Contacts of the helix formed by residues 356 - 376 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I GLN 3.5 4.9 + - - +
355I LEU* 1.3 77.6 - - - +
357I ARG* 1.3 63.8 + - - +
358I GLU* 3.0 10.8 + - - +
359I GLN* 3.0 46.4 + - - +
360I MET* 3.1 9.7 + - - +
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Residues in contact with ARG 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I LEU 3.8 0.2 + - - -
356I THR* 1.3 72.7 - - - +
358I GLU* 1.3 60.1 + - - +
360I MET* 3.5 24.6 - - + +
361I LEU* 3.6 14.0 + - - +
412I MET 2.8 23.4 + - - -
413I VAL* 3.7 19.5 - - + +
415I ASN* 3.7 32.4 + - - +
467I GLN 4.8 4.0 + - - -
468I PHE* 3.0 75.9 + - + +
522I PRO* 5.5 2.0 - - - +
523I PRO* 3.5 18.6 - - - +
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Residues in contact with GLU 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 3.0 8.8 + - - +
357I ARG* 1.3 77.8 - - - +
359I GLN* 1.3 55.6 + - + +
360I MET 3.3 0.4 - - - -
361I LEU* 3.4 6.1 + - + +
362I THR* 2.7 35.6 + - - +
410I LYS* 3.3 26.5 + - - +
413I VAL* 3.5 28.2 - - + +
587I GLU 5.1 1.7 - - - +
588I PHE 5.4 0.5 - - - -
589I ALA* 4.9 16.3 + - + -
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Residues in contact with GLN 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I GLN 4.7 1.0 - - - +
355I LEU* 3.4 29.7 - - + +
356I THR* 3.0 39.9 + - - +
358I GLU* 1.3 78.6 - - + +
360I MET* 1.3 64.0 + - - +
362I THR* 3.0 21.4 + - - +
363I ASN* 2.8 21.9 + - - +
309J GLU* 5.3 7.5 + - - +
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Residues in contact with MET 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I ASP* 3.9 17.0 - - + +
352I SER* 4.2 19.5 - - - +
355I LEU* 3.8 26.5 - - + +
356I THR 3.1 10.9 + - - +
357I ARG* 3.5 52.3 - - + +
358I GLU 3.3 0.2 - - - -
359I GLN* 1.3 77.9 - - - +
361I LEU* 1.3 60.8 + - - +
363I ASN* 3.5 12.4 + - - +
364I ARG* 3.3 18.7 + - - +
443I CYS 5.9 0.2 - - - -
466I ASP 5.9 2.0 - - - +
467I GLN 5.6 5.6 - - - +
468I PHE* 4.6 13.9 - - + -
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Residues in contact with LEU 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I ARG 3.6 3.5 + - - +
358I GLU* 3.4 9.8 + - + +
359I GLN 3.1 0.2 - - - -
360I MET* 1.3 76.7 - - - +
362I THR* 1.3 58.0 + - - +
364I ARG* 2.9 4.2 + - - +
365I PHE* 2.8 55.7 + - + -
409I LEU* 4.2 18.8 - - + +
413I VAL* 3.5 32.5 - - + -
443I CYS* 3.7 32.8 - - + +
468I PHE* 3.5 38.8 - - + -
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Residues in contact with THR 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I GLU* 2.7 22.8 + - - +
359I GLN* 3.0 17.0 + - - +
361I LEU* 1.3 76.5 - - - +
363I ASN* 1.3 58.7 + - - +
365I PHE* 3.5 6.8 + - - +
366I ASN* 2.7 43.5 + - - +
589I ALA* 3.5 26.1 - - + +
591I SER* 3.6 23.8 - - - +
592I ILE* 4.1 8.7 - - + +
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Residues in contact with ASN 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I LYS* 5.7 3.1 - - - +
355I LEU* 3.6 27.1 - - - +
359I GLN* 2.8 22.5 + - - +
360I MET* 3.8 8.4 - - - +
361I LEU 3.1 0.2 - - - -
362I THR* 1.3 76.9 - - - +
364I ARG* 1.3 63.0 + - - +
366I ASN* 3.3 10.2 + - - +
367I ASP* 2.7 37.2 + - - +
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Residues in contact with ARG 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I MET 3.3 10.5 + - - +
361I LEU* 2.9 10.0 + - + +
363I ASN* 1.3 78.9 - - - +
365I PHE* 1.3 64.3 + - + +
367I ASP* 3.0 16.7 + - - +
368I LEU* 2.9 38.3 + - + +
371I ARG* 4.0 19.1 - - - +
441I GLU* 2.8 49.7 + - - +
442I LEU 3.5 14.8 - - - +
443I CYS 3.2 26.2 + - - +
444I GLY* 4.2 10.3 - - - -
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Residues in contact with PHE 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I LEU* 2.8 55.5 + - + +
362I THR* 3.8 3.1 - - - +
364I ARG* 1.3 72.6 - - + +
366I ASN* 1.3 58.4 + - - +
368I LEU* 3.5 10.7 + - + +
369I LEU* 3.3 28.3 + - + +
409I LEU* 3.9 27.4 - - + -
442I LEU* 3.9 21.3 - - + -
576I LEU* 3.5 22.2 - - + +
579I LEU* 3.5 27.8 - - + -
588I PHE* 4.2 25.1 - + - -
592I ILE* 3.7 20.2 - - + -
596I ILE* 5.6 0.2 - - + -
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Residues in contact with ASN 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362I THR* 2.7 33.1 + - - +
363I ASN* 3.5 10.7 + - - +
364I ARG 3.1 0.6 - - - -
365I PHE* 1.3 76.2 - - - +
367I ASP* 1.3 56.4 + - - +
368I LEU 3.2 0.2 - - - -
369I LEU* 3.1 2.1 + - - -
370I ASP* 2.7 38.4 + - - +
