Contacts of the helix formed by residues 4721 - 4726 (chain B) 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 LYS4721 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4680B GLU* 6.4 2.2 - - + -
4717B PHE* 4.5 14.9 + - + +
4718B VAL* 3.4 11.3 + - + +
4720B ARG* 1.3 78.0 - - - +
4722B VAL* 1.3 64.3 + - - +
4723B LEU 3.5 0.2 + - - -
4724B ASP* 3.5 13.0 + - - +
4725B LYS* 3.8 10.6 + - - +
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Residues in contact with VAL4722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4679B LEU* 3.7 39.9 - - + +
4680B GLU* 5.9 2.0 - - - +
4686B ILE* 4.2 16.2 - - + -
4718B VAL 3.7 6.7 + - - +
4719B LYS* 3.2 26.7 - - + +
4721B LYS* 1.3 74.7 - - - +
4723B LEU* 1.3 71.3 + - + +
4724B ASP 3.1 3.7 + - - -
4725B LYS* 4.6 4.7 - - + +
4726B HIS* 3.1 28.3 + - + +
4735B ILE* 3.5 19.4 - - + +
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Residues in contact with LEU4723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4719B LYS 3.2 22.4 - - - +
4720B ARG* 3.8 17.3 - - + +
4721B LYS 3.2 0.8 - - - -
4722B VAL* 1.3 80.0 - - + +
4724B ASP* 1.3 56.2 + - - +
4727B GLY* 3.3 20.6 - - - -
4728B ASP 4.6 0.2 + - - -
4732B ARG* 5.9 3.6 - - + +
4735B ILE* 3.7 47.1 - - + +
4736B ALA* 4.6 10.1 - - + +
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Residues in contact with ASP4724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4720B ARG 4.3 3.8 + - - +
4721B LYS* 3.5 9.5 + - - +
4722B VAL 3.1 0.6 - - - -
4723B LEU* 1.3 79.9 - - - +
4725B LYS* 1.3 65.2 + - - +
4727B GLY 4.3 1.7 + - - -
4728B ASP* 5.0 5.7 + - - +
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Residues in contact with LYS4725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4680B GLU* 5.3 6.7 - - - +
4721B LYS 3.8 8.3 + - - +
4722B VAL* 3.4 7.0 + - + +
4724B ASP* 1.3 81.8 - - - +
4726B HIS* 1.3 78.7 + - + +
4727B GLY 3.4 1.9 + - - -
4728B ASP* 4.6 3.5 + - - +
4729B ILE* 4.1 8.0 - - - +
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Residues in contact with HIS4726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4679B LEU 4.9 4.5 - - - -
4680B GLU 4.3 10.0 + - - -
4681B PHE* 4.1 24.7 + - - -
4682B ASP* 4.6 3.2 + - - -
4686B ILE* 4.1 33.0 - - + +
4687B THR* 4.3 15.5 - - + +
4688B GLU* 6.4 0.2 - - + -
4722B VAL* 3.1 13.9 + - + +
4725B LYS* 1.3 91.9 + - + +
4727B GLY* 1.3 60.3 + - - +
4728B ASP 3.5 2.0 - - - -
4729B ILE* 3.7 24.4 + - + +
4730B TYR* 4.5 3.3 + - - +
4735B ILE* 3.8 8.3 - - - +
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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