Contacts of the helix formed by residues 506 - 523 (chain B) in PDB entry 4OSI
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 506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B GLY 4.5 4.8 + - - -
505B ILE* 1.3 79.6 - - - +
507B GLY* 1.3 60.5 + - - +
508B LYS 3.3 1.6 - - - -
509B GLN* 3.6 8.0 + - - +
510B ALA* 3.1 24.3 + - - +
541B GLY 4.7 3.1 + - - -
9G T 3.9 31.3 + - - +
10G A 3.8 16.2 + - - -
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Residues in contact with GLY 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA* 4.7 5.4 - - - +
501B ILE 3.9 16.6 - - - -
502B ALA* 4.0 14.3 - - - -
504B ASN* 2.9 20.4 + - - -
506B GLY* 1.3 70.3 - - - +
508B LYS* 1.3 60.4 + - - +
510B ALA* 3.2 3.8 + - - +
511B LEU* 2.9 37.1 + - - +
9G T 5.1 0.6 + - - -
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Residues in contact with LYS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B GLN* 3.6 35.7 + - + +
476B ALA* 4.2 7.8 - - - +
479B THR* 3.0 37.9 - - + +
482B ARG* 6.1 0.4 - - - +
507B GLY* 1.3 76.2 - - - +
509B GLN* 1.3 69.5 + - - +
511B LEU* 3.6 1.4 - - - +
512B GLU* 2.9 52.5 + - - +
9G T 3.2 28.5 + - - +
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Residues in contact with GLN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLY 3.6 8.0 + - - +
507B GLY 3.3 0.6 - - - -
508B LYS* 1.3 91.9 - - - +
510B ALA* 1.3 57.5 + - - +
512B GLU* 4.4 10.6 + - - +
513B THR* 2.9 36.4 + - - -
542B LYS* 2.9 49.4 + - + -
9G T 3.5 43.0 + - - +
10G A 3.8 15.0 - - - +
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Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ILE* 3.6 13.9 - - + +
506B GLY 3.1 15.3 + - - +
507B GLY* 3.2 10.3 + - - +
509B GLN* 1.3 72.6 - - - +
511B LEU* 1.3 67.4 + - - +
513B THR 3.9 0.2 - - - -
514B VAL* 2.9 22.7 + - - +
536B ALA* 3.3 27.8 - - + +
538B ASN 5.1 1.8 - - - +
541B GLY* 4.3 11.9 - - - +
542B LYS* 4.2 9.8 - - - +
545B LEU* 4.2 4.7 - - - +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA 4.5 0.9 - - - +
479B THR* 3.6 36.1 - - + +
480B VAL* 3.9 24.9 - - + +
483B LEU* 4.8 8.7 - - + -
487B LEU* 5.1 8.1 - - + -
498B VAL* 3.8 29.8 - - + +
501B ILE* 3.7 23.8 - - + -
502B ALA* 4.3 4.3 - - + -
507B GLY 2.9 20.6 + - - +
508B LYS* 3.6 4.3 - - - +
510B ALA* 1.3 68.5 - - - +
512B GLU* 1.3 58.6 + - - +
514B VAL* 2.3 43.1 + - + +
515B GLN* 2.9 9.5 + - - -
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Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B THR* 3.9 11.1 - - - +
482B ARG* 3.3 25.8 + - - -
483B LEU* 4.5 5.1 - - - +
508B LYS* 2.9 37.2 + - - +
509B GLN* 3.9 13.1 + - - +
511B LEU* 1.3 75.7 - - - +
513B THR* 1.3 57.5 + - - +
515B GLN* 3.1 21.6 + - - +
516B ARG* 2.9 35.6 + - + +
542B LYS* 6.3 0.4 - - - -
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Residues in contact with THR 513 (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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509B GLN 2.9 19.6 + - - -
510B ALA 4.2 0.7 - - - -
511B LEU 2.6 3.2 + - - -
512B GLU* 1.3 73.2 - - - +
514B VAL* 1.3 56.5 + - - +
516B ARG* 3.0 35.3 + - - +
517B LEU* 2.9 32.3 + - + +
542B LYS* 3.1 38.6 - - + +
545B LEU* 3.5 32.5 - - + -
546B GLU* 4.7 0.4 - - + -
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 4.4 22.2 - - + -
493B LEU* 6.0 4.0 - - + -
501B ILE* 4.9 12.3 - - + -
510B ALA 2.9 18.2 + - - +
511B LEU* 2.3 35.9 + - + +
513B THR* 1.3 72.4 - - - +
515B GLN* 1.3 58.2 + - + +
517B LEU* 3.8 1.8 - - + +
518B LEU* 2.9 45.7 + - + +
532B VAL* 4.1 27.6 - - + +
533B VAL* 6.2 0.7 - - + -
536B ALA* 4.3 15.7 - - + -
545B LEU* 4.3 6.7 - - + -
