + +
300D GLN* 3.2 14.9 + - - +
301D LEU* 3.1 48.7 + - + +
339D GLN* 5.8 1.3 - - - +
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D HIS* 6.4 1.6 - - + -
294D GLU* 3.0 26.5 + - + +
295D ILE* 3.4 13.5 - - + +
297D LYS* 1.3 77.2 - - + +
299D TYR* 1.3 69.1 + - + +
301D LEU* 3.4 5.4 + - - +
302D MET* 3.2 43.1 + - + +
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Residues in contact with TYR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TYR* 3.8 33.4 - + - -
237D LEU* 3.5 37.0 - - + -
282D LYS* 3.2 31.9 + - + +
284D HIS* 4.4 9.6 + + - -
295D ILE* 3.1 30.4 + - + +
296D LEU 4.0 2.7 - - - +
298D ILE* 1.3 84.7 - - + +
300D GLN* 1.3 64.8 + - - +
301D LEU 3.2 2.0 + - - -
302D MET* 3.4 26.3 + - + +
304D HIS* 2.8 29.6 + + - -
310D PHE* 4.2 11.7 - + + -
340D PHE* 3.7 16.6 - - + -
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Residues in contact with GLN 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU 2.8 21.0 + - - +
297D LYS* 3.2 15.9 + - - +
299D TYR* 1.3 73.8 - - - +
301D LEU* 1.3 87.4 + - - +
302D MET 3.6 1.2 + - - +
339D GLN* 3.1 39.0 - - + +
340D PHE* 3.6 11.8 - - + -
344D LYS* 2.9 39.3 + - - +
345D CYS* 3.5 19.9 - - + -
346D PRO* 5.6 0.3 - - - +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D LYS* 3.1 47.3 + - + +
298D ILE* 3.8 5.6 - - - +
300D GLN* 1.3 101.0 - - - +
302D MET* 1.3 63.9 + - - +
303D ASP 3.9 0.2 + - - -
344D LYS 5.4 0.2 - - - +
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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