Contacts of the helix formed by residues 544 - 559 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544J ASN* 3.2 41.1 - - - +
543K ARG* 1.3 88.2 - - - +
545K ALA* 1.3 65.4 + - - +
546K ALA* 3.2 4.5 - - - +
547K THR* 3.0 24.0 + - - +
548K TRP* 3.2 12.2 + - + -
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Residues in contact with ALA 545 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543K ARG* 3.2 3.3 - - - +
544K ASN* 1.3 75.5 - - - +
546K ALA* 1.3 62.7 + - - +
548K TRP* 3.3 17.7 - - + +
549K LYS* 2.9 57.8 + - + +
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Residues in contact with ALA 546 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544K ASN* 3.2 2.0 - - - -
545K ALA* 1.3 77.7 - - - +
547K THR* 1.3 59.0 + - - +
549K LYS* 4.9 1.3 - - - +
550K ASN* 3.2 25.8 + - - +
553K ARG* 5.1 1.6 + - - -
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Residues in contact with THR 547 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C C 4.6 20.2 - - + +
12C A 3.1 30.8 + - - +
509K TYR* 5.6 0.4 - - - +
540K TYR* 6.1 0.7 - - - +
544K ASN* 3.0 20.6 + - - +
546K ALA* 1.3 78.7 - - - +
548K TRP* 1.3 68.2 + - + +
550K ASN* 3.4 8.1 + - - +
551K ALA* 3.1 19.3 + - + +
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Residues in contact with TRP 548 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509K TYR* 3.2 24.5 - - - +
531K TYR* 3.7 24.5 - + - -
534K PHE* 3.7 19.3 - + + -
535K THR* 3.4 23.1 - - + -
540K TYR* 4.9 4.9 - + + -
541K PHE* 3.2 53.4 + + + -
543K ARG 3.3 13.9 + - - +
544K ASN* 3.2 23.5 + - + -
545K ALA* 3.3 17.3 - - + +
547K THR* 1.3 79.7 - - + +
549K LYS* 1.3 92.6 + - + +
551K ALA* 3.1 3.9 + - - +
552K VAL* 2.9 40.2 + - + +
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Residues in contact with LYS 549 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528K ASN* 5.5 2.4 - - - +
531K TYR* 3.6 48.5 + - + +
535K THR* 5.6 1.6 - - - -
545K ALA* 2.9 35.1 + - + +
546K ALA* 4.9 1.1 - - - +
548K TRP* 1.3 105.9 - - + +
550K ASN* 1.3 65.3 - - - +
552K VAL* 3.3 2.9 + - - +
553K ARG* 3.0 41.6 + - - +
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Residues in contact with ASN 550 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C A 3.4 22.0 + - - +
13C A 3.1 47.9 + - - +
14C A 4.9 1.6 + - - -
10D T 4.7 2.3 - - - +
546K ALA 3.2 21.8 + - - +
547K THR* 3.4 5.8 + - - +
549K LYS* 1.3 79.8 - - - +
551K ALA* 1.3 56.1 + - - +
553K ARG* 3.3 25.8 + - - +
554K HIS* 2.8 30.0 + - - +
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Residues in contact with ALA 551 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C A 5.8 3.4 - - + -
11C C 4.9 9.9 - - + +
509K TYR* 3.5 36.3 - - + +
547K THR* 3.1 14.5 + - + +
548K TRP* 3.3 9.4 - - - +
550K ASN* 1.3 77.6 - - - +
552K VAL* 1.3 56.9 + - - +
554K HIS* 3.4 6.6 + - - +
555K ASN* 2.9 37.4 + - - +
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Residues in contact with VAL 552 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509K TYR* 4.1 8.1 - - + -
513K ILE* 3.9 13.6 - - + +
527K LEU* 4.2 9.0 - - + -
530K ILE* 4.0 23.6 - - + -
531K TYR* 4.3 7.0 - - + -
534K PHE* 3.9 27.1 - - + -
548K TRP* 2.9 34.4 + - + +
549K LYS 3.6 7.6 - - - +
550K ASN 3.3 0.2 - - - -
551K ALA* 1.3 75.9 - - - +
553K ARG* 1.3 64.1 + - - +
555K ASN* 3.2 2.4 + - - +
556K LEU* 2.9 36.6 + - + +
