Contacts of the helix formed by residues 544 - 559 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543F ARG* 1.3 75.5 - - - +
545F ALA* 1.3 62.0 + - - +
546F ALA* 2.6 19.3 + - - +
547F THR* 2.5 53.3 + - - -
548F TRP* 3.1 18.6 + - - -
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Residues in contact with ALA 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F ASN* 1.3 74.9 - - - +
546F ALA* 1.3 57.3 + - - +
548F TRP* 3.2 29.4 - - + +
549F LYS* 2.9 48.2 + - + +
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Residues in contact with ALA 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F ASN* 2.6 21.6 + - - +
545F ALA* 1.3 75.3 - - - +
547F THR* 1.3 58.3 + - - +
549F LYS* 4.2 3.4 - - - +
550F ASN* 3.4 23.2 + - - +
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Residues in contact with THR 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B T 3.5 36.9 + - - +
543F ARG* 4.3 12.7 - - + +
544F ASN* 2.5 41.0 + - - -
546F ALA* 1.3 71.9 - - - +
548F TRP* 1.3 62.8 + - - +
550F ASN* 3.3 8.1 + - - +
551F ALA* 3.0 25.5 + - - +
509G TYR* 4.4 3.1 - - - +
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Residues in contact with TRP 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544F ASN 3.1 26.5 + - - -
545F ALA* 3.2 21.4 - - + +
547F THR* 1.3 76.3 - - - +
549F LYS* 1.3 115.3 + - + +
551F ALA* 3.6 0.7 - - - +
552F VAL* 2.8 37.6 + - + +
509G TYR* 3.3 30.1 - - + +
531G TYR* 3.4 37.2 - + - -
534G PHE* 3.5 28.7 - + + -
535G THR* 3.5 23.8 - - + +
538G PHE* 3.7 42.4 - + + +
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Residues in contact with LYS 549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545F ALA* 2.9 30.1 + - + +
546F ALA* 4.2 4.5 - - - +
548F TRP* 1.3 116.9 - - + +
550F ASN* 1.3 66.1 + - - +
552F VAL* 3.3 1.9 + - - +
553F ARG* 3.2 36.3 + - - +
531G TYR* 3.7 39.5 + - + +
535G THR* 4.6 3.6 + - - -
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Residues in contact with ASN 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A G 5.8 3.2 + - - -
8A A 5.6 3.2 - - - +
14B T 4.2 12.5 + - - +
15B T 3.4 35.3 + - - +
16B T 5.5 1.8 + - - -
546F ALA 3.4 17.6 + - - +
547F THR* 3.3 5.8 + - - +
549F LYS* 1.3 81.7 - - - +
551F ALA* 1.3 68.1 + - - +
553F ARG* 3.2 27.4 + - - +
554F HIS* 3.0 23.5 + - - +
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Residues in contact with ALA 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B G 5.1 3.8 - - + -
14B T 4.1 13.5 - - + +
547F THR 3.0 13.7 + - - +
548F TRP 3.6 0.2 - - - +
550F ASN* 1.3 82.6 + - - +
552F VAL* 1.3 55.3 + - - +
554F HIS* 3.2 6.5 + - - +
555F ASN* 2.9 38.1 + - - +
509G TYR* 3.4 44.0 - - + +
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Residues in contact with VAL 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F TRP* 2.8 32.4 + - + +
549F LYS 3.7 4.9 - - - +
551F ALA* 1.3 70.3 - - - +
553F ARG* 1.3 66.7 + - - +
555F ASN* 3.4 2.8 + - - +
556F LEU* 3.0 36.7 + - + +
509G TYR* 4.1 4.5 - - + -
513G ILE* 4.0 11.4 - - + +
527G LEU* 4.3 1.1 - - + -
530G ILE* 4.1 21.3 - - + -
531G TYR* 4.3 14.8 - - + -
534G PHE* 3.7 39.9 - - + -
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Residues in contact with ARG 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A T 4.3 32.5 + - - +
7A G 3.0 36.5 + - - +
549F LYS* 3.2 27.3 + - - +
550F ASN* 3.2 28.5 + - - +
552F VAL* 1.3 76.9 - - - +
554F HIS* 1.3 63.9 + - - +
556F LEU* 3.2 9.8 + - - +
557F SER* 3.2 25.1 + - - -
527G LEU* 4.6 13.9 - - + -
531G TYR* 3.2 28.9 + - + +
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Residues in contact with HIS 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A A 5.8 3.1 - - - -
9A A 4.2 12.5 + - - -
10A A 4.2 6.7 + - - -
13B G 4.1 18.8 + + - -
14B T 3.0 37.7 + + + +
15B T 4.9 1.6 - - - -
550F ASN* 3.0 18.2 + - - +
551F ALA* 3.3 12.1 - - - +
553F ARG* 1.3 77.7 - - - +
555F ASN* 1.3 69.7 + - - +
557F SER* 3.3 8.9 + - - -
558F LEU* 3.1 62.2 + - + +
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Residues in contact with ASN 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B T 6.0 0.9 - - - +
13B G 4.5 12.3 + - - +
14B T 5.8 0.4 - - - +
551F ALA* 2.9 29.3 + - - +
552F VAL 3.9 0.2 - - - +
553F ARG 3.3 0.2 - - - -
554F HIS* 1.3 85.6 + - - +
556F LEU* 1.3 64.3 + - - +
558F LEU* 4.5 0.7 - - - -
559F HIS* 3.0 56.2 + - + -
562F PHE* 3.5 9.2 - - + -
509G TYR* 3.4 25.4 - - - +
510G ALA* 3.9 11.0 + - - +
513G ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552F VAL* 3.0 25.7 + - + +
553F ARG* 3.2 7.4 + - - +
555F ASN* 1.3 77.7 - - - +
557F SER* 1.3 59.1 + - - +
559F HIS 3.8 11.3 - - - +
562F PHE* 3.9 30.6 - - + +
573F TRP* 3.5 63.0 - - + +
601F MG 4.0 1.4 - - - -
513G ILE* 4.0 22.2 - - + -
527G LEU* 3.7 29.4 - - + -
530G ILE* 4.3 6.1 - - + -
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Residues in contact with SER 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A G 4.9 9.6 + - - +
8A A 3.7 24.0 + - - -
553F ARG 3.2 15.4 + - - -
554F HIS* 3.3 8.8 + - - -
556F LEU* 1.3 75.1 - - - +
558F LEU* 1.3 54.4 + - - +
573F TRP* 5.1 4.0 - - - -
601F MG 2.6 18.8 - - - -
583J ARG* 5.3 9.3 + - - +
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Residues in contact with LEU 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B T 5.0 10.3 - - + -
554F HIS* 3.1 44.8 + - + +
555F ASN* 4.2 3.1 - - - +
557F SER* 1.3 78.0 - - - +
559F HIS* 1.3 81.0 + - + +
560F LYS* 3.7 5.7 + - - +
601F MG 2.9 11.8 - - - -
558J LEU* 4.3 38.1 - - + -
559J HIS* 6.4 0.2 - - + -
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Residues in contact with HIS 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B T 6.3 0.2 - - + -
12B T 4.5 15.1 + - + -
555F ASN* 3.0 52.0 + - + +
556F LEU 3.8 1.9 - - - +
558F LEU* 1.3 96.3 - - + +
560F LYS* 1.3 63.4 + - - +
561F CYS* 3.8 21.3 - - - -
562F PHE* 3.3 30.3 + + + +
583F ARG* 3.8 27.0 + - - -
601F MG 3.5 6.4 - - - -
510G ALA* 4.3 10.3 - - + +
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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