Contacts of the helix formed by residues 544 - 559 (chain J) in PDB entry 2A07
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 ASN 544 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543J ARG* 1.3 88.3 - - + +
545J ALA* 1.3 65.9 + - - +
546J ALA* 3.2 4.0 - - - +
547J THR* 3.0 23.6 + - - +
548J TRP* 3.2 12.4 + - + -
544K ASN* 3.2 40.4 - - - +
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Residues in contact with ALA 545 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543J ARG 3.2 3.0 - - - -
544J ASN* 1.3 75.3 - - - +
546J ALA* 1.3 63.7 + - - +
548J TRP* 3.3 19.1 - - + +
549J LYS* 2.9 55.3 + - + +
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Residues in contact with ALA 546 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544J ASN* 3.2 2.3 + - - -
545J ALA* 1.3 78.6 - - - +
547J THR* 1.3 60.8 + - - +
549J LYS* 4.9 1.3 - - - +
550J ASN* 3.3 22.9 + - - +
553J ARG* 5.1 0.9 + - - -
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Residues in contact with THR 547 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A C 4.7 19.3 - - + +
12A A 3.2 29.3 + - - +
509J TYR* 5.7 0.2 - - - +
540J TYR* 6.1 1.1 - - - +
544J ASN* 3.0 21.2 + - - +
546J ALA* 1.3 79.5 - - - +
548J TRP* 1.3 68.3 + - + +
550J ASN* 3.4 8.6 + - - +
551J ALA* 3.1 18.7 + - + +
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Residues in contact with TRP 548 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509J TYR* 3.2 24.7 - - - +
531J TYR* 3.6 27.1 - + - -
534J PHE* 3.7 19.3 - + + -
535J THR* 3.4 23.1 - - + -
540J TYR* 4.9 4.0 - + + -
541J PHE* 3.1 52.8 + + + -
543J ARG 3.3 13.5 + - - +
544J ASN* 3.2 23.4 + - + -
545J ALA* 3.3 17.5 - - + +
547J THR* 1.3 80.4 - - + +
549J LYS* 1.3 90.3 + - + +
551J ALA* 3.2 3.3 + - - +
552J VAL* 2.9 40.8 + - + +
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Residues in contact with LYS 549 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528J ASN* 5.5 2.4 - - - +
531J TYR* 3.7 48.7 + - + +
535J THR* 5.6 1.3 - - - -
545J ALA* 2.9 38.8 + - + +
546J ALA* 4.9 1.3 - - - +
548J TRP* 1.3 101.7 - - + +
550J ASN* 1.3 60.4 + - - +
552J VAL* 3.3 2.7 + - - +
553J ARG* 3.0 46.1 + - - +
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Residues in contact with ASN 550 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A A 3.5 21.4 + - - +
13A A 3.0 49.1 + - - +
14A A 5.0 1.4 + - - -
10B T 4.7 2.4 - - - +
546J ALA 3.3 21.5 + - - +
547J THR* 3.4 5.7 + - - +
549J LYS* 1.3 78.9 - - - +
551J ALA* 1.3 56.7 + - - +
553J ARG* 3.3 25.9 + - - +
554J HIS* 2.9 29.4 + - - +
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Residues in contact with ALA 551 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 5.7 2.9 - - + -
11A C 4.9 12.1 - - + +
509J TYR* 3.5 35.9 - - + +
547J THR* 3.1 13.8 + - + +
548J TRP* 3.4 9.0 - - - +
550J ASN* 1.3 77.2 - - - +
552J VAL* 1.3 57.5 + - - +
554J HIS* 3.6 6.6 - - - +
555J ASN* 2.9 37.7 + - - +
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Residues in contact with VAL 552 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509J TYR* 4.1 8.1 - - + -
513J ILE* 3.9 11.6 - - + +
527J LEU* 4.2 9.6 - - + -
530J ILE* 4.0 19.5 - - + -
531J TYR* 4.3 5.2 - - + -
534J PHE* 4.0 24.9 - - + -
548J TRP* 2.9 37.5 + - + +
549J LYS 3.6 7.6 - - - +
550J ASN 3.2 0.2 - - - -
