Contacts of the helix formed by residues 430 - 436 (chain O) in PDB entry 6FF7
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 GLU 430 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423O GLU* 5.3 6.0 - - - +
427O LYS 5.1 0.2 + - - -
429O PHE* 1.3 81.8 - - + +
431O ARG* 1.3 62.4 + - - +
432O VAL 3.6 2.5 - - - +
433O ARG* 4.3 14.8 + - + +
434O VAL* 4.4 12.3 + - - +
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Residues in contact with ARG 431 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420O ALA* 5.9 6.8 - - + +
423O GLU* 4.5 26.2 - - + +
424O GLU* 5.4 1.6 - - - +
427O LYS 5.0 5.4 - - - +
428O GLU* 4.9 8.0 - - + -
429O PHE 3.8 1.8 - - - +
430O GLU* 1.3 76.9 - - - +
432O VAL* 1.3 63.7 + - - +
433O ARG 3.4 0.7 - - - -
434O VAL* 4.2 7.5 + - - +
435O ILE* 4.4 11.6 + - - +
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Residues in contact with VAL 432 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430O GLU* 3.6 0.8 - - - +
431O ARG* 1.3 77.2 - - - +
433O ARG* 1.3 63.4 + - - +
434O VAL 3.6 0.2 + - - -
435O ILE* 5.3 0.3 - - - +
436O TYR* 3.9 11.8 + - - +
437O LYS* 3.8 14.8 + - - +
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Residues in contact with ARG 433 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430O GLU* 4.3 15.3 + - + +
431O ARG 3.4 1.0 - - - -
432O VAL* 1.3 80.4 - - - +
434O VAL* 1.3 57.2 + - + +
437O LYS* 3.1 15.7 + - + -
438O TYR* 2.6 38.0 + - + +
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Residues in contact with VAL 434 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416O TYR* 5.3 14.3 - - + +
419O PHE* 6.1 4.7 - - + -
420O ALA* 6.1 5.2 - - + +
430O GLU 4.4 12.0 + - - +
431O ARG* 4.2 4.1 + - - +
432O VAL 3.5 0.6 - - - -
433O ARG* 1.3 80.7 - - + +
435O ILE* 1.3 62.4 + - + +
438O TYR* 3.8 21.0 + - - +
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Residues in contact with ILE 435 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416O TYR* 6.2 2.0 - - - -
420O ALA* 5.5 12.1 - - + -
431O ARG 4.4 10.3 + - - +
432O VAL 4.2 1.8 + - - +
433O ARG 3.5 0.2 - - - -
434O VAL* 1.3 80.1 - - + +
436O TYR* 1.3 60.9 + - + +
438O TYR 5.0 0.2 - - - -
439O ALA* 5.1 5.9 - - - +
446O GLN* 6.1 1.0 - - - +
455O TYR* 5.7 8.7 - - + -
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Residues in contact with TYR 436 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432O VAL 3.9 9.4 + - - +
435O ILE* 1.3 81.9 - - + +
437O LYS* 1.3 61.2 + - + +
438O TYR 3.6 0.9 - - - -
439O ALA* 3.7 18.1 - - - +
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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