Contacts of the helix formed by residues 351 - 369 (chain B) in PDB entry 1E9H
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 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 6.1 1.8 - - - +
190B GLU* 3.5 47.8 - - + +
191B VAL* 3.6 25.1 - - + -
194B LYS* 3.5 29.2 - - + -
350B TYR* 1.3 76.6 - - - +
352B PRO* 1.3 71.7 - - + +
353B SER* 3.2 4.0 - - - +
354B VAL* 2.9 23.7 + - + +
355B ILE* 3.1 11.0 + - - +
382B TYR* 5.2 4.3 - - - +
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Residues in contact with PRO 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU* 2.9 31.4 - - + +
194B LYS* 5.4 3.4 - - + -
309B PRO 4.4 11.0 - - - +
310B THR* 3.8 5.2 - - - +
311B VAL* 3.6 42.0 - - + +
314B PHE* 4.0 4.9 - - + -
350B TYR 3.8 3.6 - - - +
351B LEU* 1.3 89.8 - - + +
353B SER* 1.3 58.8 + - - -
355B ILE* 3.5 4.2 + - + -
356B ALA* 3.0 24.9 + - - +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 4.2 4.0 - - - -
190B GLU* 2.4 39.4 + - - -
314B PHE* 3.5 35.4 - - - -
318B TYR* 3.2 21.6 + - - -
351B LEU* 4.2 0.5 - - - +
352B PRO* 1.3 73.6 - - - +
354B VAL* 1.3 59.7 + - - +
356B ALA* 3.5 1.6 - - - +
357B GLY 3.2 16.8 + - - -
382B TYR* 2.8 26.3 + - - -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 4.3 11.9 - - + -
351B LEU* 2.9 22.5 + - + +
353B SER* 1.3 75.4 + - - +
355B ILE* 1.3 67.8 + - - +
356B ALA 3.0 0.9 - - - -
357B GLY* 3.0 11.5 + - - +
358B ALA* 3.0 11.6 + - - +
382B TYR* 3.6 35.4 - - + +
386B SER 5.1 6.7 - - - +
387B LEU* 3.7 14.7 - - + +
390B CYS* 4.0 23.1 - - + -
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B VAL* 4.1 24.2 - - + -
337B GLY* 4.6 7.2 - - - -
340B SER* 3.8 32.8 - - - +
347B TYR* 3.9 29.4 - - + +
350B TYR* 3.7 26.2 - - + +
351B LEU 3.1 7.0 + - - +
352B PRO* 3.9 7.2 - - + +
354B VAL* 1.3 74.8 - - - +
356B ALA* 1.3 57.6 + - - +
358B ALA* 3.3 2.3 + - - +
359B ALA* 2.8 28.6 + - + +
390B CYS* 3.9 15.9 - - - -
394B LEU* 4.3 9.8 - - + +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B VAL* 3.9 20.8 - - + +
314B PHE* 3.6 23.6 - - + -
315B LEU* 3.3 18.7 - - + +
318B TYR* 3.7 7.4 - - + -
352B PRO 3.0 18.9 + - - +
353B SER 3.5 7.0 - - - +
354B VAL 3.0 0.2 - - - -
355B ILE* 1.3 77.9 - - - +
357B GLY* 1.3 56.5 + - - +
359B ALA* 4.5 0.7 - - - -
360B PHE* 3.0 26.0 + - - +
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Residues in contact with GLY 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TYR* 3.5 2.0 - - - -
353B SER 3.2 6.1 + - - -
354B VAL 3.0 7.5 + - - -
356B ALA* 1.3 75.8 - - - +
358B ALA* 1.3 66.3 + - - +
360B PHE 3.3 0.3 + - - -
361B HIS* 3.0 23.4 + - - +
372B TRP* 3.5 35.5 - - - -
382B TYR* 5.7 0.7 - - - -
387B LEU* 3.9 12.3 - - - +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B VAL 3.0 11.8 + - - +
355B ILE 3.7 7.2 - - - +
357B GLY* 1.3 76.4 - - - +
359B ALA* 1.3 57.8 + - - +
361B HIS 3.3 0.2 + - - -
362B LEU* 2.9 26.9 + - - +
387B LEU* 4.0 3.4 - - + +
390B CYS* 3.8 23.1 - - + -
391B LEU* 3.3 43.2 - - + +
394B LEU* 3.8 9.6 - - + -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.4 4.3 - - + -
333B ALA* 3.7 22.2 - - - +
336B LEU* 3.5 14.1 - - + +
337B GLY* 4.0 9.6 - - - +
355B ILE 2.8 18.6 + - - +
356B ALA* 3.9 4.0 - - - +
358B ALA* 1.3 77.2 - - - +
360B PHE* 1.3 56.8 + - - +
363B ALA* 2.8 30.7 + - - +
394B LEU* 3.4 19.2 - - + +
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Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.1 6.5 - - + +
318B TYR* 3.6 29.6 - - + -
319B PHE* 3.6 33.4 - + - -
321B HIS 5.2 0.2 - - - -
322B GLN* 4.3 20.4 - - + -
329B VAL* 3.7 23.3 - - + -
333B ALA* 4.1 5.6 - - + -
356B ALA 3.0 18.3 + - - +
357B GLY 3.8 2.9 - - - +
