Contacts of the helix formed by residues 443 - 448 (chain B) in PDB entry 6GYK
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 ASN 443 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B TYR* 3.8 10.1 + - - +
441B ASP 5.5 0.2 - - - +
442B PHE* 1.3 83.7 - - - +
444B MET* 1.3 70.7 + - - +
445B LYS* 3.3 31.4 + - - +
446B LEU* 3.4 31.6 + - + +
447B ALA* 3.5 22.0 + - - +
194M SER 4.6 5.7 - - - +
195M LEU* 3.6 25.6 + - - +
197M HIS* 5.9 5.2 - - + +
272R SER* 5.7 1.4 + - - -
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Residues in contact with MET 444 (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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90B ILE* 5.9 2.2 - - + -
132B VAL* 4.5 10.8 - - + +
134B LYS* 2.9 39.0 - - - +
163B GLY* 6.2 1.1 - - - -
165B VAL* 3.7 36.5 - - + +
442B PHE* 3.5 15.0 - - + -
443B ASN* 1.3 76.4 + - - +
445B LYS* 1.3 63.7 + - + +
446B LEU 3.4 0.2 - - - -
447B ALA* 4.1 2.5 - - + +
448B ILE* 3.7 43.4 + - + +
275R SER* 5.9 1.8 - - - +
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Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ASN* 3.2 19.4 - - - +
444B MET* 1.3 81.4 - - + +
446B LEU* 1.3 60.0 + - - +
448B ILE 3.9 11.1 - - - +
449B ASN* 4.3 1.7 + - - -
139M ALA* 3.2 29.2 - - + +
194M SER* 4.7 13.9 - - - -
195M LEU* 3.7 30.3 - - + -
265R HIS 4.6 3.4 + - - -
266R THR 3.5 11.3 + - - +
267R GLY* 2.4 39.7 + - - +
268R MET* 4.0 8.5 - - - +
269R SER* 4.3 7.0 - - - +
271R ARG 5.2 9.9 + - - -
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Residues in contact with LEU 446 (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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431B TYR* 3.4 45.4 - - + +
443B ASN* 3.4 19.1 + - + +
445B LYS* 1.3 82.3 - - - +
447B ALA* 1.3 63.0 + - - +
449B ASN* 4.1 13.9 + - - +
135M MET* 4.4 13.2 - - + +
136M LEU* 3.6 33.0 - - + -
139M ALA* 4.4 6.3 - - + -
195M LEU* 3.7 29.4 - - + +
196M ILE* 6.1 1.8 - - + -
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Residues in contact with ALA 447 (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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90B ILE* 6.2 0.2 - - + -
427B ASP* 4.8 1.7 - - - +
428B ILE* 3.5 29.1 + - + +
431B TYR* 3.5 31.1 - - + +
442B PHE* 3.6 22.4 - - + -
443B ASN 3.5 7.5 + - - +
444B MET* 3.9 3.5 + - + +
445B LYS 3.5 0.2 - - - -
446B LEU* 1.3 80.5 - - - +
448B ILE* 1.3 69.8 + - + +
449B ASN* 3.6 8.8 + - - +
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Residues in contact with ILE 448 (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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90B ILE* 6.3 1.1 - - + -
92B PHE* 4.7 1.8 - - + -
132B VAL* 3.7 35.2 - - + -
165B VAL* 3.7 30.1 - - + +
166B PHE 4.3 10.6 - - - +
167B ILE* 4.5 12.8 - - + -
424B LEU* 4.4 5.6 - - + -
428B ILE* 3.6 32.3 - - + -
444B MET* 3.7 25.1 + - + +
445B LYS* 3.9 13.2 - - - +
447B ALA* 1.3 80.2 - - + +
449B ASN* 1.3 70.0 + - - +
450B ALA 4.2 0.3 + - - -
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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