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Residues in contact with ARG 553 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C A 5.9 0.6 - - - +
8D A 4.3 13.1 + - + -
9D A 3.6 38.0 + - + +
10D T 3.3 21.2 + - + +
527K LEU* 3.9 20.4 - - + -
531K TYR* 2.9 35.1 + - - +
546K ALA 5.1 1.4 + - - -
549K LYS* 3.0 27.0 + - - +
550K ASN* 3.4 36.5 + - - +
552K VAL* 1.3 77.3 - - - +
554K HIS* 1.3 62.3 + - - +
556K LEU* 3.3 9.1 + - - +
557K SER* 3.1 19.6 + - - -
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Residues in contact with HIS 554 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C A 4.6 7.5 + + - -
11C C 3.1 32.1 + + + -
12C A 3.6 5.6 + - - +
13C A 4.7 5.8 - - - +
10D T 3.9 9.8 - - - +
11D T 2.9 25.4 + + + +
12D T 3.0 24.4 + + + -
13D G 4.3 1.3 - - - -
550K ASN* 2.8 19.9 + - - +
551K ALA* 3.6 6.3 - - - +
553K ARG* 1.3 77.9 - - - +
555K ASN* 1.3 73.2 + - - +
557K SER* 3.9 1.0 - - - -
558K LEU* 2.9 63.7 + - + +
559K HIS* 5.8 0.4 - - - -
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Residues in contact with ASN 555 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C A 6.0 1.2 - - - +
10C A 4.4 9.2 + - - -
509K TYR* 3.4 29.7 - - - +
510K ALA* 3.8 10.7 - - - +
513K ILE* 3.8 15.3 - - + -
551K ALA* 2.9 26.6 + - - +
552K VAL 3.7 3.6 - - - +
554K HIS* 1.3 86.3 - - - +
556K LEU* 1.3 65.3 + - - +
558K LEU* 4.6 0.2 - - - -
559K HIS* 3.0 58.7 + - + -
562K PHE* 3.5 7.9 - - + -
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Residues in contact with LEU 556 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513K ILE* 3.6 31.4 - - + -
527K LEU* 3.6 31.0 - - + -
530K ILE* 4.2 4.7 - - + -
552K VAL* 2.9 27.0 + - + +
553K ARG* 3.6 5.8 - - - +
555K ASN* 1.3 78.4 - - - +
557K SER* 1.3 50.8 + - - +
559K HIS 3.5 1.4 - - - +
562K PHE* 3.5 22.2 - - + +
573K TRP* 3.6 55.0 - - + +
606K MG 2.3 30.7 - - - -
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Residues in contact with SER 557 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D A 3.0 21.1 - - - +
10D T 2.6 41.1 + - - +
11D T 3.8 21.1 - - - -
553K ARG 3.1 10.7 + - - -
556K LEU* 1.3 75.7 - - - +
558K LEU* 1.3 66.4 + - - +
559K HIS 4.3 0.3 - - - -
560K LYS* 5.5 1.4 - - - +
573K TRP* 4.6 0.7 - - - -
606K MG 3.1 11.8 - - - -
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Residues in contact with LEU 558 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C A 6.2 0.4 - - - +
11D T 4.2 5.1 - - + +
12D T 4.2 23.6 - - + -
558I LEU* 4.3 33.4 - - + -
559I HIS* 6.3 0.9 - - + -
554K HIS* 2.9 48.1 + - + +
555K ASN 4.3 1.1 - - - +
557K SER* 1.3 75.9 - - - +
559K HIS* 1.3 83.5 + - + +
560K LYS* 3.6 9.2 + - - +
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Residues in contact with HIS 559 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C A 5.0 12.0 - - - +
510K ALA* 4.4 7.6 - - + +
554K HIS* 5.8 0.4 - - - -
555K ASN* 3.0 54.9 + - + +
556K LEU 3.5 1.7 - - - +
557K SER 4.3 0.2 - - - -
558K LEU* 1.3 98.0 - - + +
560K LYS* 1.3 61.1 + - - +
561K CYS* 3.8 20.6 - - - -
562K PHE* 3.1 13.7 + + + +
584K ARG* 5.1 9.1 + - - +
606K MG 2.5 25.3 - - - -
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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
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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