Contacts of the helix formed by residues 597 - 603 (chain B) in PDB entry 3BYH
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 LEU 597 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B ARG* 0.8 246.8 - - + +
399B ARG* 5.6 1.1 - - - +
400B LEU* 2.2 44.6 - - + -
584B VAL* 4.8 0.7 - - - -
596B LEU* 1.3 79.4 - - - +
598B PRO* 1.3 64.0 - - + +
599B GLU* 3.2 8.7 - - - +
600B ASP* 2.6 38.9 + - - +
601B ILE* 3.9 1.0 + - - +
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Residues in contact with PRO 598 (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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396B ARG* 4.3 0.7 - - - +
577B ARG* 4.0 17.0 - - - +
580B ALA* 3.2 32.3 - - + +
581B THR* 3.5 37.7 - - + +
584B VAL* 4.4 16.3 - - + -
596B LEU 4.5 1.8 - - - +
597B LEU* 1.3 87.1 - - + +
599B GLU* 1.3 69.9 + - - +
601B ILE* 3.0 17.7 + - + +
602B VAL* 3.4 4.8 + - - +
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Residues in contact with GLU 599 (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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396B ARG* 3.1 31.3 + - - +
577B ARG* 3.0 32.6 + - + +
597B LEU* 3.2 7.9 - - - +
598B PRO* 1.3 96.2 - - - +
600B ASP* 1.3 58.3 + - - +
601B ILE 3.1 0.7 - - - -
602B VAL* 3.7 12.6 - - + -
603B GLU* 3.0 50.6 + - + +
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Residues in contact with ASP 600 (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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396B ARG* 3.2 19.0 + - - -
397B CYS* 4.8 12.5 - - - +
400B LEU* 4.9 0.9 - - - +
596B LEU* 3.2 24.3 - - + +
597B LEU* 2.6 40.8 + - - +
599B GLU* 1.3 73.3 - - - +
601B ILE* 1.3 56.0 + - - +
603B GLU* 5.1 3.0 - - - +
604B VAL* 3.3 2.8 + - - -
605B ASN* 2.9 44.0 + - + +
608B MET* 3.9 19.0 - - + +
609B ILE* 4.1 5.2 - - - +
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Residues in contact with ILE 601 (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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544B LEU* 3.9 18.5 - - - +
545B SER* 3.3 15.9 + - - +
547B GLY* 4.7 3.6 - - - -
550B PHE* 4.1 18.8 - - + -
580B ALA* 4.1 19.7 - - + +
583B ILE* 3.8 41.1 - - + -
584B VAL* 4.3 10.3 - - + -
596B LEU* 3.9 15.5 - - + -
597B LEU 4.7 0.9 - - - +
598B PRO 3.0 7.7 + - - +
600B ASP* 1.3 79.3 - - - +
602B VAL* 1.3 63.1 + - - +
603B GLU 3.2 2.0 - - - -
604B VAL* 3.2 12.0 + - - +
609B ILE* 4.3 10.7 - - + +
612B LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 602 (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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545B SER* 3.2 25.1 - - - +
573B ASP* 5.1 12.3 - - + +
576B LYS* 4.0 49.8 + - + +
577B ARG* 4.0 10.8 - - + +
580B ALA* 4.0 4.7 - - + -
598B PRO 3.4 14.3 + - - +
599B GLU* 3.5 12.1 + - + +
601B ILE* 1.3 78.1 - - - +
603B GLU* 1.3 62.9 + - + +
604B VAL* 4.3 0.2 - - - +
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Residues in contact with GLU 603 (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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393B ARG* 4.6 29.0 + - - -
599B GLU* 3.0 33.1 + - + +
600B ASP* 5.0 3.8 - - - +
602B VAL* 1.3 82.4 - - + +
604B VAL* 1.3 74.0 + - - +
605B ASN* 3.7 2.2 - - + +
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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