Contacts of the helix formed by residues 383 - 396 (chain G) 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 ASP 383 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376G PHE* 4.0 2.0 - - - -
381G SER 3.9 1.8 + - - -
382G ALA* 1.3 71.3 - - - +
384G ILE* 1.3 67.1 + - - +
385G GLU* 2.9 43.0 + - - +
386G GLU* 3.2 34.6 + - - +
387G TRP* 3.1 19.2 - - - +
566G LYS* 4.6 4.9 - - - +
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Residues in contact with ILE 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376G PHE* 3.4 41.7 - - + -
382G ALA 3.7 2.0 + - - -
383G ASP* 1.3 75.0 + - - +
385G GLU* 1.3 65.4 + - + +
387G TRP* 3.4 0.6 + - - -
388G MET* 3.0 40.2 + - + +
577G LEU* 4.3 21.3 - - + -
599G TRP* 5.0 3.8 - - + -
602G ARG* 4.6 17.0 - - + +
603G LEU* 4.9 11.0 - - + -
606G GLU* 4.6 19.5 - - + +
607G PHE* 4.1 16.8 - - + -
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Residues in contact with GLU 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383G ASP* 2.9 20.1 + - - +
384G ILE* 1.3 81.6 - - + +
386G GLU* 1.3 60.9 + - + +
388G MET* 3.4 4.0 + - - +
389G ALA* 3.1 21.1 + - - +
607G PHE* 3.4 30.8 - - + -
611G VAL* 5.9 1.4 - - - +
615G MET* 4.4 0.5 - - - +
626G LEU* 3.5 34.3 - - + +
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Residues in contact with GLU 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383G ASP* 3.2 25.9 + - + +
385G GLU* 1.3 74.6 - - + +
387G TRP* 1.3 61.0 + - + +
389G ALA* 3.0 7.7 + - - +
390G GLY 3.0 22.0 + - - -
562G PHE* 3.1 38.0 - - + +
563G LEU* 3.6 8.0 - - - +
566G LYS* 2.7 40.3 + - - +
568G ILE* 3.8 15.2 - - + +
626G LEU* 4.1 16.6 - - + -
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Residues in contact with TRP 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375G MET* 3.5 27.5 - - + +
376G PHE* 3.8 14.6 - + + -
382G ALA* 4.1 10.6 - - + +
383G ASP 3.1 25.2 - - - +
384G ILE 3.4 4.9 + - - +
385G GLU 3.4 0.6 - - - -
386G GLU* 1.3 81.1 + - + +
388G MET* 1.3 59.8 + - - +
390G GLY* 3.4 2.3 + - - -
391G VAL* 3.1 26.0 + - - +
566G LYS* 4.3 14.2 - - + +
567G ARG 3.9 9.9 - - - -
568G ILE* 3.7 38.2 - - + +
571G SER* 3.2 34.1 - - - -
573G ILE* 3.5 23.8 - - + -
574G ALA* 3.9 15.0 - - - +
577G LEU* 3.6 18.4 - - + +
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Residues in contact with MET 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384G ILE* 3.0 36.1 + - + +
385G GLU* 3.6 6.5 - - - +
387G TRP* 1.3 74.9 - - - +
389G ALA* 1.3 64.2 + - - +
391G VAL* 3.4 23.4 + - + +
392G ALA* 3.5 4.2 + - - +
577G LEU* 3.5 49.1 - - + +
581G TRP* 3.5 34.5 - - + -
603G LEU* 3.7 15.3 - - + -
607G PHE* 4.2 14.8 - - + -
612G TYR* 4.0 6.2 - - - -
615G MET* 3.8 23.4 - - + +
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Residues in contact with ALA 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385G GLU 3.1 13.0 + - - +
386G GLU* 3.0 14.1 + - - +
388G MET* 1.3 76.8 - - - +
390G GLY* 1.3 62.6 + - - +
392G ALA* 3.0 15.3 + - - +
393G TRP* 3.1 12.8 + - - +
562G PHE* 4.2 2.5 - - + -
563G LEU* 4.4 1.6 - - - -
615G MET* 3.7 9.6 - - - -
625G VAL* 3.4 33.8 - - + +
626G LEU* 3.6 16.4 - - + -
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Residues in contact with GLY 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386G GLU 3.0 9.9 + - - -
