Contacts of the helix formed by residues 356 - 376 (chain D) in PDB entry 4E2I
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 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354D GLN 3.5 4.4 + - - +
355D LEU* 1.3 77.9 - - - +
357D ARG* 1.3 64.1 + - - +
358D GLU* 3.0 10.2 + - - +
359D GLN* 3.0 45.4 + - - +
360D MET* 3.1 10.2 + - - +
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Residues in contact with ARG 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D THR* 1.3 73.8 - - - +
358D GLU* 1.3 59.3 + - - +
360D MET* 3.5 24.0 + - + +
361D LEU* 3.6 15.2 + - - +
412D MET 2.8 22.4 + - - -
413D VAL* 3.7 19.5 - - + +
415D ASN* 3.7 32.7 + - - +
467D GLN 4.8 4.0 + - - -
468D PHE* 3.0 75.3 + - + +
522D PRO* 5.5 2.0 - - - +
523D PRO* 3.5 19.9 - - - +
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Residues in contact with GLU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D THR* 3.0 8.2 + - - +
357D ARG* 1.3 77.6 - - - +
359D GLN* 1.3 56.5 + - + +
360D MET 3.3 0.4 - - - -
361D LEU* 3.3 7.4 + - + +
362D THR* 2.7 35.5 + - - +
410D LYS* 3.3 26.4 + - - +
413D VAL* 3.5 30.0 - - + +
587D GLU 5.1 1.6 - - - +
588D PHE 5.3 0.5 - - - -
589D ALA* 4.9 15.9 + - + -
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Residues in contact with GLN 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D GLN 4.6 1.2 - - - +
355D LEU* 3.4 29.1 - - + +
356D THR* 3.0 39.8 + - - +
358D GLU* 1.3 76.7 - - + +
360D MET* 1.3 64.2 + - - +
362D THR* 3.0 21.2 + - - +
363D ASN* 2.8 22.0 + - - +
309E GLU* 5.5 4.8 + - - +
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Residues in contact with MET 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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351D ASP* 4.0 17.0 - - + +
352D SER* 4.2 19.1 - - - +
355D LEU* 3.8 25.8 - - + +
356D THR 3.1 11.7 + - - +
357D ARG* 3.5 51.4 - - + +
358D GLU 3.3 0.2 - - - -
359D GLN* 1.3 78.4 - - - +
361D LEU* 1.3 61.4 + - - +
363D ASN* 3.5 11.9 + - - +
364D ARG* 3.3 18.5 + - - +
443D CYS 5.9 0.4 - - - -
466D ASP 5.9 1.8 - - - +
467D GLN 5.6 5.2 - - - +
468D PHE* 4.5 14.8 - - + -
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Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D ARG 3.6 3.3 + - - +
358D GLU* 3.3 9.1 + - + +
359D GLN 3.1 0.2 - - - -
360D MET* 1.3 77.3 - - - +
362D THR* 1.3 58.6 + - - +
364D ARG* 2.9 4.1 + - - +
365D PHE* 2.8 56.1 + - + -
409D LEU* 4.2 18.8 - - + +
413D VAL* 3.5 32.3 - - + -
443D CYS* 3.7 32.3 - - + +
468D PHE* 3.5 39.0 - - + -
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Residues in contact with THR 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D GLU* 2.7 22.5 + - - +
359D GLN* 3.0 16.3 + - - +
361D LEU* 1.3 77.0 - - - +
363D ASN* 1.3 59.7 + - - +
365D PHE* 3.5 7.9 + - - +
366D ASN* 2.7 43.9 + - - +
589D ALA* 3.6 25.5 - - + +
591D SER* 3.6 24.2 - - - +
592D ILE* 4.1 8.2 - - + +
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Residues in contact with ASN 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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281D LYS* 5.7 3.1 - - - +
355D LEU* 3.6 28.7 - - - +
359D GLN* 2.8 22.5 + - - +
360D MET* 3.7 8.1 - - - +
361D LEU 3.1 0.2 - - - -
362D THR* 1.3 75.6 - - - +
364D ARG* 1.3 61.5 + - - +
366D ASN* 3.2 10.1 + - - +
367D ASP* 2.7 37.9 + - - +
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Residues in contact with ARG 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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360D MET 3.3 9.6 + - - +
361D LEU* 2.9 9.8 + - - +
363D ASN* 1.3 78.7 - - - +
365D PHE* 1.3 64.0 + - + +
367D ASP* 3.0 16.1 + - - +
368D LEU* 2.9 39.1 + - + +
371D ARG* 4.0 18.7 - - - +
441D GLU* 2.8 49.9 + - - +
442D LEU 3.5 14.8 - - - +
443D CYS 3.2 28.0 + - - +
444D GLY* 4.2 9.6 - - - -
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Residues in contact with PHE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D LEU* 2.8 55.7 + - + +
362D THR* 3.8 2.9 - - - +
364D ARG* 1.3 73.4 - - + +
366D ASN* 1.3 61.2 + - - +
368D LEU* 3.6 10.0 + - + +
369D LEU* 3.3 27.9 + - - +
409D LEU* 3.9 27.8 - - + -
442D LEU* 3.9 20.9 - - + -
576D LEU* 3.5 21.6 - - + +
579D LEU* 3.5 28.0 - - + -
588D PHE* 4.2 24.7 - + - -
592D ILE* 3.7 20.4 - - + -
596D ILE* 5.6 0.2 - - + -
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Residues in contact with ASN 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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362D THR* 2.7 32.5 + - - +
363D ASN* 3.2 11.1 + - - +
364D ARG 3.1 0.8 - - - -
365D PHE* 1.3 76.0 - - - +
367D ASP* 1.3 57.2 + - - +
368D LEU 3.2 0.2 - - - -
369D LEU* 3.1 2.2 + - - -
