Contacts of the helix formed by residues 672 - 687 (chain A) in PDB entry 2REI
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 THR 672 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A GLY 4.9 2.9 - - - +
671A TYR* 1.3 85.2 - - - +
673A GLU* 1.3 64.1 + - - +
674A LYS* 3.4 10.3 + - - +
675A GLN* 3.0 38.3 + - - +
676A ARG 3.2 16.3 + - - -
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Residues in contact with GLU 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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618A ASN* 5.5 6.7 - - - +
671A TYR* 5.0 4.2 - - - -
672A THR* 1.3 73.1 - - - +
674A LYS* 1.3 61.3 + - - +
676A ARG* 3.3 13.5 + - + +
677A ARG* 2.9 40.5 + - - +
703A ARG* 3.5 32.9 + - - +
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Residues in contact with LYS 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A THR* 3.4 8.4 + - - +
673A GLU* 1.3 77.5 - - - +
675A GLN* 1.3 61.3 + - + +
677A ARG* 3.3 30.8 + - - +
678A ASP* 2.8 58.2 + - - +
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Residues in contact with GLN 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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644A PHE* 3.3 24.7 - - + -
667A LEU* 4.5 3.6 - - + -
670A GLY 4.4 1.7 - - - +
671A TYR* 3.4 14.6 - - + -
672A THR* 3.0 43.3 + - - +
674A LYS* 1.3 76.0 - - + +
676A ARG* 1.3 60.2 + - - +
678A ASP* 4.5 2.2 - - - +
679A PHE* 2.8 34.2 + - - +
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Residues in contact with ARG 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ASN* 3.2 31.3 + - - +
621A VAL* 6.2 0.2 - - - +
622A HIS* 4.5 10.3 + - - -
667A LEU* 3.6 20.8 - - + +
671A TYR* 3.8 26.9 - - + -
672A THR 3.2 14.7 + - - +
673A GLU* 3.6 15.1 + - - +
674A LYS 3.3 0.2 - - - -
675A GLN* 1.3 74.9 - - - +
677A ARG* 1.3 57.8 + - - +
679A PHE* 3.7 0.5 - - - +
680A LEU* 2.8 54.0 + - + +
702A THR* 3.0 44.9 + - - +
703A ARG* 3.2 43.6 - - - +
707A VAL* 4.6 2.2 - - + +
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Residues in contact with ARG 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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612A GLU* 6.1 2.5 - - + +
617A PRO* 3.4 37.0 - - + +
618A ASN* 4.5 15.4 + - - +
621A VAL* 5.8 0.4 - - - +
673A GLU* 2.9 28.9 + - - +
674A LYS* 3.4 39.5 + - - +
676A ARG* 1.3 76.5 - - - +
678A ASP* 1.3 70.7 + - - +
680A LEU* 3.8 3.0 - - - +
681A CYS* 3.0 31.3 + - - -
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Residues in contact with ASP 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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612A GLU* 5.1 6.1 - - - +
644A PHE* 3.7 22.1 - - + -
674A LYS* 2.8 52.0 + - - +
675A GLN* 3.9 2.2 - - - +
677A ARG* 1.3 82.4 + - - +
679A PHE* 1.3 63.8 + - - +
681A CYS* 3.4 20.5 - - - +
682A GLU* 4.1 2.8 + - - +
778A GLY* 5.3 5.0 - - - -
779A LEU 5.4 2.1 + - - -
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Residues in contact with PHE 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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644A PHE* 3.5 42.5 - + + -
665A LYS* 3.3 43.7 - - + -
666A THR 3.9 16.6 - - - -
667A LEU* 3.8 25.6 - - + -
675A GLN 2.8 22.0 + - - +
676A ARG 3.7 1.8 - - - +
678A ASP* 1.3 74.6 - - - +
680A LEU* 1.3 73.3 + - + +
681A CYS 3.3 1.0 + - - -
682A GLU* 3.3 14.8 + - - +
707A VAL* 4.0 14.6 - - + -
708A MET 4.1 0.7 - - - -
709A ILE* 3.3 45.3 - - + +
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ASN* 5.3 0.9 - - - +
621A VAL* 3.6 24.7 - - + +
676A ARG* 2.8 62.2 + - + +
677A ARG* 4.2 3.1 - - - +
679A PHE* 1.3 90.1 - - + +
681A CYS* 1.3 65.1 + - - +
682A GLU 3.1 2.7 - - - -
683A ALA* 2.9 15.5 + - - +
684A SER* 3.1 11.7 + - - -