387G TRP 3.4 4.6 + - - -
388G MET 3.3 0.4 - - - -
389G ALA* 1.3 73.7 - - - +
391G VAL* 1.3 57.7 + - - +
392G ALA 3.0 2.0 - - - -
393G TRP* 3.2 6.1 + - - +
394G LEU* 2.8 42.6 + - - +
563G LEU* 3.6 19.9 - - - +
568G ILE* 4.2 8.5 - - - -
569G ILE* 4.8 3.8 - - - -
574G ALA* 5.6 0.7 - - - -
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Residues in contact with VAL 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387G TRP 3.1 18.6 + - - +
388G MET* 3.5 28.3 - - + +
389G ALA 3.2 0.4 - - - -
390G GLY* 1.3 75.8 - - - +
392G ALA* 1.3 55.0 + - - +
394G LEU* 4.0 9.1 - - - +
395G HIS* 3.2 26.2 + - - +
574G ALA* 3.8 19.7 - - - +
577G LEU* 3.9 5.4 - - + +
578G MET* 3.5 34.7 - - + +
581G TRP* 5.2 2.5 - - + -
582G TYR* 4.5 2.5 - - + -
612G TYR* 3.3 22.5 + - + +
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Residues in contact with ALA 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388G MET 3.5 4.8 + - - +
389G ALA 3.0 13.8 + - - +
390G GLY 3.0 0.4 - - - -
391G VAL* 1.3 78.4 - - - +
393G TRP* 1.3 65.5 + - - +
395G HIS* 3.2 3.1 + - - +
396G CYS* 3.1 29.9 + - - -
612G TYR* 4.5 6.5 - - + -
615G MET* 4.1 11.9 - - + -
616G LYS* 3.5 40.3 - - + +
619G VAL* 4.6 2.9 - - + -
625G VAL* 4.9 0.4 - - + -
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Residues in contact with TRP 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389G ALA 3.1 7.8 + - - +
390G GLY* 3.7 5.2 - - - +
392G ALA* 1.3 78.8 - - - +
394G LEU* 1.3 74.8 + - + +
396G CYS* 3.1 16.7 + - - +
397G LEU* 3.3 27.1 + - + +
430G SER 5.3 1.6 - - - -
431G GLY* 5.2 2.9 - - - -
434G THR* 3.9 17.0 - - + -
553G LEU* 3.2 55.2 + - + +
556G CYS* 3.4 26.2 - - - -
557G LEU* 3.7 25.8 - - + +
563G LEU* 4.4 11.2 - - + -
569G ILE* 3.5 44.6 - - + -
619G VAL* 4.3 5.5 - - + +
625G VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390G GLY 2.8 21.7 + - - +
391G VAL* 4.1 5.8 - - - +
393G TRP* 1.3 92.7 - - + +
395G HIS* 1.3 58.8 + - - +
397G LEU* 3.2 30.0 - - + +
401G MET* 3.2 21.3 - - + +
434G THR* 4.8 2.7 - - + +
435G LEU* 5.5 6.3 - - + -
438G ALA* 5.9 0.2 - - + -
569G ILE* 3.1 33.7 - - - +
571G SER 5.3 0.2 - - - +
574G ALA* 3.9 30.7 - - + -
575G LEU* 4.0 23.1 - - + -
578G MET* 4.4 9.6 - - - -
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Residues in contact with HIS 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147 ILE* 4.3 17.4 - - + +
391G VAL 3.2 18.4 + - - +
392G ALA 3.2 5.9 + - - +
394G LEU* 1.3 74.9 - - - +
396G CYS* 1.3 57.2 + - - +
397G LEU 3.2 2.9 - - - -
398G LEU 3.4 16.9 - - - +
400G LYS* 4.6 14.8 - - - -
401G MET* 3.9 7.8 + - + -
402G ASP* 2.9 39.1 + - + -
578G MET* 4.5 4.2 - - - -
582G TYR* 3.3 31.3 - + - +
616G LYS* 2.9 30.3 + - - +
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Residues in contact with CYS 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147 ILE* 4.2 11.4 - - + -
157 PHE* 4.1 19.7 - - - -
392G ALA 3.1 22.0 + - - +
393G TRP 3.1 9.3 + - - +
395G HIS* 1.3 76.1 - - - +
397G LEU* 1.3 59.0 + - - +
398G LEU 3.6 0.4 - - - -
550G LYS* 3.6 2.3 + - - -
552G TYR* 2.7 30.0 + - + +
553G LEU* 3.4 8.3 - - + +
616G LYS* 4.1 22.2 - - - -
619G VAL* 3.6 36.1 - - + -
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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