Contacts of the helix formed by residues 351 - 369 (chain D) in PDB entry 1H26
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D ARG* 6.1 0.9 - - - +
190D GLU* 3.4 52.5 - - + +
191D VAL* 4.1 18.6 - - + -
194D LYS* 3.7 28.0 - - + +
349D LYS 4.4 0.2 + - - -
350D TYR* 1.3 75.7 - - - +
352D PRO* 1.3 77.8 - - + +
353D SER* 4.0 5.8 - - - +
354D VAL* 3.0 21.9 + - + +
355D ILE* 3.1 11.7 + - - +
382D TYR* 5.0 5.8 - - - +
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Residues in contact with PRO 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLU* 2.7 26.2 - - + +
194D LYS* 5.9 2.0 - - + -
237D ASN* 6.4 0.4 - - - +
309D PRO 4.1 15.9 - - - +
310D THR* 3.7 6.7 - - - +
311D VAL* 3.5 38.9 - - + +
314D PHE* 4.1 4.5 - - + -
350D TYR 3.8 2.7 - - - +
351D LEU* 1.3 92.8 - - + +
353D SER* 1.3 55.1 + - - +
355D ILE* 4.6 2.5 - - + -
356D ALA* 2.8 29.1 + - - +
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Residues in contact with SER 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ARG* 4.1 2.9 - - - -
190D GLU* 2.6 32.7 + - - -
314D PHE* 3.6 24.7 - - - -
318D TYR* 2.8 30.1 + - - -
351D LEU* 4.0 3.5 - - - +
352D PRO* 1.3 75.0 - - - +
354D VAL* 1.3 64.0 + - - +
356D ALA* 3.7 2.2 - - - -
357D GLY* 3.4 11.6 + - - -
382D TYR* 2.9 27.9 + - - -
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 4.3 13.0 - - + -
351D LEU* 3.0 19.7 + - + +
353D SER* 1.3 78.0 + - - +
355D ILE* 1.3 72.6 + - - +
356D ALA 3.0 0.4 - - - -
357D GLY* 2.7 12.1 + - - -
358D ALA* 2.9 9.5 + - - +
382D TYR* 3.5 34.5 - - + +
386D SER 5.7 2.9 - - - +
387D LEU* 4.1 17.8 - - + +
390D CYS* 3.7 26.2 - - + -
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Residues in contact with ILE 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D VAL* 3.8 23.1 - - + -
337D GLY* 4.4 11.7 - - - -
340D SER* 3.6 30.1 - - - +
347D TYR* 3.9 34.3 - - + +
350D TYR* 4.0 15.7 - - + +
351D LEU 3.1 9.0 + - - +
352D PRO* 4.0 1.8 - - + +
354D VAL* 1.3 76.0 - - - +
356D ALA* 1.3 70.2 + - - +
357D GLY 2.6 1.6 + - - -
358D ALA 2.8 9.4 + - - -
359D ALA* 2.9 11.4 + - + -
390D CYS* 3.6 23.6 - - - -
394D LEU* 5.0 8.7 - - + -
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Residues in contact with ALA 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D VAL* 3.8 20.6 - - - +
314D PHE* 3.7 15.5 - - + -
315D LEU* 3.3 16.5 - - + +
318D TYR* 3.5 20.5 - - + -
352D PRO 2.8 21.6 + - - +
353D SER 3.8 1.1 - - - +
354D VAL 3.0 0.6 + - - -
355D ILE* 1.3 80.5 - - - +
357D GLY* 1.3 55.9 + - - +
359D ALA* 3.6 1.3 + - - +
360D PHE* 3.0 27.9 + - - +
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Residues in contact with GLY 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D TYR* 3.6 6.2 - - - -
353D SER 3.4 6.4 + - - -
354D VAL 2.7 10.0 + - - -
355D ILE 2.6 3.4 + - - -
356D ALA* 1.3 69.8 - - - +
358D ALA* 1.3 66.6 + - - -
360D PHE 2.7 1.2 + - - -
361D HIS* 2.6 25.3 + - - +
372D TRP* 3.7 25.0 - - - -
382D TYR* 6.1 0.2 - - - -
387D LEU* 4.0 14.1 - - - -
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Residues in contact with ALA 358 (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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354D VAL 2.9 5.2 + - - +
355D ILE 2.8 10.8 + - - +
357D GLY* 1.3 73.5 - - - +
359D ALA* 1.3 66.6 + - - +
360D PHE 2.7 0.2 + - - -
361D HIS* 4.5 2.2 - - - -
362D LEU* 2.7 22.4 + - - +
387D LEU* 4.2 6.9 - - + +
390D CYS* 3.6 28.5 - - + -
391D LEU* 3.9 30.1 - - + +
394D LEU* 3.7 12.8 - - + -
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Residues in contact with ALA 359 (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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315D LEU* 4.7 2.5 - - + -
333D ALA* 3.7 15.9 - - + +
336D LEU* 3.2 37.0 - - + +
337D GLY* 3.8 11.4 - - - +
355D ILE* 2.9 16.4 + - + +
356D ALA* 4.1 4.0 - - - +
358D ALA* 1.3 75.1 - - - +
360D PHE* 1.3 56.5 + - - +
362D LEU* 4.3 0.2 - - - -
363D ALA* 3.0 25.1 + - - +
394D LEU* 3.5 14.7 - - + +
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Residues in contact with PHE 360 (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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315D LEU* 4.2 3.6 - - + -
318D TYR* 3.7 26.7 - - + -
319D PHE* 3.5 37.7 - + - -
321D HIS* 4.9 1.3 - - + -
322D GLN* 4.3 18.4 - - + -
329D VAL* 4.4 17.0 - - + -
333D ALA* 4.2 4.7 - - + -
356D ALA 3.0 19.6 + - - +
357D GLY* 2.7 6.1 + - - +
358D ALA 2.7 1.0 + - - -
359D ALA* 1.3 74.2 - - - +
361D HIS* 1.3 71.7 + - - +
363D ALA* 3.0 4.2 + - - +
364D LEU* 2.8 29.6 + - + +
