Contacts of the helix formed by residues 617 - 622 (chain A) in PDB entry 3WSZ
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 ALA 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PRO 4.4 0.2 - - - -
90A ILE* 4.2 27.8 - - + -
548A ILE* 3.8 25.2 - - + +
550A THR* 5.7 1.3 - - + -
561A LEU* 6.2 0.2 - - + -
595A THR* 3.0 22.1 + - - +
597A PHE* 4.2 11.2 - - + -
615A VAL* 4.9 2.2 - - + -
616A ASN* 1.3 72.7 + - - +
618A THR* 1.3 66.0 + - - +
619A ASP 3.2 3.1 - - - -
620A ALA* 3.2 16.5 + - + +
621A LEU* 3.9 3.3 + - - +
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Residues in contact with THR 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A THR* 2.7 30.5 + - + +
616A ASN* 3.2 13.6 + - - -
617A ALA* 1.3 74.6 - - - +
619A ASP* 1.3 59.8 + - - +
621A LEU* 2.9 10.4 + - - +
622A GLY 2.9 22.5 + - - +
661A PHE* 4.0 31.0 - - + -
803A NAG 3.3 32.0 + - - +
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Residues in contact with ASP 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU 4.3 6.1 - - - +
89A PRO* 3.2 29.2 + - + +
91A LYS* 4.2 14.4 + - - +
616A ASN 5.1 0.6 + - - -
617A ALA 3.2 1.2 - - - -
618A THR* 1.3 75.4 - - - +
620A ALA* 1.3 62.8 + - - +
621A LEU 3.3 0.2 - - - -
622A GLY* 3.7 17.2 + - - +
803A NAG 3.4 29.6 + - - -
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO* 3.3 15.2 + - + +
90A ILE* 4.7 3.1 - - + -
548A ILE* 4.0 13.9 - - + -
563A TYR* 3.8 29.8 - - + -
565A THR* 4.2 8.6 - - + +
617A ALA 3.2 12.7 + - - +
618A THR 3.1 1.0 - - - -
619A ASP* 1.3 76.9 - - - +
621A LEU* 1.3 60.9 + - + +
659A THR* 3.3 20.3 - - - +
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Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ASP* 3.2 40.6 - - + +
547A GLY 4.7 6.5 - - - +
548A ILE* 3.5 41.7 - - + -
565A THR* 4.3 8.1 - - + -
595A THR* 4.1 9.6 - - + -
617A ALA 4.1 4.9 - - - +
618A THR 2.9 8.8 + - - +
620A ALA* 1.3 80.2 - - + +
622A GLY* 1.3 57.7 + - - +
623A VAL* 2.9 9.3 + - - +
654A ARG* 5.6 0.7 - - - +
659A THR* 3.4 15.1 - - - +
660A CYS* 3.2 38.5 + - - +
661A PHE* 3.2 17.0 - - + -
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Residues in contact with GLY 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A THR* 2.9 13.7 + - - +
619A ASP* 3.7 19.0 - - - +
620A ALA 3.4 1.2 - - - -
621A LEU* 1.3 74.7 - - - +
623A VAL* 1.3 64.9 + - - +
624A PRO* 4.8 0.3 - - - +
661A PHE* 3.6 12.0 - - - -
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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