Contacts of the helix formed by residues 460 - 474 (chain B) in PDB entry 6IEH
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 460 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A HIS* 5.3 1.6 - - - +
440B GLN* 3.8 22.2 - - + +
441B VAL* 5.9 3.1 - - + +
459B LEU* 1.3 80.1 - - + +
461B PRO* 1.3 68.4 - - + +
462B ILE* 3.4 10.1 - - + +
463B LEU* 3.3 35.0 + - + +
464B LYS* 2.9 24.9 + - - +
979B PHE* 4.5 9.4 - - + -
990B GLU* 3.1 47.3 - - + +
991B GLY* 4.7 0.7 - - - -
994B ILE* 4.4 14.6 - - + -
1034B ILE* 4.9 9.4 - - + -
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Residues in contact with PRO 461 (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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459B LEU 3.7 4.7 - - - +
460B LEU* 1.3 86.6 - - + +
462B ILE* 1.3 65.1 + - - +
464B LYS* 3.2 30.0 + - + +
465B GLU* 3.2 26.6 + - - +
991B GLY* 4.9 2.9 - - - +
994B ILE* 4.2 33.4 - - + -
1034B ILE 5.8 3.6 - - - +
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Residues in contact with ILE 462 (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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427B ALA* 4.4 18.8 - - + +
428B ILE* 5.3 4.0 - - + -
430B CYS* 5.7 4.5 - - + -
431B LEU* 4.0 38.4 - - + -
441B VAL* 5.3 2.5 - - + -
460B LEU* 4.6 8.7 - - + -
461B PRO* 1.3 79.6 - - - +
463B LEU* 1.3 77.0 + - + +
465B GLU* 3.9 7.8 + - - +
466B THR* 3.4 21.4 + - - +
1034B ILE* 4.3 14.2 + - + +
1037B ALA* 3.8 26.9 - - + -
1039B SER* 3.6 27.4 - - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 5.3 2.7 - - + +
424B PHE* 4.5 23.6 - - + -
428B ILE* 5.3 6.1 - - + -
440B GLN 3.5 24.9 - - - +
441B VAL* 4.1 23.6 - - + -
444B VAL* 4.4 11.7 - - + -
459B LEU* 5.6 5.4 - - + -
460B LEU* 3.3 29.8 + - + +
462B ILE* 1.3 86.0 - - + +
464B LYS* 1.3 64.7 + - - +
465B GLU 3.2 0.2 - - - -
466B THR* 3.3 8.0 + - + -
467B ILE* 3.2 35.9 + - + +
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Residues in contact with LYS 464 (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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455B HIS* 3.4 35.3 + - + +
456B HIS 3.7 18.8 - - - +
457B GLY* 4.5 5.3 - - - -
459B LEU* 3.5 28.3 - - + +
460B LEU 2.9 14.9 + - - +
461B PRO* 3.2 24.0 + - + +
463B LEU* 1.3 76.8 - - - +
465B GLU* 1.3 64.2 + - + +
467B ILE* 3.4 9.0 + - + +
468B GLU* 3.3 27.6 + - - +
995B ARG* 4.3 16.2 - - - +
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B PRO* 3.2 20.1 + - - +
462B ILE* 4.1 3.2 - - - +
464B LYS* 1.3 79.2 - - + +
466B THR* 1.3 60.2 + - - +
468B GLU* 3.2 18.9 + - - +
469B ILE* 2.9 33.6 + - + +
1038B ALA* 4.1 2.5 - - - -
1039B SER* 3.2 18.7 + - - +
1040B LEU* 1.6 70.5 + - + +
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Residues in contact with THR 466 (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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423B VAL 4.8 0.8 + - - +
424B PHE* 4.3 26.9 + - + -
427B ALA* 3.1 30.8 - - - +
448B LEU* 4.3 4.3 - - + -
462B ILE* 3.4 15.7 + - - +
463B LEU* 3.3 12.7 + - + +
464B LYS 3.2 0.4 - - - -
465B GLU* 1.3 80.3 - - - +
467B ILE* 1.3 58.2 + - + +
469B ILE* 3.2 9.7 + - - +
470B LEU* 2.9 44.4 + - + +
1039B SER* 4.8 1.8 + - - -
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Residues in contact with ILE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B VAL* 6.0 4.5 - - + -
448B LEU* 4.1 25.8 - - + -
453B GLY* 4.3 11.4 - - - -
454B ILE* 3.4 36.1 - - + +
455B HIS* 5.0 5.6 - - + -
