Contacts of the helix formed by residues 604 - 609 (chain F) in PDB entry 7C17
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 SER 604 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A GLU* 4.6 3.1 + - - -
906C PHE* 4.3 4.8 - - - -
547F VAL* 5.5 4.5 - - - -
597F LYS 5.1 0.2 + - - -
598F LEU* 2.4 49.2 + - - -
600F HIS 3.2 13.9 + - - -
601F PRO* 5.0 0.6 - - - +
603F ARG* 1.3 74.6 - - - +
605F GLU* 1.3 53.3 + - - +
606F VAL* 3.2 3.6 - - - +
607F LEU* 3.1 19.3 + - - +
608F ARG* 2.7 32.6 + - - +
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Residues in contact with GLU 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F PRO* 3.3 44.3 - - - +
602F SER 4.5 5.6 - - - +
603F ARG* 3.2 4.3 - - - -
604F SER* 1.3 75.2 - - - +
606F VAL* 1.3 55.3 + - - +
608F ARG* 3.3 24.7 - - - +
609F SER* 2.7 39.2 + - - -
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Residues in contact with VAL 606 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D THR* 4.9 18.6 - - - +
393D THR* 5.5 0.4 - - - -
543F ALA* 5.3 7.2 - - + -
547F VAL* 4.7 9.4 - - + -
603F ARG 4.4 13.0 + - - +
604F SER 4.8 0.2 - - - -
605F GLU* 1.3 78.3 - - - +
607F LEU* 1.3 74.3 + - + +
609F SER* 3.7 11.5 + - - -
610F PHE* 3.2 35.0 + - + -
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Residues in contact with LEU 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C LEU* 5.8 1.8 - - + -
902C LEU* 4.4 10.7 - - + +
905C ILE* 5.3 14.6 - - + -
906C PHE* 3.4 19.7 - - + -
540F LEU* 3.8 25.1 - - + -
543F ALA* 3.9 25.4 - - + +
544F THR* 4.3 14.1 - - + -
547F VAL* 3.8 33.2 - - + -
598F LEU* 5.8 2.0 - - + -
604F SER* 3.1 21.8 + - - +
606F VAL* 1.3 85.8 - - + +
608F ARG* 1.3 62.6 + - - +
610F PHE* 3.6 16.0 + - - +
611F LEU 4.6 0.2 + - - -
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Residues in contact with ARG 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906C PHE* 3.6 43.6 - - + +
599F ARG 4.8 6.7 + - - -
601F PRO* 5.3 8.7 - - - +
604F SER 2.7 16.0 + - - +
605F GLU* 3.2 34.1 + - - +
607F LEU* 1.3 74.7 - - - +
609F SER* 1.3 59.7 + - - +
610F PHE 3.1 3.2 + - - -
611F LEU* 3.3 45.4 + - + +
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Residues in contact with SER 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D THR* 3.3 36.5 + - - +
393D THR* 3.4 19.3 - - - +
395D LYS* 5.8 0.2 - - - +
396D ALA* 5.5 1.6 - - - +
605F GLU* 2.7 22.4 + - - +
606F VAL* 4.0 6.9 - - - -
607F LEU 3.3 0.6 - - - -
608F ARG* 1.3 76.3 - - - +
610F PHE* 1.3 55.8 + - - +
611F LEU* 3.2 7.1 + - - +
612F ASP* 4.2 13.7 + - - +
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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