Contacts of the helix formed by residues 46 - 57 (chain 7) 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 HIS 46 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427 SER 2.7 15.2 + - - -
437 TYR* 3.8 3.9 + - - +
447 MET 3.6 0.6 - - - -
457 GLY* 1.3 67.7 - - - +
477 PHE* 1.3 69.5 + - - +
487 ASP 2.9 4.1 + - - -
497 LEU* 2.9 15.2 + - - -
507 LEU 3.1 7.8 + - - -
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Residues in contact with PHE 47 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353 GLY* 6.3 2.7 - - - -
437 TYR 5.5 0.4 - - - -
447 MET 5.3 2.0 - - - -
457 GLY 3.0 10.0 + - - -
467 HIS* 1.3 72.3 - - - +
487 ASP* 1.3 67.4 + - - +
507 LEU* 3.0 3.5 + - - -
517 ASN* 2.9 13.9 + - - -
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Residues in contact with ASP 48 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10983 GLY 5.8 2.1 + - - -
10993 GLU* 6.0 2.5 - - - +
11003 THR* 5.3 11.7 - - - +
11223 LEU 6.5 0.7 - - - -
11233 SER* 6.3 2.5 - - - +
467 HIS 2.9 1.4 + - - -
477 PHE* 1.3 71.5 - - - +
497 LEU* 1.3 55.6 + - - +
517 ASN* 2.4 29.4 + - - +
527 TYR* 2.8 9.5 + - - -
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Residues in contact with LEU 49 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10493 LYS 5.0 11.4 - - - -
10503 PHE* 6.1 2.2 - - - +
11003 THR* 5.7 2.2 - - - +
437 TYR* 5.8 3.1 - - - +
467 HIS* 2.9 11.5 + - - +
487 ASP* 1.3 69.2 - - - +
507 LEU* 1.3 66.4 + - - +
527 TYR* 3.1 10.3 + - - +
537 PHE* 3.1 9.0 + - - -
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Residues in contact with LEU 50 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437 TYR* 4.1 15.9 + - - +
467 HIS 3.1 7.5 + - - -
477 PHE* 3.0 7.1 + - - +
487 ASP 2.7 5.1 + - - -
497 LEU* 1.3 72.7 - - - +
517 ASN* 1.3 54.1 + - - +
537 PHE* 2.7 25.1 + - - -
547 ALA* 2.9 9.5 + - - -
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Residues in contact with ASN 51 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477 PHE 2.9 7.6 + - - -
487 ASP* 2.4 18.2 + - - +
507 LEU* 1.3 68.1 - - - +
527 TYR* 1.3 64.8 + - - +
547 ALA* 3.1 3.9 + - - +
557 ILE* 2.9 18.7 + - - -
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Residues in contact with TYR 52 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487 ASP 2.8 10.6 + - - -
497 LEU* 3.4 6.3 - - - +
507 LEU 3.0 0.4 - - - -
517 ASN* 1.3 78.6 - - - +
537 PHE* 1.3 66.1 + - - +
557 ILE* 3.0 7.3 + - - -
567 ALA* 3.1 9.5 + - - -
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Residues in contact with PHE 53 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497 LEU 3.1 8.0 + - - -
507 LEU 2.7 14.0 + - - -
527 TYR* 1.3 69.5 - - - +
547 ALA* 1.3 63.2 + - - +
567 ALA* 2.8 13.9 + - - +
577 GLU 3.1 13.4 + - - +
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Residues in contact with ALA 54 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507 LEU 2.9 11.4 + - - -
517 ASN* 3.1 4.9 + - - +
537 PHE* 1.3 76.1 - - - +
557 ILE* 1.3 59.4 + - - +
577 GLU 2.6 24.5 - - - +
587 ASN* 3.6 6.2 - - - -
597 GLU 3.8 7.8 + - - +
607 SER 5.1 12.1 - - - -
617 LYS* 5.8 2.9 - - - +
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Residues in contact with ILE 55 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8043 HIS 5.8 0.2 + - - -
517 ASN 2.9 13.5 + - - -
527 TYR 3.5 2.7 - - - -
547 ALA* 1.3 78.4 - - - +
567 ALA* 1.3 68.6 + - - +
577 GLU 3.9 1.2 - - - -
587 ASN* 4.0 4.2 + - - -
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Residues in contact with ALA 56 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13021 TYR* 6.1 4.7 - - - +
13031 ILE 5.8 1.3 - - - -
13041 LEU* 5.0 19.5 - - - +
8043 HIS* 4.6 12.6 + - - -
527 TYR 3.1 7.9 + - - -
537 PHE 2.8 12.5 + - - -
557 ILE* 1.3 75.1 - - - +
577 GLU* 1.3 57.4 + - - +
587 ASN 3.4 2.4 + - - -
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Residues in contact with GLU 57 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8043 HIS* 5.7 1.6 - - - +
537 PHE 3.1 8.6 + - - +
547 ALA* 2.6 22.5 - - - +
567 ALA* 1.3 69.6 - - - +
587 ASN* 1.3 61.2 + - - +
597 GLU* 3.1 2.6 + - - -
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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