Contacts of the helix formed by residues 671 - 682 (chain A) in PDB entry 5LUQ
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 SER 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A LEU* 3.3 6.4 - - - +
670A LEU* 1.3 81.1 + - - +
672A ILE* 1.3 71.8 + - - +
673A THR 3.4 0.7 - - - -
674A VAL* 4.4 2.0 - - - +
675A ARG* 2.9 35.7 + - - +
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Residues in contact with ILE 672 (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 ARG* 6.2 2.0 - - + -
635A PRO* 5.9 5.2 - - + -
669A LEU* 3.7 39.5 - - + +
671A SER* 1.3 82.9 + - - +
673A THR* 1.3 62.8 + - + +
675A ARG* 4.0 21.0 - - - +
676A ASN* 2.9 52.1 + - - +
704A PHE* 6.2 0.2 - - + -
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Residues in contact with THR 673 (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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638A GLN* 3.6 31.9 - - + +
669A LEU* 2.4 38.7 + - + +
670A LEU* 3.9 4.2 - - - -
672A ILE* 1.3 77.5 - - + +
674A VAL* 1.3 57.9 + - - -
676A ASN* 3.7 1.4 - - - +
677A ALA* 2.9 30.7 + - - +
704A PHE* 4.0 27.3 - - + -
707A PHE* 5.0 9.0 - - + -
740A ILE* 4.4 12.3 + - + +
741A ILE* 5.4 7.7 - - - +
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Residues in contact with VAL 674 (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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670A LEU* 3.1 32.1 - - + +
671A SER* 3.7 3.2 + - - +
672A ILE 3.4 0.2 - - - -
673A THR* 1.3 78.1 + - - +
675A ARG* 1.3 67.4 + - - +
677A ALA* 3.1 7.6 + - - +
678A LYS* 2.9 22.3 + - - +
740A ILE 3.6 23.1 - - - +
741A ILE* 4.3 8.3 - - - +
742A GLU* 4.0 13.9 - - + +
743A LEU* 3.4 31.3 - - + +
783A HIS* 3.7 10.5 - - + +
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Residues in contact with ARG 675 (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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671A SER 2.9 27.0 + - - +
672A ILE* 4.0 22.4 - - - +
674A VAL* 1.3 76.4 - - - +
676A ASN* 1.3 73.5 + - - +
678A LYS* 3.4 12.4 + - + +
679A LYS* 3.0 40.0 + - - +
743A LEU* 5.5 0.2 - - - -
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Residues in contact with ASN 676 (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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672A ILE* 2.9 39.4 + - - +
673A THR 3.7 3.8 - - - +
675A ARG* 1.3 87.4 + - - +
677A ALA* 1.3 63.9 + - - +
679A LYS* 2.8 25.5 + - - +
680A ILE* 2.9 18.1 + - + +
700A LYS* 6.0 4.4 - - - +
701A TYR* 4.4 7.2 - - + -
704A PHE* 3.9 31.1 - - + -
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Residues in contact with ALA 677 (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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673A THR 2.9 19.1 + - - +
674A VAL* 3.6 6.5 - - - +
676A ASN* 1.3 73.7 - - - +
678A LYS* 1.3 64.6 + - - +
680A ILE* 2.9 27.8 + - + +
681A LYS* 3.0 13.7 + - - +
704A PHE* 4.9 6.9 - - + -
741A ILE* 5.4 2.0 - - + +
743A LEU* 5.3 1.1 - - + -
744A ASP* 3.2 34.1 - - - +
746A ARG* 4.4 2.6 + - - -
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Residues in contact with LYS 678 (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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674A VAL 2.9 7.0 + - - +
675A ARG* 3.6 14.6 - - + +
677A ALA* 1.3 74.9 - - - +
679A LYS* 1.3 63.1 + - - +
681A LYS* 3.0 2.4 + - - -
682A TYR* 3.0 61.7 + - + -
743A LEU* 3.6 34.0 - - + +
746A ARG* 3.8 13.1 - - - +
784A VAL* 5.7 6.1 - - - +
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Residues in contact with LYS 679 (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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675A ARG* 3.0 29.4 + - - +
676A ASN* 2.8 23.7 + - - +
678A LYS* 1.3 75.0 - - - +
680A ILE* 1.3 60.7 + - - +
682A TYR* 3.9 13.4 + - - +
701A TYR* 3.7 25.3 + - + +
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Residues in contact with ILE 680 (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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676A ASN 3.1 12.3 - - - +
677A ALA* 2.9 20.5 + - + +
679A LYS* 1.3 79.6 - - - +
681A LYS* 1.3 63.2 + - - +
682A TYR 4.7 1.6 - - - -
701A TYR* 3.2 39.0 - - + +
704A PHE* 3.4 36.6 - - + -
705A ALA 6.2 0.4 - - - +
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Residues in contact with LYS 681 (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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677A ALA 3.0 8.2 + - - +
678A LYS 3.0 1.5 + - - +
680A ILE* 1.3 80.1 - - - +
682A TYR* 1.3 77.9 + - + +
746A ARG* 3.3 50.8 - - - +
1324A PRO* 5.3 15.6 - - + +
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Residues in contact with TYR 682 (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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678A LYS* 3.0 64.2 + - + +
679A LYS* 3.9 10.9 + - - +
680A ILE 3.4 2.5 - - - -
681A LYS* 1.3 99.7 - - + +
746A ARG* 5.2 3.4 - - - -
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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