Contacts of the helix formed by residues 500 - 506 (chain K) in PDB entry 6X5A
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 500 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146K GLU* 3.8 10.8 - - - -
149K LYS* 3.4 18.4 + - - -
496K GLU 3.7 2.2 + - - -
497K ARG 3.9 5.9 + - - -
498K ASN 3.5 3.6 + - - -
499K ASN* 1.3 78.4 - - - +
501K PHE* 1.3 77.7 + - - +
502K PRO 3.5 0.2 - - - -
505K ASP* 4.2 3.6 - - - +
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Residues in contact with PHE 501 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K GLU* 3.4 28.9 - - + +
149K LYS* 4.6 4.8 + - - +
150K LEU* 4.9 20.4 - - + -
404K LEU* 4.1 22.7 - - + -
446K SER* 5.4 7.6 - - - -
449K PHE* 3.3 39.0 - + - -
453K LEU* 4.9 8.7 - - + -
496K GLU* 3.5 20.2 + - + -
497K ARG* 5.5 8.1 - - + -
500K GLY* 1.3 77.9 - - - +
502K PRO* 1.3 69.5 - - - +
503K ILE 3.3 2.9 - - - +
504K PHE* 3.2 34.2 + + + +
505K ASP* 3.6 7.4 + - - +
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Residues in contact with PRO 502 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495K TYR* 5.1 9.0 - - + +
496K GLU* 4.1 14.6 - - - +
499K ASN* 3.2 47.8 - - + +
500K GLY 3.5 0.4 - - - +
501K PHE* 1.3 89.0 - - - +
503K ILE* 1.3 63.9 + - + +
505K ASP* 2.7 45.9 + - + +
506K LYS* 4.0 1.7 + - - +
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Residues in contact with ILE 503 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404K LEU* 4.3 8.1 - - + -
407K GLN* 3.4 41.9 - - + +
408K LEU* 4.6 2.5 - - + +
411K GLU* 3.1 25.6 - - + +
495K TYR* 4.7 7.9 - - + +
496K GLU* 3.0 34.8 - - - +
501K PHE 3.3 1.0 - - - -
502K PRO* 1.3 85.6 - - + +
504K PHE* 1.3 57.7 + - - +
506K LYS* 3.1 39.2 - - + +
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Residues in contact with PHE 504 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LYS* 5.5 7.9 - - + +
150K LEU* 3.4 32.8 - - + -
153K VAL* 3.4 47.1 - - + +
400K LEU* 3.9 19.5 - - + -
403K TYR* 4.9 7.0 - + + -
404K LEU* 3.5 53.8 - - + -
407K GLN* 4.4 9.6 - - - -
449K PHE* 6.3 0.7 - + - -
501K PHE* 3.2 28.0 + + + +
502K PRO 3.0 1.2 - - - -
503K ILE* 1.3 78.8 - - - +
505K ASP* 1.3 56.4 + - - +
506K LYS* 3.0 18.9 + - - +
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Residues in contact with ASP 505 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LYS* 3.8 28.0 + - - +
499K ASN 5.4 0.7 - - - +
500K GLY 4.2 4.5 - - - +
501K PHE 3.6 6.2 - - - +
502K PRO* 2.7 37.6 + - + +
504K PHE* 1.3 68.4 - - - +
506K LYS* 1.3 63.9 - - - +
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Residues in contact with LYS 506 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K VAL* 6.0 0.2 - - - +
407K GLN* 3.2 40.1 + - - +
410K LYS* 4.4 9.7 - - - +
502K PRO 4.6 0.9 - - - +
503K ILE* 3.1 30.7 + - + +
504K PHE 3.0 9.1 - - - +
505K ASP* 1.3 83.8 - - - +
507K LEU* 1.3 79.2 + - - +
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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