Contacts of the helix formed by residues 546 - 563 (chain 1) in PDB entry 6AH0
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 ASP 546 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1121 ILE* 4.9 12.4 - - - +
1131 ALA 5.8 0.6 + - - +
5451 GLU* 1.3 69.9 - - - +
5471 GLN* 1.3 68.7 + - - +
5491 ARG* 2.8 15.4 + - - -
5501 HIS* 2.9 10.3 + - - -
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Residues in contact with GLN 547 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5451 GLU* 4.5 0.4 - - - +
5461 ASP* 1.3 71.4 - - - +
5481 GLU* 1.3 65.8 + - - +
5501 HIS* 2.7 16.3 + - - +
5511 LEU* 2.8 13.0 + - - -
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Residues in contact with GLU 548 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5051 LYS* 5.4 12.3 - - - +
5451 GLU* 4.6 9.1 - - - +
5461 ASP 3.2 1.0 - - - -
5471 GLN* 1.3 73.2 - - - +
5491 ARG* 1.3 65.1 + - - +
5511 LEU* 3.9 1.7 - - - +
5521 LEU* 3.0 17.3 + - - -
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Residues in contact with ARG 549 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5391 LEU* 6.5 1.3 - - - +
5441 LEU* 5.8 1.2 - - - +
5451 GLU 4.5 10.3 + - - +
5461 ASP 2.8 9.8 + - - -
5481 GLU* 1.3 79.3 - - - +
5501 HIS* 1.3 64.4 + - - +
5521 LEU* 2.9 9.9 + - - +
5531 VAL* 2.9 10.6 + - - -
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Residues in contact with HIS 550 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5461 ASP 2.9 8.2 + - - -
5471 GLN* 2.7 12.0 + - - +
5491 ARG* 1.3 70.5 - - - +
5511 LEU* 1.3 61.0 + - - +
5531 VAL* 3.2 4.3 + - - +
5541 LYS* 3.0 15.8 + - - -
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Residues in contact with LEU 551 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5471 GLN 2.8 16.9 + - - -
5481 GLU* 3.9 1.6 - - - +
5501 HIS* 1.3 69.7 - - - +
5521 LEU* 1.3 53.4 + - - +
5541 LYS* 2.3 29.7 + - - +
5551 VAL 2.9 9.4 + - - -
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Residues in contact with LEU 552 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5481 GLU 3.0 10.2 + - - -
5491 ARG 2.9 9.6 + - - -
5511 LEU* 1.3 70.3 - - - +
5531 VAL* 1.3 66.0 + - - +
5551 VAL* 3.2 4.9 + - - +
5561 ILE* 3.0 15.1 + - - -
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Residues in contact with VAL 553 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5491 ARG 2.9 12.6 + - - -
5501 HIS* 3.4 6.1 - - - +
5521 LEU* 1.3 75.3 - - - +
5541 LYS* 1.3 53.8 + - - +
5561 ILE* 2.5 26.7 + - - +
5571 ASP* 2.9 10.6 + - - -
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Residues in contact with LYS 554 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5501 HIS 3.0 9.3 + - - -
5511 LEU* 2.3 19.5 + - - +
5531 VAL* 1.3 67.1 - - - +
5551 VAL* 1.3 61.4 + - - +
5571 ASP* 3.5 1.5 + - - +
5581 ARG* 2.9 22.2 + - - -
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Residues in contact with VAL 555 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5511 LEU 2.9 9.9 + - - -
5521 LEU* 3.2 5.2 + - - +
5531 VAL 3.0 0.4 - - - -
5541 LYS* 1.3 77.2 - - - +
5561 ILE* 1.3 61.9 + - - +
5581 ARG* 5.1 0.4 - - - +
5591 ILE* 3.0 23.3 + - - +
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Residues in contact with ILE 556 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5521 LEU 3.0 8.8 + - - -
5531 VAL* 2.5 18.0 + - - +
5551 VAL* 1.3 69.3 - - - +
5571 ASP* 1.3 64.6 + - - +
5591 ILE 4.0 0.2 - - - -
5601 LEU* 3.0 15.8 + - - -
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Residues in contact with ASP 557 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5531 VAL 2.9 10.6 + - - -
5541 LYS* 4.0 1.8 - - - +
5561 ILE* 1.3 73.8 - - - +
5581 ARG* 1.3 55.2 + - - +
5601 LEU* 2.4 28.3 + - - +
5611 TYR* 2.9 9.4 + - - -
5961 ILE* 5.8 8.5 - - - +
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Residues in contact with ARG 558 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5201 THR* 6.1 2.7 - - - -
5541 LYS 2.9 20.8 + - - -
5551 VAL* 3.9 0.7 - - - +
5571 ASP* 1.3 69.2 - - - +
5591 ILE* 1.3 62.9 + - - +
5611 TYR* 2.8 16.1 + - - +
5621 LYS 3.8 2.3 + - - -
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Residues in contact with ILE 559 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5201 THR* 5.9 6.7 - - - +
5231 ALA* 6.0 6.1 - - - +
5551 VAL 3.0 14.8 + - - -
5561 ILE 4.0 0.4 - - - -
5581 ARG* 1.3 75.6 - - - +
5601 LEU* 1.3 58.1 + - - +
5621 LYS* 3.1 15.0 + - - +
5631 LEU* 3.3 12.8 + - - -
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Residues in contact with LEU 560 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5561 ILE 3.0 11.9 + - - -
5571 ASP* 2.4 23.4 + - - +
5591 ILE* 1.3 67.7 - - - +
5611 TYR* 1.3 62.7 + - - -
5621 LYS* 3.1 0.9 - - - -
5631 LEU 3.9 13.0 - - - +
5991 ASN* 4.8 11.7 - - - +
6031 ALA* 5.9 1.0 - - - -
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Residues in contact with TYR 561 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5571 ASP 2.9 5.0 + - - -
5581 ARG 2.8 12.5 + - - -
5601 LEU* 1.3 79.1 - - - +
5621 LYS* 1.3 61.3 + - - +
5631 LEU 4.8 0.2 - - - -
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Residues in contact with LYS 562 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5581 ARG 3.8 2.2 + - - -
5591 ILE* 3.1 8.8 + - - +
5611 TYR* 1.3 80.2 - - - +
5631 LEU* 1.3 68.0 + - - +
5641 ASP* 3.3 2.8 + - - -
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Residues in contact with LEU 563 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5591 ILE 3.3 11.3 + - - -
5601 LEU* 3.9 14.9 - - - +
5621 LYS* 1.3 75.4 - - - +
5641 ASP* 1.3 59.0 + - - +
5661 LEU* 4.6 5.6 - - - +
5671 VAL* 5.2 2.7 - - - +
6031 ALA* 5.6 2.8 - - - -
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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