Contacts of the helix formed by residues 544 - 549 (chain I) in PDB entry 6ALH
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 GLY 544 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A A 5.5 2.5 + - - -
18A C 5.1 14.1 - - - -
542I ARG 3.7 2.4 + - - -
543I ALA* 1.3 74.0 - - - +
545I PHE* 1.3 66.2 + - - +
546I GLU* 3.2 10.2 + - - -
547I VAL* 4.0 10.8 - - - +
548I ARG* 2.8 24.5 + - - +
788J LEU* 6.4 0.4 - - - -
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Residues in contact with PHE 545 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544I GLY* 1.3 73.2 - - - -
546I GLU* 1.3 78.4 + - + +
548I ARG* 3.5 7.7 + - + +
549I ASP* 3.3 40.6 + - + +
750J PRO* 4.9 9.6 - - + -
781J LYS* 3.5 36.8 - - + -
784J ALA* 3.9 26.7 - - + -
785J ASP* 3.8 21.3 - - - -
788J LEU* 6.3 2.8 - - + +
933J ARG* 3.5 31.9 - - - +
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Residues in contact with GLU 546 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A G 6.1 0.9 - - - +
18A C 5.0 5.9 + - - -
446I ASP* 3.5 30.1 - - - +
544I GLY* 3.2 6.6 - - - -
545I PHE* 1.3 97.1 + - + +
547I VAL* 1.3 65.2 + - + +
549I ASP* 3.1 24.2 + - - +
933J ARG* 5.9 1.0 + - - -
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Residues in contact with VAL 547 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A G 3.5 44.9 - - + +
446I ASP* 3.5 13.2 - - - +
451I ARG* 3.6 14.4 + - - +
538I LEU* 3.8 21.3 - - + -
543I ALA* 4.1 14.4 - - + -
544I GLY* 4.0 16.6 - - - +
546I GLU* 1.3 76.2 - - + +
548I ARG* 1.3 67.8 + - - +
549I ASP 3.2 4.0 + - - +
570I GLY 3.7 10.9 - - - +
571I LEU* 4.3 6.2 - - + +
573I ASN* 5.1 2.3 + - - -
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Residues in contact with ARG 548 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540I ARG 2.8 28.5 + - - -
541I GLU 4.1 5.1 + - - -
543I ALA* 2.6 42.2 + - + +
544I GLY 2.8 16.9 + - - +
545I PHE* 3.5 10.8 + - + +
546I GLU 3.2 0.6 - - - -
547I VAL* 1.3 78.9 - - - +
549I ASP* 1.3 61.6 + - - +
567I PRO 5.5 3.2 + - - -
568I ASN* 5.3 3.2 - - - +
569I ILE* 3.3 31.0 + - + +
570I GLY* 3.3 22.2 - - - +
571I LEU* 4.0 17.1 - - + +
780J ARG* 3.5 13.1 + - + +
784J ALA* 4.8 21.1 - - + -
788J LEU* 5.2 11.3 - - - +
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Residues in contact with ASP 549 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446I ASP* 5.7 1.9 - - - +
545I PHE* 3.3 36.3 + - + +
546I GLU* 3.1 19.9 + - - +
547I VAL* 3.9 4.7 - - - +
548I ARG* 1.3 81.4 - - - +
550I VAL* 1.3 95.8 + - - +
551I HIS* 3.8 1.9 + - - +
554I HIS* 4.1 7.8 - - - -
750J PRO* 3.3 28.3 - - + +
777J HIS* 4.2 12.4 + - - +
780J ARG* 4.2 9.8 - - - +
781J LYS* 4.8 6.9 - - - +
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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