551J ALA* 1.3 76.0 - - - +
553J ARG* 1.3 63.5 + - - +
555J ASN* 3.3 2.4 + - - +
556J LEU* 2.9 40.5 + - + +
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Residues in contact with ARG 553 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A A 5.9 0.6 - - - +
8B A 4.3 13.2 + - - -
9B A 3.6 38.3 + - + +
10B T 3.4 20.2 + - + +
527J LEU* 4.0 20.0 - - + -
531J TYR* 2.9 30.5 + - - +
546J ALA 5.1 1.4 + - - -
549J LYS* 3.0 31.8 + - - +
550J ASN* 3.5 35.4 + - - +
552J VAL* 1.3 75.5 - - - +
554J HIS* 1.3 63.1 + - - +
556J LEU* 3.3 10.1 + - - +
557J SER* 3.1 19.8 + - - -
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Residues in contact with HIS 554 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 4.6 7.5 + + - -
11A C 3.0 32.4 + + + -
12A A 3.7 4.7 + - - +
13A A 4.7 5.8 - - - +
10B T 3.9 10.5 - - - +
11B T 2.9 23.7 + + - +
12B T 3.1 22.5 + + + -
13B G 4.4 1.3 - - - -
550J ASN* 2.9 18.7 + - - +
551J ALA* 3.6 6.1 - - - +
553J ARG* 1.3 77.7 - - - +
555J ASN* 1.3 71.5 + - - +
557J SER* 3.8 1.2 - - - -
558J LEU* 2.8 67.4 + - + +
559J HIS* 5.8 0.2 - - - -
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Residues in contact with ASN 555 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A A 6.0 1.2 - - - +
10A A 4.4 8.5 + - - -
509J TYR* 3.4 29.9 - - - +
510J ALA* 3.8 9.9 - - - +
513J ILE* 3.6 19.3 - - + -
551J ALA* 2.9 26.9 + - - +
554J HIS* 1.3 86.2 - - - +
556J LEU* 1.3 65.8 + - - +
558J LEU* 4.6 0.2 - - - -
559J HIS* 3.0 58.3 + - + -
562J PHE* 3.5 7.6 - - + -
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Residues in contact with LEU 556 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J ILE* 3.6 31.9 - - + -
527J LEU* 3.7 29.8 - - + -
530J ILE* 4.2 5.6 - - + -
552J VAL* 2.9 27.5 + - + +
553J ARG* 3.3 6.3 + - - +
555J ASN* 1.3 76.9 - - - +
557J SER* 1.3 51.5 + - - +
559J HIS 3.5 1.4 - - - +
562J PHE* 3.5 14.2 - - + +
573J TRP* 3.5 62.5 - - + +
605J MG 2.3 31.5 - - - -
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Residues in contact with SER 557 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B A 3.0 20.8 - - - +
10B T 2.6 41.7 + - - +
11B T 3.8 23.1 - - - -
553J ARG 3.1 11.7 + - - -
556J LEU* 1.3 76.8 - - - +
558J LEU* 1.3 65.9 + - - +
559J HIS 4.4 0.2 - - - -
560J LYS* 5.7 2.6 + - - +
573J TRP* 4.6 0.7 - - - -
605J MG 3.2 10.2 - - - -
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Residues in contact with LEU 558 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 6.2 0.9 - - - +
11B T 4.2 5.5 - - + +
12B T 4.3 23.6 - - + -
558F LEU* 4.3 32.5 - - + -
559F HIS* 6.5 0.2 - - + -
554J HIS* 2.8 47.7 + - + +
555J ASN 4.2 1.6 - - - +
557J SER* 1.3 76.3 - - - +
559J HIS* 1.3 84.1 + - + +
560J LYS* 3.6 12.1 + - - +
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Residues in contact with HIS 559 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A A 5.0 12.4 - - - +
558F LEU* 6.4 0.2 - - + -
510J ALA* 4.5 6.0 - - + +
554J HIS* 5.8 0.4 + - - -
555J ASN* 3.0 53.8 + - + +
556J LEU 3.5 1.7 - - - +
557J SER 4.4 0.2 - - - -
558J LEU* 1.3 99.7 + - + +
560J LYS* 1.3 61.1 + - - +
561J CYS* 3.8 21.1 - - - -
562J PHE* 3.1 15.4 + + + +
584J ARG* 4.9 10.6 + - - +
605J MG 2.4 25.9 - - - -
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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