358B ALA 3.3 0.2 - - - -
359B ALA* 1.3 74.4 - - - +
361B HIS* 1.3 60.8 + - - +
363B ALA* 3.5 0.3 - - - +
364B LEU* 2.8 44.9 + - + +
372B TRP* 3.7 24.2 - + + -
373B PRO* 4.1 15.3 - - + -
376B LEU* 3.7 13.9 - - + -
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLY 3.0 17.4 + - - +
358B ALA* 3.8 3.4 - - - +
360B PHE* 1.3 78.9 - - - +
362B LEU* 1.3 58.9 + - - +
364B LEU* 3.3 5.1 + - - +
365B TYR* 2.7 48.4 + + + +
370B GLN 4.4 2.5 - - - -
371B SER* 3.3 33.5 - - - -
372B TRP* 2.9 34.6 + - + +
384B LEU* 3.4 28.2 - - + +
387B LEU* 5.2 1.3 - - + -
391B LEU* 4.1 20.6 - - + -
430B LEU* 5.3 6.4 + - + +
432B LEU* 4.6 9.2 - - + +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 4.4 0.9 - - - +
336B LEU* 3.8 21.8 - - + -
358B ALA 2.9 17.1 + - - +
361B HIS* 1.3 78.2 - - - +
363B ALA* 1.3 63.5 + - - +
365B TYR* 4.5 2.2 - - + -
366B THR* 2.6 41.3 + - - +
391B LEU* 4.1 7.9 - - + -
394B LEU* 4.0 14.6 - - + +
395B HIS* 3.7 39.7 - - + +
398B TYR* 4.2 13.0 - - + -
427B PRO* 4.8 2.0 - - + -
430B LEU* 3.4 34.5 - - + -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 3.5 15.9 - - + +
332B LEU* 3.7 15.5 - - + +
333B ALA* 3.4 31.4 - - + +
336B LEU* 4.0 0.6 - - - +
359B ALA 2.8 20.2 + - - +
360B PHE 3.5 4.0 - - - +
361B HIS 3.2 0.2 - - - -
362B LEU* 1.3 79.4 - - - +
364B LEU* 1.3 64.1 + - - +
366B THR* 3.5 1.9 - - - -
367B VAL* 3.0 27.1 + - - +
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Residues in contact with LEU 364 (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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322B GLN* 4.0 14.1 - - + +
329B VAL* 3.9 23.7 - - + +
360B PHE* 2.8 42.0 + - + +
361B HIS* 3.5 4.3 - - - +
363B ALA* 1.3 76.5 - - - +
365B TYR* 1.3 55.9 + - - +
367B VAL* 4.0 0.2 - - - +
368B THR* 2.8 41.9 + - - +
370B GLN* 3.2 42.6 - - + +
371B SER 4.1 22.9 - - - +
372B TRP* 4.6 0.7 - - - +
373B PRO* 4.2 7.6 - - + -
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Residues in contact with TYR 365 (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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361B HIS* 2.7 33.9 + + + +
362B LEU* 4.2 3.1 - - + +
364B LEU* 1.3 73.2 - - - +
366B THR* 1.3 62.2 + - - +
369B GLY* 2.8 48.6 + - - +
370B GLN 3.0 16.3 + - - +
371B SER* 4.5 7.9 - - - -
427B PRO* 4.1 14.6 - - + -
429B THR 3.6 21.3 + - - -
430B LEU* 3.8 32.8 - - + -
431B ASN* 3.2 26.4 + - + -
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Residues in contact with THR 366 (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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332B LEU* 3.9 17.7 - - + -
362B LEU* 2.6 28.3 + - - +
363B ALA 3.5 3.6 - - - -
365B TYR* 1.3 80.6 - - - +
367B VAL* 1.3 63.1 + - + +
369B GLY 4.8 0.2 + - - -
398B TYR* 4.2 9.6 - - - +
424B LEU* 5.1 6.5 - - + -
425B ASN 3.8 15.3 - - - +
427B PRO* 3.2 40.2 - - + +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 4.0 12.1 - - - +
328B LYS* 4.0 33.4 - - + +
329B VAL* 3.8 21.1 - - + -
332B LEU* 4.0 17.9 - - + -
363B ALA 3.0 15.4 + - - +
366B THR* 1.3 80.0 - - - +
368B THR* 1.3 65.3 + - + +
424B LEU* 4.0 20.0 - - + -
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 3.9 19.3 - - + +
329B VAL* 4.2 7.4 - - + -
364B LEU* 2.8 23.3 + - + +
367B VAL* 1.3 89.5 - - + +
369B GLY* 1.3 58.1 + - - +
370B GLN* 2.6 42.1 + - - +
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU 3.4 0.4 + - - -
365B TYR* 2.8 37.5 + - - -
366B THR 4.8 0.2 + - - -
367B VAL 3.8 0.2 - - - -
368B THR* 1.3 78.3 + - - +
370B GLN* 1.3 64.8 + - - +
371B SER* 4.4 2.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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