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Residues in contact with GLN 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 5.1 1.6 + - - +
483B LEU* 3.9 33.5 - - + +
486B VAL* 5.2 14.5 - - + +
487B LEU* 4.9 13.2 - - + -
511B LEU 2.9 6.6 + - - +
512B GLU* 3.2 23.0 - - - +
514B VAL* 1.3 79.8 - - + +
516B ARG* 1.3 67.8 + - - +
517B LEU 3.4 0.3 + - - -
518B LEU* 5.3 0.7 - - - -
519B PRO* 3.9 13.3 - - - +
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Residues in contact with ARG 516 (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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512B GLU* 2.9 22.5 + - + +
513B THR* 3.0 42.6 + - - +
515B GLN* 1.3 81.7 + - - +
517B LEU* 1.3 81.0 + - - +
519B PRO* 4.3 4.3 - - - +
520B VAL* 3.7 15.6 - - - +
542B LYS* 4.9 2.6 - - - +
546B GLU* 3.2 23.1 + - - +
549B GLN* 4.5 5.7 + - - +
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B THR* 2.9 31.2 + - + +
514B VAL* 4.9 2.0 - - + -
515B GLN 3.3 0.2 - - - -
516B ARG* 1.3 101.3 - - + +
518B LEU* 1.3 68.4 + - - +
519B PRO* 3.2 4.3 - - - -
520B VAL* 3.0 26.5 + - + -
521B LEU* 2.8 39.7 + - + +
545B LEU* 4.3 27.6 - - + +
546B GLU* 4.4 3.6 - - + +
549B GLN* 3.3 30.5 - - - +
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 5.8 0.9 - - + -
492B GLY* 5.1 9.0 - - - +
493B LEU* 3.6 32.3 - - + -
514B VAL* 2.9 27.0 + - + +
515B GLN* 5.3 0.4 - - - -
517B LEU* 1.3 74.2 - - - +
519B PRO* 1.3 72.8 - - + +
521B LEU* 4.8 3.6 - - - -
522B CYS* 3.2 37.6 + - + +
529B PRO* 4.7 14.1 - - + -
532B VAL* 4.2 24.9 - - + +
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Residues in contact with PRO 519 (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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515B GLN 3.9 15.9 - - - +
516B ARG 4.3 3.6 - - - +
517B LEU 3.4 2.7 - - - -
518B LEU* 1.3 92.0 - - + +
520B VAL* 1.3 59.6 + - + +
521B LEU 2.7 1.4 + - - -
522B CYS* 2.6 30.7 + - + -
523B GLN* 2.8 36.6 + - + +
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ARG 3.7 22.7 - - - +
517B LEU* 3.0 28.3 + - + +
519B PRO* 1.3 74.3 - - + +
521B LEU* 1.3 65.6 + - + +
522B CYS 3.5 0.2 - - - -
523B GLN* 4.3 6.9 - - - +
524B ALA* 3.5 22.8 - - - +
525B HIS* 3.5 7.5 + - + -
549B GLN* 4.1 17.7 - - + +
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Residues in contact with LEU 521 (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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517B LEU* 2.8 36.2 + - + +
518B LEU* 4.3 3.6 - - - +
519B PRO 2.7 5.3 + - - -
520B VAL* 1.3 77.7 - - + +
522B CYS* 1.3 58.5 + - - +
524B ALA 4.1 0.4 - - - -
525B HIS* 3.4 17.6 + - + +
526B GLY* 3.2 24.3 + - - -
527B LEU* 4.1 20.4 + - + +
532B VAL* 3.9 36.8 - - + -
535B ILE* 5.4 1.6 - - + -
545B LEU* 4.6 14.1 - - + +
548B VAL* 4.6 14.1 - - + -
549B GLN* 4.2 29.2 - - + +
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Residues in contact with CYS 522 (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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518B LEU* 3.2 21.5 + - + +
519B PRO* 2.6 9.1 + - + -
521B LEU* 1.3 73.7 - - - +
523B GLN* 1.3 62.3 + - - +
524B ALA 3.1 1.3 - - - -
526B GLY* 4.8 8.0 - - - +
527B LEU 2.7 32.0 + - - +
529B PRO* 4.0 20.9 - - - -
532B VAL* 4.0 20.0 - - - -
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Residues in contact with GLN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B PRO* 2.8 39.6 + - + +
520B VAL* 4.3 3.8 - - - +
522B CYS* 1.3 78.5 - - - +
524B ALA* 1.3 62.3 + - + +
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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
------------------------------------------------------------
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