Contacts of the helix formed by residues 4696 - 4700 (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 LYS4696 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4671H ARG* 4.1 27.8 + - - +
4695H VAL* 1.3 85.0 - - + +
4697H GLY* 1.3 62.5 + - - +
4698H GLN 3.3 0.9 - - - -
4699H TRP* 3.5 16.5 + - - +
4700H ASP* 3.5 11.6 + - - +
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Residues in contact with GLY4697 (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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4684H LEU* 3.3 29.9 - - - +
4685H TYR* 5.1 1.4 - - - -
4695H VAL 3.4 4.2 - - - +
4696H LYS* 1.3 78.5 - - - +
4698H GLN* 1.3 61.2 + - - +
4700H ASP* 3.3 8.9 + - - +
4701H ARG 4.1 0.2 + - - -
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Residues in contact with GLN4698 (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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4685H TYR* 3.3 28.2 + - - -
4695H VAL* 4.0 11.3 + - - +
4696H LYS 3.3 0.8 - - - -
4697H GLY* 1.3 74.9 - - - +
4699H TRP* 1.3 65.5 + - - +
4701H ARG* 3.2 18.8 + - - +
4702H LEU 4.9 0.2 + - - -
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Residues in contact with TRP4699 (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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4695H VAL 4.1 5.9 + - - +
4696H LYS* 3.5 14.1 + - - +
4697H GLY 3.3 0.8 - - - -
4698H GLN* 1.3 77.7 - - - +
4700H ASP* 1.3 56.1 + - - +
4701H ARG 3.1 5.8 + - - -
4702H LEU* 3.5 11.9 + - + +
4775H ILE* 3.5 25.0 + - + -
4776H TRP* 3.3 37.4 + + - +
4779H GLY* 3.6 21.9 - - - -
4780H VAL* 4.3 12.8 - - + -
4783H THR* 6.2 4.5 - - + -
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Residues in contact with ASP4700 (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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4671H ARG* 5.9 4.5 - - - +
4675H LEU* 4.6 13.0 - - + +
4684H LEU* 3.7 15.7 - - + +
4696H LYS 3.5 9.8 + - - +
4697H GLY* 3.3 14.3 + - - +
4698H GLN 3.1 1.4 - - - -
4699H TRP* 1.3 75.6 - - - +
4701H ARG* 1.3 57.7 + - - +
4702H LEU 3.3 0.9 - - - -
4703H VAL* 3.2 20.9 - - + +
4704H LEU* 3.5 11.4 - - - +
4776H TRP* 3.6 16.4 - - + +
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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