Contacts of the helix formed by residues 546 - 559 (chain B) in PDB entry 4P0S
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 546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528B ALA* 3.1 15.1 + - - -
544B ARG* 3.5 6.4 - - - +
545B ILE* 1.3 86.3 - - - +
547B PRO* 1.3 75.7 - - - +
548B GLU 3.6 1.6 - - - -
549B LEU 3.9 1.9 + - - -
550B SER* 3.3 21.0 + - - -
45J G 3.1 16.4 - - - -
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Residues in contact with PRO 547 (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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524B GLN* 5.0 2.3 - - - +
525B ASN* 5.3 12.4 - - - +
528B ALA* 4.2 13.4 - - + -
544B ARG* 4.2 15.0 - - - +
546B GLY* 1.3 82.2 - - - +
548B GLU* 1.3 67.0 + - - +
550B SER* 3.4 3.9 + - - -
551B ARG* 3.2 18.7 + - - +
45J G 3.2 29.4 - - + +
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Residues in contact with GLU 548 (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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491B ARG* 3.4 7.5 + - - -
547B PRO* 1.3 81.9 - - - +
549B LEU* 1.3 62.4 + - - +
551B ARG* 2.8 38.9 + - + +
552B ARG* 2.9 50.3 + - - +
566B LEU 4.5 2.8 - - - +
44J A 2.9 31.0 - - - +
45J G 2.8 27.7 + - - +
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Residues in contact with LEU 549 (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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489B LEU* 5.7 2.2 - - + -
490B ASN 4.9 0.4 - - - +
491B ARG* 4.9 7.6 - - + +
492B VAL* 3.9 25.6 - - + -
496B MET* 4.0 27.4 - - + -
500B VAL* 6.1 0.4 - - + -
545B ILE* 3.7 42.2 - - + +
546B GLY 3.9 2.4 + - - +
547B PRO 3.3 0.2 - - - -
548B GLU* 1.3 82.5 + - - +
550B SER* 1.3 66.1 + - - +
551B ARG 2.9 2.1 + - - -
552B ARG* 3.4 16.7 + - + +
553B ILE* 3.2 44.5 + - + +
45J G 4.8 3.5 + - - -
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Residues in contact with SER 550 (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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514B TYR* 4.7 1.9 + - - -
523B ARG 4.8 0.2 + - - -
524B GLN 2.6 27.8 + - - +
525B ASN* 3.5 1.9 - - - -
526B LEU* 3.6 0.5 + - - +
527B LEU* 3.1 33.4 + - - +
528B ALA* 3.4 20.2 + - - -
545B ILE* 4.5 1.7 - - - +
546B GLY 3.3 16.9 + - - -
547B PRO 3.4 6.0 + - - -
549B LEU* 1.3 78.8 - - - +
551B ARG* 1.3 55.9 + - - +
553B ILE* 3.6 5.3 + - - +
554B TYR* 3.0 24.9 + - - +
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Residues in contact with ARG 551 (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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524B GLN* 4.0 32.7 + - + +
547B PRO 3.2 8.3 + - - +
548B GLU* 2.8 28.7 + - - +
549B LEU 2.9 0.8 - - - -
550B SER* 1.3 74.6 - - - +
552B ARG* 1.3 71.7 + - - +
553B ILE 3.1 1.3 - - - -
554B TYR* 3.9 2.2 - - - +
555B LEU* 2.9 57.5 + - + +
564B LEU* 5.9 3.8 - - - +
565B SER 4.8 6.5 + - - -
566B LEU* 4.3 15.6 + - - +
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Residues in contact with ARG 552 (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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489B LEU* 4.1 14.1 - - + +
490B ASN* 2.5 55.1 + - - +
491B ARG* 2.6 31.5 - - - +
492B VAL* 5.3 0.2 - - - +
548B GLU* 2.9 44.1 + - - +
549B LEU* 3.4 15.4 + - + +
551B ARG* 1.3 84.2 - - + +
553B ILE* 1.3 52.2 + - + +
555B LEU* 3.6 7.3 - - - +
556B GLN* 2.6 39.6 + - - +
566B LEU* 3.5 51.0 - - + +
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Residues in contact with ILE 553 (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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486B ILE* 5.2 14.8 - - + -
