Contacts of the helix formed by residues 472 - 488 (chain B) in PDB entry 4OSV
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 GLY 472 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B ILE 3.3 3.7 + - - -
471B GLY* 1.3 78.6 - - - +
473B GLY* 1.3 66.3 + - - +
475B GLN* 3.7 6.4 + - - +
476B ALA* 3.0 36.1 + - - -
502B ALA 3.2 11.7 - - - -
503B SER 3.0 5.5 + - - -
504B ASN 3.0 10.7 + - - -
507B GLY 4.3 3.4 - - - -
5G T 5.8 0.3 - - - +
6G T 4.2 6.2 + - - -
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Residues in contact with GLY 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ALA* 4.4 6.1 - - - -
467B ILE 2.9 10.6 + - - -
468B ALA* 3.8 17.7 + - - -
471B GLY 3.2 4.9 - - - -
472B GLY* 1.3 78.2 - - - +
474B LYS* 1.3 62.5 + - - -
476B ALA* 3.8 0.3 - - - +
477B LEU* 3.0 31.4 + - - +
5G T 5.6 0.9 - - - -
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Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLY 5.5 0.2 + - - -
441B GLN* 3.0 43.7 + - + +
442B ALA* 4.2 6.4 - - - +
445B THR* 3.1 33.2 - - - +
448B ARG* 4.5 3.6 - - - +
472B GLY 3.7 0.2 + - - -
473B GLY* 1.3 71.0 - - - -
475B GLN* 1.3 78.0 + - - +
477B LEU* 3.2 3.3 + - - +
478B GLU* 3.0 46.9 + - - +
5G T 3.4 24.3 + - - +
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Residues in contact with GLN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B GLY 3.7 1.5 + - - +
473B GLY 3.3 0.8 - - - -
474B LYS* 1.3 94.3 - - - +
476B ALA* 1.3 53.5 + - - +
478B GLU* 3.5 12.9 + - - +
479B THR* 2.6 38.3 + - - -
508B LYS* 3.3 35.1 + - + +
5G T 2.9 55.1 + - - +
6G T 3.5 16.8 - - - +
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ILE* 3.6 9.9 - - + -
472B GLY* 3.0 40.7 + - - +
475B GLN* 1.3 75.3 - - - +
477B LEU* 1.3 60.6 + - - +
479B THR* 3.7 3.2 - - - -
480B VAL* 2.8 34.8 + - - +
502B ALA* 3.4 18.2 - - + +
508B LYS* 4.0 17.0 - - - +
511B LEU* 5.3 0.2 - - - -
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ALA 4.2 2.7 - - - +
445B THR* 3.8 27.4 - - + +
446B VAL* 3.5 28.7 - - + +
449B LEU* 4.0 8.9 - - + +
453B LEU* 3.9 25.1 - - + +
464B VAL* 3.8 21.1 - - + +
467B ILE* 3.8 25.1 - - + +
468B ALA* 4.0 8.3 - - + -
473B GLY 3.0 21.4 + - - +
474B LYS 3.2 6.5 + - - +
476B ALA* 1.3 77.3 - - - +
478B GLU* 1.3 62.4 + - - +
480B VAL* 3.4 4.2 + - - +
481B GLN* 3.1 21.1 + - - +
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Residues in contact with GLU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B THR* 4.1 10.5 - - + -
448B ARG* 2.8 29.8 + - - +
449B LEU* 4.2 11.2 - - + -
474B LYS* 3.0 38.5 + - - +
475B GLN* 3.9 14.2 + - - +
477B LEU* 1.3 75.1 - - - +
479B THR* 1.3 63.6 + - - +
481B GLN* 3.4 9.5 + - - +
482B ARG* 3.2 21.5 + - - +
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Residues in contact with THR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B GLN 2.6 23.1 + - - -
476B ALA 3.2 4.0 + - - -
478B GLU* 1.3 74.0 - - - +
480B VAL* 1.3 55.8 + - - +
482B ARG* 3.3 9.9 + - - +
483B LEU* 2.7 59.5 + - + +
508B LYS* 3.3 25.2 - - - +
511B LEU* 3.8 20.4 - - + -
512B GLU* 4.1 16.7 + - + +
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU* 4.3 5.8 - - + -
