Contacts of the helix formed by residues 458 - 472 (chain B) in PDB entry 5AM8
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 ARG 458 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLY 5.3 0.4 + - - -
453B ARG 3.5 13.3 + - - -
454B THR* 3.8 1.8 - - - -
455B PRO* 2.8 52.0 + - + +
457B SER* 1.3 83.8 + - - +
459B TYR* 1.3 63.8 + - - +
460B ASN 3.3 2.7 - - - -
461B PHE* 3.6 32.1 - - + -
462B ASP* 3.0 38.2 + - - +
481B GLU* 3.4 6.7 - - - -
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Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LYS* 3.8 19.1 - - + -
175B TYR* 3.9 21.7 + + - -
176B GLU* 3.5 40.3 + - + +
179B THR* 4.2 3.1 + - - +
445B TRP* 3.0 31.1 + + + -
449B VAL* 3.8 31.9 - - + +
454B THR* 3.9 12.3 - - + -
455B PRO 3.3 14.9 + - - -
456B PRO* 3.2 34.9 + - + +
458B ARG* 1.3 75.4 - - - +
460B ASN* 1.3 59.2 + - + +
463B TRP* 3.1 12.8 + - - +
481B GLU* 3.5 2.7 + - - +
483B HIS 5.6 0.4 - - - +
484B PHE* 3.5 29.2 - + + -
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Residues in contact with ASN 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TYR* 1.3 74.3 - - + +
461B PHE* 1.3 67.2 + - - +
462B ASP 3.2 1.6 - - - -
463B TRP* 4.1 3.2 - - - +
464B TRP* 2.9 43.4 + - - +
479B ARG* 3.6 10.9 - - - +
480B ASN 3.6 17.3 + - - +
481B GLU* 3.0 19.3 + - - +
483B HIS* 3.4 18.0 - - - +
484B PHE* 3.6 1.6 - - - -
485B ASP* 2.8 53.2 + - - +
486B ALA 4.3 1.9 + - - -
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Residues in contact with PHE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B SER 5.2 0.2 - - - +
458B ARG* 3.6 31.2 - - + +
460B ASN* 1.3 75.2 - - - +
462B ASP* 1.3 76.0 + - - +
464B TRP* 3.6 3.1 + - - +
465B TYR* 3.0 30.5 + + + +
481B GLU* 2.8 19.5 + - - +
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Residues in contact with ASP 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B TRP* 3.9 7.4 - - + -
453B ARG* 4.4 11.1 + - - +
454B THR* 2.7 38.8 + - + +
458B ARG* 3.0 28.0 + - - +
461B PHE* 1.3 93.0 - - - +
463B TRP* 1.3 66.9 + - - +
465B TYR* 3.6 9.7 - - + +
466B LEU* 3.1 31.1 + - + +
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Residues in contact with TRP 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B HIS* 6.0 0.6 + - - -
257B TRP* 5.9 2.5 - + - -
438B PHE* 4.2 22.2 - + - -
441B LEU* 4.0 15.9 - - + -
442B VAL* 4.2 18.2 - - + -
445B TRP* 3.5 32.9 - + + +
459B TYR 3.1 20.3 + - - +
460B ASN* 3.5 7.4 - - - +
462B ASP* 1.3 78.7 - - - +
464B TRP* 1.3 83.0 + + - +
466B LEU* 3.2 3.4 + - - +
467B ARG* 2.9 65.7 + - + +
485B ASP* 3.8 22.8 - - + +
486B ALA* 3.6 37.7 - - + -
489B LYS* 5.1 8.3 - - + -
492B VAL* 5.5 1.6 - - + -
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Residues in contact with TRP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TRP* 3.7 30.3 - + - -
164B HIS* 5.6 0.2 - - - -
250B ALA* 4.1 3.4 - - + -
460B ASN* 2.9 38.5 + - - +
461B PHE* 4.2 2.9 - - - +
463B TRP* 1.3 92.1 - + - +
465B TYR* 1.3 66.2 + - - +
467B ARG* 3.6 49.4 - - + -
468B THR* 2.9 32.5 + - - +
473B ILE* 4.2 13.7 - - + -
474B CYS 4.1 4.5 - - - -
475B PRO* 3.7 42.0 - - + -
479B ARG* 4.0 8.9 - - + +
485B ASP* 2.8 24.1 + - + -
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Residues in contact with TYR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B PHE* 3.0 22.9 + + + +
