Contacts of the helix formed by residues 471 - 485 (chain B) in PDB entry 5SUY
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 GLU 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B TYR* 3.4 19.8 - - - +
469B PHE* 3.3 2.6 - - - +
470B PRO* 1.3 79.7 - - + +
472B ARG* 1.3 65.8 + - - +
473B ARG* 4.3 18.3 + - - +
474B GLU* 2.9 44.5 + - - +
475B ALA 3.7 4.7 + - - -
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Residues in contact with ARG 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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456B SER* 3.9 6.1 + - - +
459B VAL* 3.4 26.0 - - + +
460B ASP* 3.4 27.7 + - - +
463B TYR* 3.5 36.6 + - + +
471B GLU* 1.3 76.6 + - - +
473B ARG* 1.3 58.5 + - - +
475B ALA* 2.9 21.5 + - - +
476B ARG* 3.0 12.2 + - - +
499B GLU* 2.8 41.8 + - - -
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLU* 3.3 17.3 + - - +
472B ARG* 1.3 77.5 - - - +
474B GLU* 1.3 80.3 + - - +
476B ARG* 3.2 13.1 + - + +
477B LYS* 3.0 25.6 + - - +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE* 3.7 18.8 - - + -
470B PRO* 3.2 24.9 - - + +
471B GLU* 2.9 50.8 + - - +
472B ARG 3.1 1.0 - - - -
473B ARG* 1.3 100.7 + - - +
475B ALA* 1.3 59.8 + - - +
477B LYS* 3.4 9.1 + - + +
478B TYR* 3.1 26.0 + - - +
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Residues in contact with ALA 475 (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 VAL* 4.0 15.0 - - + +
462B LEU* 3.8 6.2 - - + +
463B TYR* 4.0 31.9 - - + +
469B PHE* 3.8 28.9 - - + -
471B GLU 3.7 2.2 + - - -
472B ARG 2.9 11.1 + - - +
474B GLU* 1.3 74.5 - - - +
476B ARG* 1.3 61.7 + - - +
478B TYR* 3.4 2.9 + - - +
479B ALA* 3.1 23.0 + - - +
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Residues in contact with ARG 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B VAL* 3.9 12.0 - - + +
472B ARG* 3.0 12.4 + - - +
473B ARG* 3.2 15.7 + - - +
475B ALA* 1.3 77.0 - - - +
477B LYS* 1.3 62.3 + - - +
479B ALA* 3.3 4.3 + - - +
480B SER* 3.2 20.8 + - - -
496B THR* 5.5 1.6 - - - +
497B PHE* 3.1 42.4 + - + -
498B SER* 4.1 3.0 - - - +
499B GLU* 3.6 47.8 + - - +
500B GLN* 5.3 2.6 + - - -
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ARG 3.0 13.1 + - - +
474B GLU* 3.4 11.9 + - + +
475B ALA 3.3 0.2 - - - -
476B ARG* 1.3 72.4 - - - +
478B TYR* 1.3 66.3 + - - +
480B SER* 3.3 18.5 + - - -
481B GLY* 3.0 18.4 + - - +
484B LYS* 4.0 22.0 - - - +
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Residues in contact with TYR 478 (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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418A SER 5.1 1.2 + - - -
419A VAL* 5.1 18.2 - - + -
421A THR 4.3 4.6 + - - -
423A MET* 3.2 39.2 - - + +
426A VAL* 3.6 29.1 - - + +
462B LEU* 3.8 32.1 - - + -
466B VAL* 5.3 3.6 - - + -
469B PHE* 3.8 25.4 - + + -
474B GLU 3.1 13.4 + - - +
475B ALA 3.5 9.0 - - - +
477B LYS* 1.3 76.9 - - - +
479B ALA* 1.3 61.9 + - - +
481B GLY* 3.0 5.0 + - - +
482B LEU* 3.0 28.7 + - + +
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Residues in contact with ALA 479 (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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458B VAL* 4.0 12.3 - - + -
459B VAL* 4.1 6.1 - - + -
462B LEU* 4.0 16.7 - - + +
475B ALA 3.1 13.6 + - - +
476B ARG 3.3 8.7 + - - +
478B TYR* 1.3 76.1 - - - +
480B SER* 1.3 56.8 + - - +
482B LEU* 3.0 24.6 + - - +
483B LEU* 3.1 12.6 + - - +
488B ILE* 4.0 5.2 - - - +
497B PHE* 3.9 25.8 - - + -
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Residues in contact with SER 480 (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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476B ARG* 3.2 13.4 + - - -
477B LYS* 3.5 22.8 + - - -
479B ALA* 1.3 75.4 - - - +
481B GLY* 1.3 57.5 + - - +
483B LEU* 3.4 4.9 + - - +
484B LYS* 3.1 44.5 + - - +
497B PHE* 3.9 30.0 + - - +
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Residues in contact with GLY 481 (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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423A MET* 4.0 13.0 - - - +
477B LYS* 3.0 13.4 + - - +
478B TYR* 3.0 6.2 + - - -
480B SER* 1.3 73.8 - - - +
482B LEU* 1.3 63.7 + - - +
484B LYS* 3.5 11.4 + - - +
485B ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 482 (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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423A MET* 3.9 30.5 - - + +
426A VAL* 5.8 1.1 - - + -
427A THR* 3.3 26.2 - - - +
430A MET* 4.6 12.6 - - + -
458B VAL* 4.5 10.8 - - + -
462B LEU* 4.3 18.2 - - + -
478B TYR* 3.0 25.2 + - + +
479B ALA* 3.0 20.0 + - - +
481B GLY* 1.3 76.4 - - - +
483B LEU* 1.3 60.7 + - - +
485B ALA* 3.2 2.4 + - - -
486B GLY 3.2 3.6 + - - -
487B LEU* 3.1 37.5 + - + +
488B ILE* 3.9 15.7 - - + -
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Residues in contact with LEU 483 (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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479B ALA 3.1 11.0 + - - +
480B SER* 3.6 7.9 - - - +
481B GLY 3.3 0.2 - - - -
482B LEU* 1.3 74.1 - - - +
484B LYS* 1.3 65.4 + - - +
486B GLY* 3.1 14.2 + - - -
488B ILE* 3.6 31.2 - - + +
489B ARG* 4.0 1.6 - - - -
490B HIS* 3.8 38.6 - - + +
494B LYS 5.5 0.4 - - - +
495B ILE 3.6 23.3 - - - +
497B PHE* 3.8 33.2 - - + +
503B TYR* 4.0 7.6 - - + -
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Residues in contact with LYS 484 (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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477B LYS* 4.0 19.4 - - - +
480B SER* 3.1 28.9 + - - +
481B GLY* 3.5 12.5 + - - +
483B LEU* 1.3 75.2 - - - +
485B ALA* 1.3 61.2 + - - +
486B GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 485 (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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423A MET* 3.9 20.4 - - + -
481B GLY 3.0 17.6 + - - +
482B LEU 3.8 4.5 - - - +
483B LEU 3.2 0.8 - - - -
484B LYS* 1.3 75.4 - - - +
486B GLY* 1.3 59.4 + - - +
487B LEU* 3.3 13.1 + - + +
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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