459B LEU* 4.0 18.8 - - + -
467B ILE* 3.9 11.9 - - + -
476B ALA 2.8 19.5 + - - +
477B LEU* 3.8 4.5 - - - +
479B THR* 1.3 74.0 - - - +
481B GLN* 1.3 65.5 + - - +
483B LEU* 4.3 1.1 - - - +
484B LEU* 2.9 54.3 + - + +
498B VAL* 4.1 11.2 - - + -
499B VAL* 5.8 0.7 - - + -
502B ALA* 3.4 29.6 - - + -
511B LEU* 3.7 9.9 - - + -
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Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ARG* 5.0 2.8 + - - -
449B LEU* 3.5 33.7 - - + +
452B VAL* 4.2 13.9 - - + +
453B LEU* 4.0 17.5 - - + +
457B HIS* 3.3 31.9 + - + -
477B LEU 3.1 13.3 + - - +
478B GLU* 3.4 13.6 - - - +
479B THR 3.3 0.2 - - - -
480B VAL* 1.3 77.5 - - - +
482B ARG* 1.3 63.7 + - + +
485B PRO* 3.4 7.6 - - - +
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Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLU 3.2 10.5 + - - +
479B THR* 3.7 12.4 + - - +
480B VAL 3.2 0.2 - - - -
481B GLN* 1.3 83.0 - - + +
483B LEU* 1.3 79.9 + - + +
485B PRO* 3.4 17.6 - - - +
486B VAL* 3.9 10.0 - - + +
512B GLU* 3.5 25.5 + - - +
515B GLN* 4.2 17.8 + - - +
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B THR* 2.7 43.3 + - + +
480B VAL* 5.0 1.6 - - - -
482B ARG* 1.3 94.1 - - + +
484B LEU* 1.3 59.8 + - - +
485B PRO 3.4 0.9 - - - -
486B VAL* 3.0 14.1 + - + -
487B LEU* 2.8 44.7 + - + +
498B VAL* 5.6 1.8 - - + -
511B LEU* 4.0 29.2 - - + +
512B GLU* 4.3 6.7 - - + +
515B GLN* 3.4 42.0 - - + +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU* 4.9 0.2 - - + -
457B HIS* 3.6 42.8 - - + +
459B LEU* 4.0 13.0 - - + -
480B VAL* 2.9 41.6 + - + +
483B LEU* 1.3 76.0 - - - +
485B PRO* 1.3 63.6 - - + +
486B VAL 3.0 0.2 + - - -
488B CYS* 3.0 61.8 + - - +
495B PRO* 4.2 13.2 - - + -
498B VAL* 3.9 22.6 - - + +
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Residues in contact with PRO 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B HIS* 4.2 13.0 - - + +
481B GLN 3.4 12.8 - - - +
482B ARG* 3.4 17.7 - - - +
484B LEU* 1.3 92.5 - - + +
486B VAL* 1.3 59.7 + - + +
488B CYS* 4.6 0.7 - - + -
489B GLN* 3.4 29.3 + - - +
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 3.9 16.2 - - + +
483B LEU* 3.0 18.1 + - + +
484B LEU 3.0 0.6 - - - -
485B PRO* 1.3 85.1 - - + +
487B LEU* 1.3 71.2 + - + +
488B CYS 3.5 0.4 - - - -
489B GLN* 4.3 12.1 + - - +
515B GLN* 3.6 26.0 - - + +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.8 29.4 + - + +
486B VAL* 1.3 80.7 - - + +
488B CYS* 1.3 53.1 + - - +
489B GLN 3.3 8.0 + - - -
492B GLY* 3.6 3.3 - - - -
493B LEU* 2.7 57.6 + - + +
498B VAL* 4.5 9.2 - - + -
511B LEU* 4.1 35.7 - - + +
514B VAL* 4.7 9.4 - - + -
515B GLN* 4.2 33.0 - - + +
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Residues in contact with CYS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 3.0 45.8 + - + +
485B PRO* 5.3 0.4 - - + -
486B VAL 3.5 0.4 - - - -
487B LEU* 1.3 76.8 - - - +
489B GLN* 1.3 73.2 + - - +
493B LEU 3.1 20.6 - - - +
495B PRO* 3.5 26.9 - - + -
498B VAL* 3.6 13.0 - - - -
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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