Contacts of the helix formed by residues 502 - 506 (chain B) in PDB entry 6EBT
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 LYS 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B ALA* 5.0 2.0 - - - +
498B ASP 3.8 14.1 - - - +
499B GLU* 3.8 24.0 - - - +
500B TRP 3.5 5.1 + - - +
501B VAL* 1.3 78.2 - - - +
503B PRO* 1.3 67.9 - - - +
504B LYS* 3.1 5.8 - - + +
505B ASP* 3.0 40.3 + - - +
506B MET* 3.7 9.4 - - - +
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Residues in contact with PRO 503 (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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229B ILE* 4.0 15.5 - - + -
241B PRO* 4.9 1.5 - - + +
449B MET* 3.6 32.8 - - + -
455B LEU* 3.8 19.3 - - + -
501B VAL* 3.7 10.1 - - + +
502B LYS* 1.3 83.1 - - - +
504B LYS* 1.3 62.0 + - - +
506B MET* 2.9 27.6 + - - +
507B LEU* 3.5 14.0 - - - +
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Residues in contact with LYS 504 (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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229B ILE* 3.8 18.8 - - + +
502B LYS* 3.1 5.5 + - + +
503B PRO* 1.3 79.3 - - - +
505B ASP* 1.3 64.9 + - - +
506B MET 3.3 0.6 + - - -
507B LEU* 3.7 17.2 + - + +
510B LYS* 5.1 2.3 + - - -
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Residues in contact with ASP 505 (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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283A LEU* 4.6 3.6 - - - +
502B LYS* 3.0 37.2 + - + +
504B LYS* 1.3 80.1 - - - +
506B MET* 1.3 61.1 + - + +
507B LEU 3.5 2.6 + - - -
510B LYS* 3.3 36.0 + - - +
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Residues in contact with MET 506 (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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281A THR* 4.5 0.9 + - - -
283A LEU* 3.6 40.0 - - + +
240B VAL* 5.5 2.7 - - + -
241B PRO* 3.9 27.9 - - + +
454B MET 5.1 1.8 - - - +
455B LEU* 3.8 39.3 - - + +
457B THR* 4.0 20.6 - - - +
458B ALA* 4.8 15.0 - - + -
501B VAL* 5.8 0.9 - - - -
502B LYS 3.7 12.3 - - - +
503B PRO* 2.9 18.9 + - - +
505B ASP* 1.3 81.0 - - + +
507B LEU* 1.3 65.4 + - - +
508B GLY 3.6 2.5 - - - -
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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