Contacts of the helix formed by residues 667 - 670 (chain A) in PDB entry 3TJP
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 VAL 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A LEU 3.8 1.8 - - - +
664A VAL* 3.3 16.6 - - - +
665A GLN 3.0 0.4 - - - -
666A ALA* 1.3 79.7 - - - +
668A LYS* 1.3 52.3 + - - +
670A GLU* 3.1 15.6 + - + +
673A HIS 5.6 0.2 - - - +
675A SER* 5.3 1.1 - - - +
677A LEU* 4.2 13.2 - - + -
678A ALA* 4.8 8.7 - - + +
681A LEU* 3.7 28.5 - - + -
699A LEU* 6.3 0.2 - - + -
712A ARG* 2.7 49.6 + - - +
713A PHE* 3.5 23.1 - - + -
716A ILE* 4.0 15.9 - - + -
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Residues in contact with LYS 668 (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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499A ALA* 4.2 19.5 - - + -
500A ASP* 5.1 5.4 + - - +
502A LEU* 4.5 5.5 - - - +
665A GLN* 3.1 36.2 + - - +
667A VAL* 1.3 78.3 - - - +
669A PHE* 1.3 62.4 + - + +
670A GLU 3.3 2.0 - - - +
702A GLU* 3.0 28.0 + - - -
706A SER* 5.2 3.7 + - - -
709A TYR* 3.1 69.4 + - + +
712A ARG* 4.1 2.3 + - - -
713A PHE* 3.8 23.1 - - + -
839A ARG* 4.5 4.8 - - - +
1037A THR* 3.8 17.8 + - - -
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Residues in contact with PHE 669 (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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499A ALA* 4.1 20.9 - - + -
502A LEU* 3.8 16.5 - - + +
631A LEU 3.3 25.1 - - - +
632A ASP* 3.5 18.8 - - - +
633A CYS* 3.7 27.5 - - + +
635A PHE 4.8 1.6 - - - +
636A SER* 5.6 1.2 + - - -
641A ARG* 3.7 10.1 + - - +
666A ALA* 3.1 22.6 + - + +
667A VAL 3.1 1.0 - - - -
668A LYS* 1.3 79.7 - - - +
670A GLU* 1.3 64.2 + - - +
671A PRO* 3.4 8.3 - - - +
1033A MET* 4.1 18.8 - - + -
1036A MET* 3.8 24.0 - - + -
1037A THR* 3.5 27.4 - - + -
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Residues in contact with GLU 670 (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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631A LEU* 4.2 2.9 - - - +
638A GLU* 5.2 5.5 - - - +
641A ARG* 2.5 48.0 + - - +
666A ALA 4.2 0.2 - - - +
667A VAL* 3.1 25.4 + - + +
668A LYS 4.1 2.3 - - - +
669A PHE* 1.3 77.6 - - - +
671A PRO* 1.3 71.6 - - - +
672A TYR 3.8 12.3 + - - +
675A SER* 3.3 31.2 - - - +
676A ALA 5.5 0.2 - - - -
677A LEU* 3.9 19.0 + - + +
712A ARG* 2.7 32.6 + - - +
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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