Contacts of the helix formed by residues 624 - 630 (chain B) in PDB entry 3ODX
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 LEU 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B LEU* 3.4 17.9 + - + +
623B ASP* 1.3 75.1 + - - +
625B SER* 1.3 70.9 + - - +
626B HIS 2.7 16.2 + - - -
627B LEU* 3.1 28.0 + - + +
628B ARG* 3.5 54.7 + - + +
639B LYS 5.1 0.4 - - - +
640B ASN* 4.9 6.5 - - - +
641B LEU 6.0 1.3 - - - +
684B ARG* 6.0 0.4 - - - +
687B LEU* 6.2 0.7 - - - -
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Residues in contact with SER 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B ASP* 3.0 19.7 + - - -
624B LEU* 1.3 88.0 - - - +
626B HIS* 1.3 85.7 + - - +
627B LEU 3.4 0.2 - - - -
628B ARG* 3.0 22.6 + - - +
629B GLN* 3.0 21.2 + - - +
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Residues in contact with HIS 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ASP* 4.4 1.6 - - - -
624B LEU 2.7 7.2 + - - +
625B SER* 1.3 95.5 + - - +
627B LEU* 1.3 60.1 + - + +
629B GLN* 3.3 25.4 + - - +
630B SER* 2.9 33.1 + - - -
635B LEU* 5.4 0.4 - - - -
686B LEU* 3.2 34.4 - - + +
687B LEU 3.5 22.9 - - - +
688B LYS* 4.8 12.5 - - + +
689B SER* 4.4 15.0 + - - +
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Residues in contact with LEU 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B ASP 5.8 0.4 - - - +
624B LEU* 3.1 13.9 + - + +
626B HIS* 1.3 75.9 - - + +
628B ARG* 1.3 61.7 + - - +
629B GLN 3.1 2.4 + - - -
630B SER 3.3 15.6 - - - +
635B LEU* 4.1 44.4 - - + +
636B SER* 4.7 8.7 + - - -
638B PHE* 3.0 39.0 - - + +
639B LYS* 3.5 14.2 - - - +
641B LEU* 4.5 11.7 - - + +
687B LEU* 4.4 32.8 - - + +
689B SER* 5.8 0.4 - - - +
706B PRO* 4.9 4.9 - - + -
707B VAL* 4.9 4.3 - - + -
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Residues in contact with ARG 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B LEU* 3.5 51.4 - - + +
625B SER* 3.0 13.1 + - - +
627B LEU* 1.3 75.5 - - - +
629B GLN* 1.3 58.0 + - - +
630B SER 4.4 1.8 - - - +
639B LYS* 3.5 30.5 + - - +
640B ASN* 3.2 40.2 - - - +
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Residues in contact with GLN 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B SER* 3.0 16.5 + - - +
626B HIS* 3.3 49.3 + - - +
628B ARG* 1.3 79.8 - - + +
630B SER* 1.3 67.6 - - - +
631B SER* 3.6 4.5 + - - -
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Residues in contact with SER 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B HIS 2.9 21.3 + - - -
627B LEU 3.3 14.3 - - - +
628B ARG 4.4 1.7 - - - +
629B GLN* 1.3 76.2 + - - +
631B SER* 1.4 61.5 + - - +
632B ASP* 3.1 32.8 + - - +
635B LEU* 4.4 15.2 - - - +
636B SER* 5.2 7.8 + - - -
689B SER* 4.6 8.5 - - - -
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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