591I SER 5.3 2.7 + - - +
592I ILE* 3.4 27.3 - - - +
595I ARG* 3.2 32.0 + - - +
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Residues in contact with ASP 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I LYS* 3.5 27.4 + - - -
363I ASN* 2.7 27.6 + - - +
364I ARG* 3.0 19.0 + - - +
366I ASN* 1.3 76.9 - - - +
368I LEU* 1.3 64.0 + - + +
370I ASP* 3.1 27.0 + - - +
371I ARG* 3.5 20.5 + - - +
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Residues in contact with LEU 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I ARG* 2.9 36.0 + - + +
365I PHE* 3.6 11.4 - - - +
367I ASP* 1.3 77.3 - - - +
369I LEU* 1.3 60.0 + - - +
371I ARG* 3.7 12.5 + - - +
372I MET* 3.1 23.6 + - - +
441I GLU* 3.7 21.5 - - + +
442I LEU* 3.5 41.5 - - + +
572I GLY 4.6 2.9 - - - +
573I ILE* 3.3 30.6 - - + +
576I LEU* 3.5 20.4 - - + -
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Residues in contact with LEU 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE 3.3 18.1 + - - +
366I ASN* 3.1 3.0 + - - +
368I LEU* 1.3 77.7 - - - +
370I ASP* 1.3 54.5 + - - +
371I ARG 3.2 0.7 - - - -
372I MET* 3.1 27.1 + - - +
373I ASP* 2.8 36.4 + - - +
576I LEU* 3.5 13.0 - - + -
580I ILE* 3.9 16.6 - - + -
592I ILE* 4.5 10.1 - - + -
595I ARG* 3.2 49.8 - - + +
596I ILE* 4.8 9.9 - - + -
599I TRP* 3.8 20.2 - - + +
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Residues in contact with ASP 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I ASN* 2.7 25.7 + - - +
367I ASP* 3.1 25.6 + - - +
369I LEU* 1.3 77.6 - - - +
371I ARG* 1.3 62.3 + - + +
373I ASP* 3.3 11.5 + - - +
374I ILE* 3.2 25.0 + - + +
595I ARG* 3.2 17.8 + - - +
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Residues in contact with ARG 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I ARG* 4.0 24.4 - - - +
367I ASP* 3.5 19.9 + - - +
368I LEU* 3.8 15.0 - - - +
369I LEU 3.2 0.2 - - - -
370I ASP* 1.3 76.5 - - + +
372I MET* 1.3 58.6 + - - +
374I ILE* 3.1 12.3 + - - +
375I MET* 2.9 41.3 + - - +
441I GLU* 3.4 29.9 + - - +
573I ILE* 4.1 17.8 - - + +
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Residues in contact with MET 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I LEU 3.1 11.7 - - - +
369I LEU* 3.1 19.9 + - + +
371I ARG* 1.3 72.7 - - - +
373I ASP* 1.3 56.1 + - - +
374I ILE 3.0 4.9 - - - -
375I MET* 3.4 9.9 - - - -
376I PHE* 2.8 57.6 + - + +
573I ILE* 3.5 20.9 - - + -
576I LEU* 3.5 31.6 - - + -
577I LEU* 3.4 42.2 - - + -
580I ILE* 5.4 0.7 - - + -
599I TRP* 3.6 18.2 - - + -
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Residues in contact with ASP 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369I LEU* 2.8 22.0 + - - +
370I ASP* 3.3 9.0 + - - +
372I MET* 1.3 76.0 - - - +
374I ILE* 1.3 60.4 + - + +
376I PHE* 5.3 0.7 - - - -
377I GLY* 4.0 14.4 - - - +
595I ARG* 2.8 24.4 + - - -
599I TRP* 3.2 25.7 + - - -
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Residues in contact with ILE 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308I LYS 6.2 0.2 - - - +
311I PRO* 3.7 31.9 - - + -
314I TYR* 4.3 12.1 - - - +
315I LYS* 5.3 8.3 - - + +
370I ASP* 3.2 21.5 - - + +
371I ARG* 3.1 8.7 + - - +
372I MET 3.0 0.6 - - - -
373I ASP* 1.3 82.2 - - + +
375I MET* 1.3 62.9 + - - +
376I PHE 3.3 1.1 - - - -
377I GLY* 3.3 7.7 + - - -
379I THR* 3.5 27.1 + - - +
380I GLY* 3.1 23.4 + - - -
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Residues in contact with MET 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I ARG* 2.9 31.8 + - - +
372I MET* 3.4 17.5 - - - -
374I ILE* 1.3 77.6 - - - +
376I PHE* 1.3 86.8 + - + +
377I GLY 3.2 2.2 + - - +
380I GLY* 3.3 18.5 - - - +
381I SER 5.1 0.4 - - - +
382I ALA* 3.3 43.7 + - + +
387I TRP* 3.5 40.4 - - + -
573I ILE* 4.4 7.2 - - + -
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Residues in contact with PHE 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I MET* 2.8 61.7 + - + +
373I ASP* 4.6 1.1 - - - -
375I MET* 1.3 101.9 - - + +
377I GLY* 1.3 58.8 + - - +
382I ALA* 3.8 14.4 - - + -
383I ASP 4.0 0.9 - - - -
384I ILE* 3.4 53.6 - - + -
387I TRP* 3.8 25.6 - + + -
573I ILE* 4.7 0.7 - - + -
577I LEU* 4.6 0.9 - - + -
599I TRP* 3.9 17.3 - + + -
602I ARG* 3.5 30.1 + - - +
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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
------------------------------------------------------------
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