Contacts of the helix formed by residues 4997 - 5001 (chain H) in PDB entry 6X34
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 ASP4997 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4993H LEU 5.3 0.4 - - - -
4994H ILE 5.6 0.2 - - - +
4995H ASN 4.1 6.1 - - - +
4996H LYS* 1.3 81.6 - - - +
4998H GLU* 1.3 65.3 + - - +
4999H THR* 3.2 21.2 - - + +
5000H GLU* 3.3 20.7 + - + +
5001H HIS* 4.0 3.1 + - - +
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Residues in contact with GLU4998 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3890H HIS* 5.2 5.5 + - - -
4997H ASP* 1.3 76.3 - - - +
4999H THR* 1.3 59.7 + - - +
5000H GLU 3.4 0.9 + - - -
5001H HIS* 3.5 19.0 + - - +
5006H SER* 5.9 0.5 - - - -
5009H TRP* 5.2 15.7 - - + +
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Residues in contact with THR4999 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3888H GLU* 5.6 9.0 + - - +
3890H HIS* 5.5 3.6 + - - -
3962H GLU* 4.6 13.5 + - - +
3965H GLN* 5.9 0.5 + - - -
4997H ASP* 4.0 19.1 - - + +
4998H GLU* 1.3 77.6 - - - +
5000H GLU* 1.3 61.4 + - + +
5001H HIS 3.4 5.5 + - - +
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Residues in contact with GLU5000 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4992H TYR* 3.7 20.3 + - - +
4996H LYS* 4.4 15.3 - - + +
4997H ASP* 3.3 16.9 + - + +
4998H GLU 3.2 1.0 - - - -
4999H THR* 1.3 81.3 - - + +
5001H HIS* 1.3 57.6 + - - +
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Residues in contact with HIS5001 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3890H HIS* 3.3 13.4 + - + -
3965H GLN* 3.2 15.1 + - - +
4992H TYR* 5.4 3.4 - - + -
4993H LEU* 5.0 7.2 - - + -
4997H ASP 4.6 3.4 - - - +
4998H GLU* 3.5 17.2 + - - +
4999H THR 3.4 5.5 - - - +
5000H GLU* 1.3 81.8 - - - +
5002H THR* 1.3 60.3 + - - +
5005H GLU* 3.8 21.1 - - + +
5006H SER* 4.1 15.0 - - - +
5009H TRP* 6.3 0.2 - - + -
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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