462B ASP* 3.6 12.3 - - + +
464B TRP* 1.3 75.8 - - - +
466B LEU* 1.3 68.1 + - + +
468B THR* 3.9 2.2 - - - -
469B LYS* 2.8 77.7 + - + +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 4.1 19.5 - - + +
444B GLN* 4.1 16.4 - - + +
445B TRP* 3.5 45.1 - - + +
462B ASP* 3.1 16.4 + - + +
463B TRP 3.6 5.8 - - - +
465B TYR* 1.3 93.1 - - + +
467B ARG* 1.3 64.8 + - - +
469B LYS* 4.1 3.1 - - + +
470B TYR* 2.9 50.9 + - + +
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Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TRP* 4.9 2.6 - - - +
164B HIS* 4.8 11.3 + - - -
250B ALA* 4.5 5.1 - - - +
257B TRP* 2.8 39.6 + - - +
438B PHE* 3.5 10.0 - - - -
441B LEU* 4.0 14.8 - - + -
463B TRP* 2.9 63.7 + - + +
464B TRP* 3.6 41.0 - - + +
465B TYR 3.4 0.2 - - - -
466B LEU* 1.3 74.9 - - - +
468B THR* 1.3 58.9 + - - +
471B GLN* 2.8 60.3 + - - +
472B GLY 3.2 4.9 + - - -
473B ILE* 3.5 19.5 + - + +
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Residues in contact with THR 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PRO* 4.0 21.8 - - + -
464B TRP* 2.9 22.5 + - - +
465B TYR* 4.0 2.7 - - - -
467B ARG* 1.3 74.0 - - - +
469B LYS* 1.3 66.7 + - - +
472B GLY 3.0 11.2 + - - +
473B ILE 2.9 22.6 + - - +
474B CYS* 4.6 4.9 - - + +
475B PRO* 5.3 1.0 - - - +
594B TRP* 2.9 29.2 + - + +
597B TYR* 4.3 17.3 - - + +
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Residues in contact with LYS 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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444B GLN* 5.2 2.2 + - - -
465B TYR* 2.8 58.6 + - + +
466B LEU* 3.6 6.3 - - + +
468B THR* 1.3 75.0 - - - +
470B TYR* 1.3 97.5 + - + +
594B TRP* 3.5 16.9 + - - +
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Residues in contact with TYR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU* 4.7 4.8 + - - -
215B TYR* 3.7 32.4 + + - -
219B GLU* 5.6 0.9 - - - -
222B TYR* 3.4 18.0 - - - -
223B LEU* 5.7 0.2 - - - +
437B PRO* 3.5 19.8 - - + +
440B TYR* 3.6 24.4 + + - -
441B LEU* 3.9 22.2 - - + -
444B GLN* 3.0 38.8 + - - -
466B LEU* 2.9 31.1 + - + +
469B LYS* 1.3 114.5 + - + +
471B GLN* 1.3 61.7 + - - +
472B GLY 3.4 0.8 + - - -
594B TRP* 3.9 3.8 - - - -
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Residues in contact with GLN 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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222B TYR* 2.4 32.3 + - - +
226B HIS* 3.4 7.1 - - - -
257B TRP 3.7 10.3 + - - -
258B ALA* 3.0 32.3 + - - +
261B TRP* 5.8 0.2 - - - -
434B ALA 4.9 2.6 + - - -
437B PRO* 3.9 21.1 - - + -
438B PHE* 3.3 22.8 - - - +
441B LEU* 3.6 8.2 - - + +
467B ARG* 2.8 52.5 + - - +
470B TYR* 1.3 75.2 - - - +
472B GLY* 1.3 63.1 + - - +
473B ILE* 3.7 14.3 - - + +
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Residues in contact with GLY 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 2.9 13.0 + - - -
247B PRO* 3.2 6.9 - - - +
248B ILE 2.9 20.3 + - - -
467B ARG 3.2 0.6 + - - -
468B THR 3.0 12.6 + - - -
470B TYR 3.4 1.4 - - - -
471B GLN* 1.3 78.1 - - - +
473B ILE* 1.3 60.6 + - - +
594B TRP* 3.2 37.2 - - - -
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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
------------------------------------------------------------
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