459B LEU* 5.4 4.3 - - + -
463B LEU* 3.2 28.4 + - + +
464B LYS* 3.8 7.4 - - - +
466B THR* 1.3 73.9 - - + +
468B GLU* 1.3 61.7 + - - +
470B LEU* 3.5 6.7 - - - +
471B PHE* 2.9 28.7 + - + +
476B ILE* 3.7 17.7 - - + -
479B LEU* 4.3 12.6 - - + -
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Residues in contact with GLU 468 (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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455B HIS* 2.6 36.8 + - + +
464B LYS* 3.3 14.9 + - - +
465B GLU* 3.2 21.4 + - - +
467B ILE* 1.3 73.7 - - - +
469B ILE* 1.3 67.8 + - + +
471B PHE* 4.5 0.4 - - - -
472B SER* 3.4 3.5 + - - -
485B PHE* 4.3 7.2 - - + -
489B ILE* 4.5 17.0 - - + +
491B MET* 1.9 53.5 - - + +
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Residues in contact with ILE 469 (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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423B VAL* 5.6 10.1 - - + -
465B GLU* 2.9 23.6 + - + +
466B THR* 3.2 9.6 + - - +
468B GLU* 1.3 76.2 - - + +
470B LEU* 1.3 65.4 + - + +
472B SER* 2.5 26.8 + - - +
473B GLU* 3.2 19.7 + - + +
1039B SER* 5.4 4.9 - - - +
1040B LEU* 6.1 0.9 - - - -
1041B TYR* 5.0 20.6 - - + +
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Residues in contact with LEU 470 (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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420B VAL* 4.1 21.1 - - + +
423B VAL* 4.4 14.1 - - + -
424B PHE* 5.4 1.8 - - + +
448B LEU* 3.0 43.7 - - + -
466B THR* 2.9 25.8 + - + +
467B ILE* 3.5 1.1 - - - +
469B ILE* 1.3 77.4 - - + +
471B PHE* 1.3 63.9 + - - +
473B GLU* 3.1 15.5 + - + +
475B LEU* 3.3 49.8 + - + +
476B ILE* 3.4 20.4 - - + -
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Residues in contact with PHE 471 (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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388B PRO* 4.3 14.6 - - + -
389B VAL 4.5 5.8 - - - -
390B ILE* 4.3 8.5 - - + -
467B ILE 2.9 17.2 + - - +
468B GLU* 3.9 4.7 - - - +
469B ILE 3.3 0.2 - - - -
470B LEU* 1.3 73.2 - - - +
472B SER* 1.3 65.5 + - - +
474B GLY* 3.0 14.9 + - - -
476B ILE* 3.4 42.2 + - + +
479B LEU* 4.1 28.0 - - + -
485B PHE* 5.7 0.4 - + - -
491B MET* 4.1 27.1 - - + -
492B PRO 3.3 24.0 - - - -
493B ALA* 3.8 23.3 - - + -
526B ARG* 5.8 1.1 - - - -
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Residues in contact with SER 472 (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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468B GLU 3.4 8.6 + - - -
469B ILE* 2.5 26.7 + - - +
471B PHE* 1.3 84.2 - - - +
473B GLU* 1.3 65.4 + - - +
474B GLY* 3.4 0.7 + - - -
491B MET* 4.1 12.1 - - - -
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Residues in contact with GLU 473 (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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469B ILE* 3.7 23.2 - - + +
470B LEU* 3.1 11.2 + - + +
472B SER* 1.3 81.5 + - - +
474B GLY* 1.3 58.3 + - - +
475B LEU* 3.8 21.8 + - + +
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Residues in contact with GLY 474 (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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416B GLU* 4.6 8.4 - - - +
471B PHE 3.0 13.3 + - - -
472B SER 3.2 0.8 - - - -
473B GLU* 1.3 78.5 - - - +
475B LEU* 1.3 67.2 + - - +
476B ILE* 3.2 7.9 + - - -
477B LYS* 4.7 10.2 + - - +
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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