Contacts of the helix formed by residues 657 - 665 (chain r) 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 ASN 657 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656r PRO* 1.3 78.8 - - - +
658r TYR* 1.3 63.1 + - - +
659r GLU 3.3 2.7 - - - +
660r ASP* 3.4 14.9 + - + +
661r VAL* 3.3 21.0 + - - +
888r PRO* 4.6 4.5 - - + -
889r ILE* 3.7 35.1 - - + +
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Residues in contact with TYR 658 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500r LEU* 5.5 3.5 - - - +
502r CYS* 4.9 14.6 - - + -
655r LEU 4.0 13.9 - - - +
656r PRO* 3.2 2.7 - - + +
657r ASN* 1.3 79.0 - - - +
659r GLU* 1.3 57.5 + - - +
661r VAL* 3.4 7.4 + - - +
662r ALA* 2.9 26.2 + - - +
675r TYR* 5.7 7.6 - - + -
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Residues in contact with GLU 659 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657r ASN* 3.3 0.6 - - - +
658r TYR* 1.3 79.5 - - - +
660r ASP* 1.3 56.4 + - - +
662r ALA* 3.3 10.5 - - + +
663r THR* 3.0 25.6 + - - -
669r PRO* 6.4 2.0 - - + -
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Residues in contact with ASP 660 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657r ASN* 3.4 21.6 + - + +
659r GLU* 1.3 78.2 - - - +
661r VAL* 1.3 60.5 + - - +
662r ALA 3.1 0.2 - - - -
663r THR* 3.2 8.5 + - - +
664r PHE* 3.0 26.5 + - - +
889r ILE 5.8 1.6 - - - +
927r ILE* 4.8 15.1 - - + +
928r ARG* 6.0 3.8 - - + +
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Residues in contact with VAL 661 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500r LEU* 5.8 1.3 - - - -
617r ILE* 6.5 0.7 - - + -
657r ASN 3.3 10.2 + - - +
658r TYR* 3.7 9.0 - - - +
660r ASP* 1.3 77.9 - - - +
662r ALA* 1.3 58.2 + - - +
664r PHE* 3.3 9.1 + - - +
665r LEU* 3.0 30.3 + - - +
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Residues in contact with ALA 662 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500r LEU* 4.9 10.9 - - + +
658r TYR 2.9 15.2 + - - +
659r GLU* 3.3 15.0 - - - +
661r VAL* 1.3 74.0 - - - +
663r THR* 1.3 66.2 + - - +
665r LEU* 3.2 3.4 + - - -
666r ARG 3.0 3.8 + - - -
667r VAL* 2.9 49.7 + - + +
669r PRO* 5.6 5.2 - - + -
673r LEU* 5.2 11.0 - - + -
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Residues in contact with THR 663 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659r GLU 3.0 14.5 + - - -
660r ASP* 3.2 10.9 + - - -
662r ALA* 1.3 75.0 - - - +
664r PHE* 1.3 63.5 + - - +
666r ARG* 3.1 14.6 + - - +
667r VAL 5.3 1.1 - - - -
927r ILE* 4.6 14.6 - - - -
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Residues in contact with PHE 664 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632r VAL* 5.5 6.3 - - - +
660r ASP 3.0 13.7 + - - +
661r VAL* 3.4 12.8 - - - +
663r THR* 1.3 79.6 - - - +
665r LEU* 1.3 57.0 + - + +
666r ARG* 3.1 4.2 + - - +
922r TYR 5.1 7.1 - - - +
923r ALA 5.7 1.3 - - - -
924r TYR* 4.7 25.8 - - + +
927r ILE* 5.5 4.2 - - + +
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Residues in contact with LEU 665 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498r ASN* 4.0 11.1 - - + +
499r LEU 5.1 8.5 - - - +
500r LEU* 6.0 1.8 - - + -
632r VAL* 6.2 3.1 - - - -
648r LEU* 4.6 18.0 - - + +
650r GLY* 6.1 3.1 - - - +
661r VAL 3.0 15.4 + - - +
662r ALA* 3.2 3.5 + - - +
664r PHE* 1.3 74.6 - - - +
666r ARG* 1.3 70.2 + - - +
667r VAL* 3.1 8.6 + - + +
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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