372D TRP* 3.6 11.0 - + - -
373D PRO* 4.5 11.2 - - + -
376D LEU* 3.2 35.9 - - + -
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Residues in contact with HIS 361 (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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357D GLY 2.6 19.2 + - - +
358D ALA 3.6 1.8 - - - +
360D PHE* 1.3 80.2 - - - +
362D LEU* 1.3 83.3 + - + +
364D LEU* 2.6 15.5 + - - +
365D TYR* 3.1 25.8 + + + +
371D SER* 3.1 29.7 - - - -
372D TRP* 3.4 30.5 + - + +
384D LEU* 3.6 22.8 - - + +
387D LEU* 5.1 1.1 - - + -
391D LEU* 3.4 34.7 - - + +
430D LEU* 5.5 9.2 + - + +
432D LEU* 5.0 9.9 - - + +
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Residues in contact with LEU 362 (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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336D LEU* 3.8 17.9 - - + -
358D ALA 2.7 20.1 + - - +
359D ALA* 4.3 0.4 - - - -
361D HIS* 1.3 85.2 - - + +
363D ALA* 1.3 62.1 + - - +
364D LEU 2.9 0.2 + - - -
365D TYR* 2.9 15.1 + - + +
366D THR* 2.9 25.5 + - - +
391D LEU* 4.3 9.9 - - + -
394D LEU* 4.2 14.1 - - + -
395D HIS* 4.1 27.1 - - - +
398D TYR* 3.8 26.5 - - + -
427D PRO* 4.4 6.5 - - + -
430D LEU* 4.1 25.4 - - + -
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Residues in contact with ALA 363 (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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329D VAL* 3.8 13.8 - - + +
332D LEU* 3.4 26.7 - - + -
333D ALA* 3.5 26.0 - - + +
336D LEU* 3.8 0.2 - - - +
359D ALA 3.0 20.2 + - - +
360D PHE 3.6 2.9 - - - +
361D HIS 3.0 0.2 + - - -
362D LEU* 1.3 76.7 - - - +
364D LEU* 1.3 64.3 + - - +
366D THR* 3.6 0.3 - - - -
367D VAL* 3.2 26.5 + - - +
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Residues in contact with LEU 364 (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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322D GLN* 5.0 13.5 - - + -
326D ASN* 6.3 0.4 - - + -
329D VAL* 3.8 26.6 - - + +
360D PHE* 2.8 20.6 + - + +
361D HIS* 2.6 18.7 + - - +
363D ALA* 1.3 70.1 - - - +
365D TYR* 1.3 53.4 + - - +
367D VAL 3.0 3.3 + - - -
368D THR* 2.6 55.7 + - + +
370D GLN* 3.8 19.1 - - + +
371D SER 3.7 32.8 - - - +
372D TRP 4.5 0.4 - - - +
373D PRO* 4.3 12.6 - - + -
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Residues in contact with TYR 365 (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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361D HIS* 3.1 19.7 + + + +
362D LEU* 2.9 10.7 + - + +
364D LEU* 1.3 76.9 - - - +
366D THR* 1.3 69.6 + - - +
367D VAL 2.8 0.2 + - - -
369D GLY* 2.7 42.2 + - - +
370D GLN 3.2 23.4 + - - +
371D SER* 3.8 11.2 - - - -
427D PRO* 4.6 17.5 - - + -
429D THR 4.0 19.1 + - - -
430D LEU* 3.7 28.4 + - + -
431D ASN* 4.0 17.0 + - - +
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Residues in contact with THR 366 (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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332D LEU* 3.8 11.8 - - + +
362D LEU* 2.9 20.4 + - - +
363D ALA 3.6 9.6 - - - -
365D TYR* 1.3 81.7 - - - +
367D VAL* 1.3 63.8 + - + +
369D GLY 4.5 0.3 + - - -
398D TYR* 3.8 25.2 - - - +
424D LEU* 5.0 7.9 - - + -
425D ASN 4.4 8.1 - - - +
427D PRO* 3.6 31.6 - - + +
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Residues in contact with VAL 367 (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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326D ASN* 4.0 23.3 - - - +
328D LYS* 4.2 25.8 - - + +
329D VAL* 4.1 9.9 - - + +
332D LEU* 4.2 9.4 - - + -
363D ALA 3.4 16.2 - - - +
364D LEU 3.0 3.7 + - - +
365D TYR 2.8 2.4 + - - -
366D THR* 1.3 77.0 - - - +
368D THR* 1.3 63.3 + - + +
369D GLY 3.7 0.2 - - - -
424D LEU* 4.2 24.0 - - + -
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Residues in contact with THR 368 (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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326D ASN* 4.9 7.6 - - + +
329D VAL* 4.1 14.6 - - + -
364D LEU* 2.6 30.2 + - + +
367D VAL* 1.3 88.3 - - + +
369D GLY* 1.3 53.6 + - - +
370D GLN* 2.6 60.5 + - - +
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Residues in contact with GLY 369 (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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365D TYR* 2.7 41.6 + - - -
366D THR 4.5 0.4 + - - -
367D VAL 3.7 0.6 - - - -
368D THR* 1.3 69.1 - - - +
370D GLN* 1.3 63.2 + - - +
371D SER* 4.5 1.0 + - - -
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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