Contacts of the helix formed by residues 317 - 328 (chain D) in PDB entry 4H3H
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 PHE 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271D MET* 3.6 32.3 - - + -
272D SER* 3.7 37.5 - - - -
275D ILE* 4.1 23.8 - - + -
313D ALA 3.9 8.5 - - - -
314D SER 2.9 8.4 + - - +
316D GLU* 1.3 114.5 - - + +
318D GLN* 1.3 65.4 + - - +
319D ALA 3.2 3.1 - - - -
320D GLN* 3.1 29.0 + - - +
321D ILE* 3.0 25.3 + - + +
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Residues in contact with GLN 318 (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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287A PRO* 4.5 10.8 - - + +
309D LEU* 4.1 18.1 - - + +
314D SER* 3.0 8.7 + - - +
315D LEU* 3.0 35.6 + - + +
316D GLU 3.5 1.0 - - - -
317D PHE* 1.3 75.9 - - - +
319D ALA* 1.3 57.2 + - - +
321D ILE* 3.5 5.1 + - - +
322D THR* 2.8 38.5 + - - +
339D MET* 4.0 28.6 - - + +
340D PRO* 4.7 11.3 - - - +
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Residues in contact with ALA 319 (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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287A PRO 3.6 11.4 + - - +
288A THR 4.1 2.0 - - - +
289A LEU 3.4 33.9 - - - +
290A ALA* 3.8 13.0 - - + +
291A LYS* 5.0 2.7 - - + +
317D PHE 3.2 1.0 - - - -
318D GLN* 1.3 76.2 - - - +
320D GLN* 1.3 66.6 + - - +
322D THR* 3.8 0.5 - - - +
323D THR* 2.6 38.1 + - - -
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Residues in contact with GLN 320 (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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275D ILE* 3.8 18.1 - - + +
279D GLU* 3.5 29.2 + - - +
316D GLU 4.1 5.1 + - - +
317D PHE* 3.1 41.4 + - - +
319D ALA* 1.3 85.5 + - + +
321D ILE* 1.3 62.7 + - - +
323D THR* 3.6 5.8 - - - -
324D LEU* 3.1 27.2 + - - +
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Residues in contact with ILE 321 (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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275D ILE* 3.7 34.3 - - + -
305D LEU* 4.0 28.6 - - + +
308D VAL* 4.2 8.1 - - + -
309D LEU* 3.9 18.6 - - + -
314D SER* 3.7 29.6 - - - +
317D PHE* 3.0 23.6 + - + +
318D GLN 3.9 2.9 - - - +
320D GLN* 1.3 80.5 - - - +
322D THR* 1.3 59.1 + - - +
324D LEU* 3.1 7.0 + - - +
325D LEU* 2.9 44.6 + - + +
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Residues in contact with THR 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 3.0 58.8 - - + +
288A THR* 3.0 7.9 - - + +
309D LEU* 4.5 9.2 - - - +
318D GLN* 2.8 16.6 + - - +
319D ALA 3.8 0.7 - - - +
321D ILE* 1.3 76.4 - - - +
323D THR* 1.3 67.9 + - - +
325D LEU* 3.3 7.3 + - - +
326D VAL* 3.0 29.8 + - - +
335D ILE* 3.6 19.9 - - - +
339D MET* 4.8 2.4 - - - +
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Residues in contact with THR 323 (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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288A THR* 3.3 33.1 + - + -
319D ALA 2.6 25.8 + - - -
320D GLN* 3.6 7.4 - - - +
322D THR* 1.3 77.6 - - - +
324D LEU* 1.3 66.2 + - + +
326D VAL* 3.4 2.3 + - - +
327D ASP* 3.1 25.3 + - + +
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Residues in contact with LEU 324 (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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275D ILE* 4.9 2.2 - - + +
278D TYR* 4.0 21.5 - - + +
279D GLU* 4.1 24.5 - - + +
282D HIS* 3.4 38.3 - - + +
301D LEU* 5.5 0.9 - - + -
305D LEU* 3.7 32.1 - - + -
320D GLN 3.1 15.3 + - - +
321D ILE* 3.1 9.5 + - - +
323D THR* 1.3 82.3 - - + +
325D LEU* 1.3 62.1 + - - +
327D ASP* 3.2 5.3 + - + +
328D LEU* 2.9 31.1 + - + +
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Residues in contact with LEU 325 (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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302D LYS* 3.6 18.6 - - - +
305D LEU* 3.5 30.3 - - + -
306D LEU* 3.9 26.5 - - + -
309D LEU* 4.0 14.4 - - + -
321D ILE* 2.9 34.5 + - + +
322D THR* 3.3 10.3 + - - +
324D LEU* 1.3 75.9 - - - +
326D VAL* 1.3 62.0 + - - +
328D LEU* 3.2 8.4 + - - +
330D THR* 2.7 40.9 + - - +
335D ILE* 4.0 15.9 - - + -
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Residues in contact with VAL 326 (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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245A HIS* 5.9 0.9 - - - +
246A PRO* 4.1 23.1 - - + +
247A ALA* 3.9 33.4 - - + +
287A PRO* 4.9 4.7 - - + -
288A THR* 3.8 16.6 - - + -
322D THR 3.0 20.9 + - - +
323D THR 3.9 4.3 - - - +
325D LEU* 1.3 74.6 - - - +
327D ASP* 1.3 58.0 + - - +
329D GLY* 3.0 18.9 + - - +
330D THR 4.6 7.4 - - - +
335D ILE* 3.8 18.6 - - + -
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Residues in contact with ASP 327 (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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282D HIS* 2.6 36.3 + - + -
323D THR* 3.1 19.3 + - + +
324D LEU* 3.6 5.6 - - + +
326D VAL* 1.3 77.6 - - - +
328D LEU* 1.3 57.9 + - - +
329D GLY 3.3 3.8 + - - -
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D HIS* 4.2 19.7 - - + +
298D ARG* 3.9 41.3 - - + +
301D LEU* 4.0 16.2 - - + -
302D LYS* 4.1 24.5 - - + +
305D LEU* 3.8 25.8 - - + -
324D LEU* 2.9 22.4 + - + +
325D LEU* 3.2 7.4 + - - +
327D ASP* 1.3 75.9 - - - +
329D GLY* 1.3 60.1 + - - +
330D THR* 3.3 6.1 + - - +
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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