700A VAL* 4.4 10.8 - - + -
702A THR* 3.8 30.5 - - + -
707A VAL* 4.2 8.1 - - + -
708A MET 4.6 1.3 - - - +
709A ILE* 4.2 11.7 - - + -
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Residues in contact with CYS 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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611A PRO* 4.5 11.2 - - + -
612A GLU* 4.3 26.9 - - - -
617A PRO* 5.0 8.3 - - - -
621A VAL* 5.0 1.1 - - - +
677A ARG* 3.0 29.5 + - - -
678A ASP* 3.4 15.9 - - - +
679A PHE 3.2 0.4 - - - -
680A LEU* 1.3 75.5 - - - +
682A GLU* 1.3 63.2 + - - +
684A SER* 2.8 24.6 + - - -
685A ILE* 3.0 23.0 + - + +
777A PHE 4.8 0.2 - - - -
778A GLY* 5.8 2.7 - - - -
779A LEU* 5.8 3.6 - - + +
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Residues in contact with GLU 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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665A LYS* 2.8 38.1 + - - +
678A ASP 4.1 1.8 + - - +
679A PHE* 3.3 14.6 + - - +
680A LEU 3.1 0.4 - - - -
681A CYS* 1.3 78.8 - - - +
683A ALA* 1.3 57.4 + - - +
685A ILE* 3.4 1.7 + - - +
686A MET* 2.8 50.2 + - + +
709A ILE* 4.1 7.7 - - + +
711A ILE* 5.2 0.9 - - - +
775A SER* 4.9 1.6 + - - -
776A ASP* 3.5 12.4 + - - +
777A PHE* 2.9 35.6 + - + +
778A GLY* 3.8 21.2 - - - +
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Residues in contact with ALA 683 (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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621A VAL* 5.0 1.8 - - + -
625A ALA* 4.2 10.0 - - + +
680A LEU* 2.9 12.4 + - + +
682A GLU* 1.3 78.1 - - - +
684A SER* 1.3 58.4 + - - +
686A MET* 4.4 2.9 - - - +
687A GLY* 2.8 27.4 + - - -
697A LEU* 3.5 18.1 - - + +
700A VAL* 3.4 33.7 - - + -
709A ILE* 4.0 14.1 - - + +
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Residues in contact with SER 684 (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 PRO* 3.3 23.5 - - - +
617A PRO 5.3 0.5 + - - -
620A ALA* 3.9 19.5 - - - -
621A VAL* 4.0 17.4 - - - +
624A PHE* 3.6 14.6 - - - +
680A LEU 3.1 6.2 + - - -
681A CYS* 2.8 29.5 + - - -
683A ALA* 1.3 76.2 - - - +
685A ILE* 1.3 51.8 + - - +
688A GLN* 2.8 35.0 + - - +
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Residues in contact with ILE 685 (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 TYR* 3.5 26.5 - - + +
610A ASP* 5.8 0.2 - - - +
611A PRO* 3.9 18.2 - - + -
681A CYS* 3.0 20.5 + - + +
682A GLU 3.8 2.9 - - - +
684A SER* 1.3 75.7 - - - +
686A MET* 1.3 67.6 + - - +
687A GLY 3.2 1.3 - - - -
688A GLN* 3.0 25.2 + - - +
689A PHE* 3.6 25.4 - - + -
754A TYR* 3.6 22.2 - - + +
777A PHE* 3.3 31.2 - - + +
778A GLY 5.4 2.7 - - - -
779A LEU* 6.1 4.7 - - + -
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Residues in contact with MET 686 (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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682A GLU* 2.8 44.7 + - + +
683A ALA* 4.2 1.8 - - - +
685A ILE* 1.3 73.4 - - - +
687A GLY* 1.3 62.6 + - - +
688A GLN 3.1 1.4 + - - -
689A PHE* 3.1 29.7 + - + +
694A VAL* 5.5 0.4 - - + -
695A VAL* 3.3 31.4 - - + +
696A HIS 4.1 0.9 - - - -
697A LEU* 3.7 33.5 + - + +
709A ILE* 4.9 1.3 - - + -
711A ILE* 3.8 35.4 - - + -
775A SER* 5.8 2.0 - - - +
777A PHE* 4.1 19.3 - - + +
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Residues in contact with GLY 687 (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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624A PHE* 3.4 30.6 - - - +
683A ALA 2.8 16.3 + - - -
685A ILE 3.2 0.2 + - - -
686A MET* 1.3 75.9 - - - +
688A GLN* 1.3 60.9 + - - +
689A PHE 3.3 4.6 + - - +
697A LEU* 3.6 14.0 - - - +
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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