Contacts of the helix formed by residues 675 - 680 (chain x) in PDB entry 5Z58
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 675 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614x PHE* 5.6 6.3 - - + -
615x LEU 4.0 4.1 + - - +
674x THR* 1.3 73.8 - - - +
676x ILE* 1.3 54.3 + - - +
677x ALA 2.9 6.5 - - - -
678x GLU* 2.8 33.5 + - + +
679x THR 4.2 1.4 + - - -
695x CYS* 5.1 14.6 - - + -
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Residues in contact with ILE 676 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456x VAL* 5.0 15.9 - - + -
647x ILE* 6.0 4.9 - - + +
648x TYR* 5.9 7.4 - - - +
673x ALA* 6.2 0.7 - - + -
674x THR* 3.1 8.4 + - - +
675x ASN* 1.3 76.3 - - - +
677x ALA* 1.3 58.2 + - - +
678x GLU 3.2 1.2 + - - -
680x SER* 3.1 37.8 + - - +
681x LEU* 3.8 4.2 + - - +
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Residues in contact with ALA 677 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612x LEU* 6.0 5.8 - - + -
613x VAL 5.4 4.3 - - - +
647x ILE* 6.2 0.4 - - + -
671x VAL* 6.5 0.9 - - + -
673x ALA* 4.5 13.6 - - + +
674x THR 3.5 11.7 + - - +
675x ASN 2.9 1.2 - - - -
676x ILE* 1.3 77.6 - - - +
678x GLU* 1.3 62.1 + - - +
681x LEU* 3.6 15.3 - - - +
725x ARG* 5.0 11.6 - - - +
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Residues in contact with GLU 678 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424x THR* 4.5 10.0 - - - -
675x ASN* 2.8 23.0 + - + +
677x ALA* 1.3 81.7 - - - +
679x THR* 1.3 64.8 + - - +
680x SER 3.6 0.2 - - - -
681x LEU 4.2 4.9 - - - +
718x SER* 5.8 1.8 - - - +
721x GLN* 4.8 25.8 - - + +
722x ARG* 5.2 9.9 - - + +
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Residues in contact with THR 679 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424x THR* 4.6 15.0 - - - -
521x GLU* 5.7 8.5 - - - +
553x ALA* 4.7 18.8 - - - +
675x ASN 4.2 1.8 + - - -
678x GLU* 1.3 82.2 - - - +
680x SER* 1.3 63.5 + - - +
681x LEU 3.7 0.2 - - - -
721x GLN* 6.2 2.2 - - - -
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Residues in contact with SER 680 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429x THR* 5.6 6.1 - - - -
454x ARG* 5.3 7.6 - - - -
456x VAL* 6.4 0.2 - - - -
457x ALA* 3.6 32.7 - - - +
676x ILE* 3.1 29.5 + - - +
679x THR* 1.3 80.8 - - - +
681x LEU* 1.3 62.7 + - - +
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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