Contacts of the helix formed by residues 608 - 616 (chain A) in PDB entry 3Q8B
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 ASP 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A ARG 4.1 5.1 + - - -
597A HIS* 3.5 21.1 + - - -
607A ALA* 1.3 76.4 - - - +
609A GLU* 1.3 66.3 + - - +
610A SER* 3.8 13.1 - - - +
611A VAL* 3.0 21.1 + - + +
612A VAL* 2.9 21.9 + - - +
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A ALA 3.5 2.2 + - - -
608A ASP* 1.3 71.0 - - - +
610A SER* 1.3 64.3 + - - +
612A VAL* 3.2 0.9 + - - +
613A LYS* 2.9 57.2 + - - +
722A LYS* 6.2 0.2 - - - +
723A LYS 5.4 2.3 - - - +
724A ILE* 4.0 31.4 - - + +
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Residues in contact with SER 610 (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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608A ASP* 3.2 8.9 - - - +
609A GLU* 1.3 78.9 - - - +
611A VAL* 1.3 58.3 + - - +
613A LYS* 4.0 7.3 - - - +
614A GLU* 3.0 30.8 + - - +
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Residues in contact with VAL 611 (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 ARG* 4.3 33.4 - - + +
607A ALA* 4.1 11.2 - - + -
608A ASP* 3.0 26.9 + - + +
610A SER* 1.3 74.3 - - - +
612A VAL* 1.3 68.7 + - - +
614A GLU* 3.3 5.6 + - - +
615A ALA* 3.0 23.0 + - - +
635A ILE* 3.7 24.5 - - + -
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Residues in contact with VAL 612 (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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607A ALA* 4.0 20.9 - - + +
608A ASP 2.9 17.0 + - - +
609A GLU 3.8 3.1 - - - +
611A VAL* 1.3 75.9 - - + +
613A LYS* 1.3 60.4 + - - +
615A ALA* 3.1 10.0 + - - +
616A HIS* 2.7 38.6 - - + +
635A ILE* 5.0 5.6 - - + -
638A ILE* 4.2 14.8 - - + -
639A LEU* 4.9 3.4 - - + -
700A ALA* 4.1 10.8 - - + -
702A THR* 4.5 3.6 - - + -
724A ILE* 3.8 28.5 - - + -
726A ILE* 3.8 20.2 - - + -
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Residues in contact with LYS 613 (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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609A GLU* 2.9 50.4 + - - +
610A SER* 4.0 6.3 - - - +
612A VAL* 1.3 73.9 - - - +
614A GLU* 1.3 66.0 + - - +
616A HIS* 3.0 13.5 + - - +
617A ARG* 3.3 10.2 + - - +
724A ILE* 3.9 7.0 - - + -
725A LEU* 3.0 49.2 + - - +
726A ILE* 4.2 11.7 - - - +
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Residues in contact with GLU 614 (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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610A SER 3.0 20.8 + - - +
611A VAL* 3.8 5.6 - - - +
613A LYS* 1.3 76.8 - - - +
615A ALA* 1.3 58.9 + - - +
616A HIS 3.0 4.7 + - - -
617A ARG* 3.1 55.5 + - - +
618A GLU 4.8 0.3 + - - -
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Residues in contact with ALA 615 (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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611A VAL* 3.0 18.2 + - + +
612A VAL 3.1 6.2 + - - +
614A GLU* 1.3 77.3 - - - +
616A HIS* 1.3 57.9 + - + +
617A ARG 3.5 0.7 - - - -
618A GLU* 5.3 1.1 + - - +
630A ASN 3.8 18.0 - - - +
631A ILE* 3.8 12.5 - - + +
632A ASP* 5.0 4.9 + - + +
635A ILE* 3.7 35.9 - - + -
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Residues in contact with HIS 616 (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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612A VAL* 2.7 36.3 - - + +
613A LYS 3.0 8.5 + - - +
615A ALA* 1.3 80.7 - - + +
617A ARG* 1.3 66.3 + - - +
618A GLU 3.3 3.5 + - - -
619A VAL* 3.9 8.0 - - - +
629A LEU* 3.5 27.3 - - + +
631A ILE* 3.4 23.3 - - + +
635A ILE* 4.3 5.7 - - - +
639A LEU* 3.9 16.5 - - + +
642A TYR* 3.0 38.1 - + - -
700A ALA* 4.4 0.8 - - - +
726A ILE* 3.7 40.3 - - + +
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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