370D ASP* 2.7 37.3 + - - +
591D SER 5.3 2.9 + - - +
592D ILE* 3.4 27.8 - - - +
595D ARG* 3.2 32.9 + - - +
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Residues in contact with ASP 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D LYS* 3.5 27.0 + - - -
363D ASN* 2.7 28.1 + - - +
364D ARG* 3.0 18.9 + - - +
366D ASN* 1.3 76.9 - - - +
368D LEU* 1.3 62.8 + - + +
370D ASP* 3.1 28.0 + - - +
371D ARG* 3.5 19.5 + - - +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ARG* 2.9 37.8 + - + +
365D PHE* 3.7 10.8 - - + +
367D ASP* 1.3 78.5 - - - +
369D LEU* 1.3 59.6 + - - +
371D ARG* 3.7 13.4 + - - +
372D MET* 3.1 23.7 + - - +
441D GLU* 3.7 21.8 - - + +
442D LEU* 3.5 40.8 - - + +
572D GLY 4.6 3.1 - - - +
573D ILE* 3.3 30.3 - - + +
576D LEU* 3.5 20.6 - - + -
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Residues in contact with LEU 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 PHE 3.3 17.7 + - - +
366D ASN* 3.1 3.2 + - - +
368D LEU* 1.3 77.5 - - - +
370D ASP* 1.3 54.2 + - - +
371D ARG 3.2 0.7 - - - -
372D MET* 3.1 26.7 + - - +
373D ASP* 2.8 36.4 + - - +
576D LEU* 3.5 12.8 - - + -
580D ILE* 3.9 17.0 - - + -
592D ILE* 4.5 9.9 - - + -
595D ARG* 3.2 50.3 - - + +
596D ILE* 4.8 9.6 - - + -
599D TRP* 3.8 20.0 - - + +
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Residues in contact with ASP 370 (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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366D ASN* 2.7 25.2 + - - +
367D ASP* 3.1 25.5 - - - +
369D LEU* 1.3 77.5 - - - +
371D ARG* 1.3 62.2 + - + +
373D ASP* 3.3 11.7 + - - +
374D ILE* 3.2 26.1 - - + +
595D ARG* 3.2 18.3 + - - +
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Residues in contact with ARG 371 (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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506C LYS* 6.2 0.4 - - - +
364D ARG* 4.0 24.5 - - - +
367D ASP* 3.5 19.4 + - - +
368D LEU* 3.8 14.4 - - - +
370D ASP* 1.3 76.5 - - + +
372D MET* 1.3 57.9 + - - +
374D ILE* 3.1 12.8 + - - +
375D MET* 2.9 40.8 + - - +
441D GLU* 3.4 29.9 + - - +
573D ILE* 4.1 18.6 - - + +
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Residues in contact with MET 372 (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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368D LEU 3.1 11.9 - - - +
369D LEU* 3.1 33.6 + - + +
371D ARG* 1.3 72.1 - - - +
373D ASP* 1.3 56.5 + - - +
374D ILE 3.0 4.9 - - - -
375D MET* 3.4 9.0 - - - -
376D PHE* 2.8 59.0 + - + +
573D ILE* 3.5 20.9 - - + -
576D LEU* 3.5 18.6 - - + -
577D LEU* 3.4 39.7 - - + -
580D ILE* 5.5 0.4 - - + -
599D TRP* 3.6 18.6 - - + -
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Residues in contact with ASP 373 (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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369D LEU 2.8 21.5 + - - +
370D ASP* 3.3 9.7 + - - +
372D MET* 1.3 75.1 - - - +
374D ILE* 1.3 60.1 + - + +
376D PHE* 5.3 0.9 - - - -
377D GLY* 4.0 14.5 - - - -
595D ARG* 2.8 24.6 + - - -
599D TRP* 3.2 24.8 + - - -
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Residues in contact with ILE 374 (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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311D PRO* 3.7 31.2 - - + -
314D TYR* 4.3 11.4 - - - +
315D LYS* 5.4 8.3 - - + +
370D ASP* 3.2 22.7 - - + +
371D ARG* 3.5 8.3 - - - +
372D MET 3.0 0.8 - - - -
373D ASP* 1.3 81.6 - - + +
375D MET* 1.3 63.6 + - - +
376D PHE 3.3 1.1 - - - -
377D GLY* 3.2 7.6 + - - -
379D THR* 3.5 27.7 + - - +
380D GLY* 3.1 23.8 + - - -
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Residues in contact with MET 375 (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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371D ARG* 2.9 34.3 + - - +
372D MET* 3.4 14.4 - - - -
374D ILE* 1.3 77.7 - - - +
376D PHE* 1.3 86.7 + - + +
377D GLY 3.2 1.4 + - - +
380D GLY* 3.3 18.7 - - - +
381D SER 5.1 0.7 - - - +
382D ALA* 3.3 44.7 + - + +
387D TRP* 3.5 39.5 - - + -
573D ILE* 4.4 7.2 - - + -
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Residues in contact with PHE 376 (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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372D MET* 2.8 59.1 + - + +
373D ASP* 4.6 1.6 - - - -
375D MET* 1.3 103.1 - - + +
377D GLY* 1.3 57.8 + - - +
382D ALA* 3.8 14.1 - - + -
383D ASP 4.0 1.3 - - - -
384D ILE* 3.4 51.6 - - + -
387D TRP* 3.8 25.6 - + + -
573D ILE* 4.7 0.9 - - + -
577D LEU* 4.6 0.9 - - + -
599D TRP* 3.9 17.3 - + + -
602D ARG* 3.5 30.7 + - - +
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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