Contacts of the helix formed by residues 667 - 677 (chain E) in PDB entry 3LVQ
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 HIS 667 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630E ALA 3.3 18.8 + - - +
631E LEU 3.1 28.7 + - - -
632E TYR* 4.7 0.7 - - - -
633E ASN* 3.1 47.5 + - - +
662E ALA* 3.2 6.9 + - - +
665E LYS* 3.3 39.9 + - + +
666E HIS* 1.3 70.4 - - - +
668E LYS* 1.3 62.6 + - - +
669E GLU 3.3 2.7 - - - -
670E CYS* 3.3 23.9 + - + +
671E GLU* 3.3 15.1 + - - +
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Residues in contact with LYS 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666E HIS* 2.9 20.2 + - - +
667E HIS* 1.3 69.9 - - - +
669E GLU* 1.3 63.9 + - - +
671E GLU* 3.2 22.6 + - + +
672E GLU* 3.1 32.4 + - + +
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Residues in contact with GLU 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633E ASN* 5.6 5.7 + - - +
635E PRO* 3.4 38.0 - - + +
636E ASP* 4.7 4.9 - - - +
639E LYS* 5.2 6.9 + - - -
667E HIS 3.3 1.9 + - - -
668E LYS* 1.3 74.3 - - - +
670E CYS* 1.3 66.4 + - - +
671E GLU 3.5 0.2 + - - -
672E GLU* 3.5 19.9 + - - +
673E LEU* 3.7 19.9 + - + +
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Residues in contact with CYS 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629E ALA 4.0 11.7 - - - -
630E ALA* 4.4 9.4 - - - -
633E ASN* 4.4 11.0 - - - -
634E GLN 4.5 6.7 - - - -
635E PRO* 4.6 7.4 - - - +
638E LEU* 3.7 35.1 - - + +
662E ALA* 4.7 2.7 - - + -
667E HIS* 3.3 26.0 + - + +
669E GLU* 1.3 76.9 - - - +
671E GLU* 1.3 61.4 + - - +
673E LEU* 3.3 9.4 + - - +
674E LEU* 3.1 33.1 + - + +
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Residues in contact with GLU 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659E LEU* 4.3 8.5 - - + +
662E ALA* 3.3 36.2 - - + +
663E ARG* 3.9 32.7 + - - +
666E HIS* 3.6 21.7 + - - +
667E HIS 3.3 12.3 - - - +
668E LYS* 3.2 25.8 + - + +
670E CYS* 1.3 74.3 - - - +
672E GLU* 1.3 63.1 + - - +
674E LEU* 3.5 8.3 + - - +
675E GLU* 3.2 29.0 + - + +
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Residues in contact with GLU 672 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E LYS* 3.1 25.2 + - + +
669E GLU* 3.8 15.4 - - - +
670E CYS 3.3 0.6 - - - -
671E GLU* 1.3 76.3 - - + +
673E LEU* 1.3 62.4 + - + +
675E GLU* 3.8 6.6 + - - +
676E GLN* 3.7 18.9 + - - +
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Residues in contact with LEU 673 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635E PRO* 4.4 12.6 - - + +
638E LEU* 4.8 12.8 - - + -
639E LYS* 4.1 42.6 - - + +
642E LEU* 4.6 13.6 - - + +
669E GLU* 3.7 22.6 + - + +
670E CYS* 3.3 9.2 + - - +
671E GLU 3.3 0.2 - - - -
672E GLU* 1.3 77.0 - - + +
674E LEU* 1.3 65.0 + - - +
676E GLN* 3.6 9.7 + - - +
677E ALA* 3.2 22.6 + - - +
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Residues in contact with LEU 674 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626E LEU* 3.9 15.9 - - + -
630E ALA* 4.5 3.6 - - + -
638E LEU* 4.0 13.5 - - + -
642E LEU* 5.8 2.5 - - + -
648E VAL* 4.4 13.5 - - + -
658E ALA* 3.8 33.9 - - + +
659E LEU* 3.8 27.8 - - + +
662E ALA* 3.8 28.5 - - + -
670E CYS 3.1 22.5 + - - +
671E GLU 3.8 0.4 - - - +
672E GLU 3.4 0.2 - - - -
673E LEU* 1.3 76.5 - - - +
675E GLU* 1.3 62.6 + - - +
677E ALA* 3.3 15.7 + - + +
678E GLN* 2.9 24.2 + - - +
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Residues in contact with GLU 675 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659E LEU* 5.0 15.5 - - + -
663E ARG* 5.6 3.5 + - - +
671E GLU* 3.2 20.3 + - + +
672E GLU* 4.0 7.4 - - - +
673E LEU 3.3 0.4 - - - -
674E LEU* 1.3 77.0 - - - +
676E GLN* 1.3 59.1 + - - +
678E GLN* 3.1 27.7 + - - +
679E ALA 4.5 0.9 + - - -
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Residues in contact with GLN 676 (chain E).
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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672E GLU 3.7 12.1 + - - +
673E LEU* 3.6 10.7 + - - +
674E LEU 3.4 0.4 - - - -
675E GLU* 1.3 73.1 - - - +
677E ALA* 1.3 59.8 + - - +
678E GLN 3.1 6.8 + - - -
679E ALA 3.3 24.9 + - - +
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Residues in contact with ALA 677 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642E LEU* 4.0 28.7 - - + -
648E VAL* 4.3 19.3 - - + +
673E LEU 3.2 15.7 + - - +
674E LEU* 3.4 17.7 - - + +
675E GLU 3.2 0.4 - - - -
676E GLN* 1.3 77.7 - - - +
678E GLN* 1.3 61.4 + - - +
679E ALA 5.1 0.2 - - - -
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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