489B LEU* 4.9 12.6 - - + -
500B VAL* 4.1 22.0 - - + -
510B LEU* 4.9 8.1 - - + -
514B TYR* 4.1 5.6 + - - +
527B LEU* 3.6 33.4 - - + -
545B ILE* 5.7 0.9 - - + -
549B LEU* 3.2 36.9 + - + +
550B SER* 3.7 4.7 - - - +
551B ARG 3.1 0.6 - - - -
552B ARG* 1.3 73.7 - - - +
554B TYR* 1.3 67.8 + - - +
556B GLN* 3.7 4.2 - - - +
557B MET* 3.3 30.1 + - + +
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Residues in contact with TYR 554 (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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514B TYR* 3.5 31.6 + + - +
520B ASP* 2.7 40.7 + - + +
523B ARG* 3.4 47.1 + - + +
524B GLN* 3.7 23.6 - - + -
550B SER 3.0 19.0 + - - +
551B ARG 4.0 3.1 - - - +
553B ILE* 1.3 79.0 - - - +
555B LEU* 1.3 81.8 + - + +
557B MET* 3.4 5.4 + - - +
558B THR* 3.1 45.0 + - + +
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Residues in contact with LEU 555 (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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524B GLN* 5.7 3.4 - - - +
551B ARG* 2.9 66.7 + - + +
552B ARG* 3.6 5.8 - - + +
554B TYR* 1.3 95.9 - - + +
556B GLN* 1.3 63.8 + - - +
557B MET 3.2 0.9 + - - -
558B THR* 3.4 11.9 + - - +
559B THR* 3.5 24.9 + - - +
564B LEU* 4.5 25.4 - - + -
565B SER 5.2 6.3 - - - +
566B LEU* 5.5 6.3 - - + -
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Residues in contact with GLN 556 (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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472A ARG 4.9 5.2 + - - +
474A VAL* 2.7 49.7 - - + +
475A PHE* 3.2 22.0 - - - +
478A GLN* 3.2 27.0 + - - +
499A THR* 4.3 1.9 + - - -
500A PRO* 3.0 26.6 - - - +
489B LEU* 4.2 9.0 - - + -
552B ARG 2.6 22.4 + - - +
553B ILE* 3.7 7.9 - - - +
554B TYR 3.3 0.2 - - - -
555B LEU* 1.3 75.9 - - - +
557B MET* 1.3 62.9 + - + +
558B THR 3.7 0.2 + - - -
559B THR* 5.2 1.4 - - - +
566B LEU* 4.3 7.8 - - + +
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Residues in contact with MET 557 (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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478A GLN* 4.0 24.0 - - - +
500A PRO* 3.5 32.4 - - + +
501A ALA* 3.3 20.0 + - - +
504A LEU* 4.4 15.7 - - + +
544A TYR* 4.8 17.7 - - + -
482B TRP* 4.8 20.0 - - + -
485B GLN* 5.9 0.7 - - - +
507B PRO* 5.6 2.5 - - + -
510B LEU* 4.8 19.3 - - + -
511B VAL* 5.9 0.2 - - - +
514B TYR* 5.1 4.0 - - + -
553B ILE* 3.3 21.4 + - + +
554B TYR 4.4 1.8 - - - +
555B LEU 3.2 1.0 - - - -
556B GLN* 1.3 79.0 - - + +
558B THR* 1.3 63.1 + - + +
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Residues in contact with THR 558 (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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501A ALA* 2.8 24.8 - - - +
511B VAL* 6.1 4.9 - - + -
514B TYR* 4.3 20.6 - - + -
523B ARG* 5.7 1.1 - - - -
554B TYR* 3.1 48.0 + - + +
555B LEU* 3.4 3.8 + - - -
556B GLN 3.5 0.4 - - - -
557B MET* 1.3 84.1 - - + +
559B THR* 1.3 69.9 + - - +
560B LEU* 3.6 2.6 + - - +
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Residues in contact with THR 559 (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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472A ARG 6.1 1.1 - - - +
499A THR* 2.1 39.1 + - - +
555B LEU* 3.5 20.7 + - - +
556B GLN* 5.2 1.8 - - - +
558B THR* 1.3 82.2 + - - +
560B LEU* 1.3 51.8 + - - +
561B GLN* 3.0 48.8 + - + +
564B LEU* 4.2 17.0 - - + -
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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
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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