Contacts of the helix formed by residues 653 - 668 (chain A) in PDB entry 5IA2
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 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A GLY 4.8 3.6 - - - +
652A TYR* 1.3 83.3 - - - +
654A GLU* 1.3 64.9 + - - +
655A LYS* 3.5 8.0 + - - +
656A GLN* 2.8 42.7 + - - +
657A ARG* 3.0 17.7 + - - +
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Residues in contact with GLU 654 (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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653A THR* 1.3 74.2 - - - +
655A LYS* 1.3 64.4 - - - +
657A ARG* 3.1 31.8 + - - +
658A VAL* 2.9 34.8 + - + +
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Residues in contact with LYS 655 (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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653A THR* 3.3 8.1 + - - +
654A GLU* 1.3 79.2 - - - +
656A GLN* 1.3 61.7 + - + +
658A VAL* 3.3 5.5 + - - +
659A ASP* 2.9 55.7 + - - +
761A SER* 3.3 24.6 + - - -
765A GLU* 4.2 15.5 - - - -
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Residues in contact with GLN 656 (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* 3.1 51.9 - - - -
648A LEU* 4.0 9.8 - - + +
651A GLY 4.6 0.7 - - - +
652A TYR* 3.2 18.2 - - + +
653A THR* 2.8 51.4 + - - +
655A LYS* 1.3 79.4 - - + +
657A ARG* 1.3 57.0 + - - +
659A ASP* 3.8 6.2 - - - +
660A PHE* 2.8 32.4 + - - +
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Residues in contact with ARG 657 (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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598A ASN* 5.6 3.3 - - - +
648A LEU* 4.1 10.0 - - - +
652A TYR* 3.7 18.3 - - + +
653A THR 3.0 13.5 + - - +
654A GLU* 3.1 30.1 + - - +
656A GLN* 1.3 76.2 - - - +
658A VAL* 1.3 74.6 + - - +
661A LEU* 2.9 47.2 + - + +
688A MET* 3.4 22.7 - - + -
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Residues in contact with VAL 658 (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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598A ASN* 2.9 23.6 + - - +
654A GLU* 2.9 30.0 + - + +
655A LYS* 3.8 6.5 - - - +
657A ARG* 1.3 97.4 - - - +
659A ASP* 1.3 63.9 + - - +
662A GLY* 2.8 26.2 + - - -
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Residues in contact with ASP 659 (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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655A LYS* 2.9 54.1 + - - +
656A GLN* 3.8 5.9 - - - +
658A VAL* 1.3 83.1 - - - +
660A PHE* 1.3 61.6 + - - +
662A GLY* 3.3 1.5 + - - -
663A GLU 3.1 17.8 + - - -
759A GLY* 5.5 0.5 - - - -
760A LEU* 5.7 2.9 - - - +
761A SER* 3.9 10.2 + - - -
762A ARG* 3.6 38.3 - - + +
765A GLU* 4.2 6.6 - - - +
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Residues in contact with PHE 660 (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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646A LYS* 3.4 52.0 - - + +
647A THR 3.9 13.0 - - - -
648A LEU* 3.8 36.1 - - + -
656A GLN 2.8 23.1 + - - +
657A ARG 3.8 1.3 - - - +
659A ASP* 1.3 72.5 - - - +
661A LEU* 1.3 77.0 + - + +
663A GLU* 3.3 9.5 + - - +
688A MET* 3.8 28.3 - - + -
689A MET 3.9 6.7 - - - -
690A ILE* 3.3 45.1 - - + +
762A ARG* 5.0 5.6 - - - +
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Residues in contact with LEU 661 (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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598A ASN* 3.8 13.3 - - + +
602A LEU* 4.0 25.9 - - + +
657A ARG* 2.9 42.9 + - + +
660A PHE* 1.3 88.5 - - + +
662A GLY* 1.3 57.7 + - - +
664A ALA* 3.1 7.9 + - + +
665A GLY* 2.9 23.7 + - - -
681A VAL* 4.9 16.4 - - + -
682A ILE 5.0 1.6 - - - +
683A SER* 4.1 27.1 - - - -
688A MET* 3.9 19.1 - - + -
690A ILE* 5.5 0.4 - - + -
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Residues in contact with GLY 662 (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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598A ASN* 3.3 17.5 - - - +
601A VAL* 5.5 0.8 - - - +
658A VAL 2.8 21.6 + - - -
659A ASP* 3.7 2.2 - - - -
660A PHE 3.2 0.6 - - - -
661A LEU* 1.3 77.2 - - - +
663A GLU* 1.3 62.3 + - - +
665A GLY* 3.2 2.7 + - - -
666A ILE* 3.0 32.8 + - - +
759A GLY* 5.3 0.9 - - - -
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Residues in contact with GLU 663 (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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646A LYS* 3.7 17.5 + - - -
659A ASP 3.1 11.6 + - - +
660A PHE* 3.6 9.9 - - - +
661A LEU 3.2 0.4 - - - -
662A GLY* 1.3 75.5 - - - +
664A ALA* 1.3 56.9 + - - +
666A ILE* 3.2 3.8 + - - +
667A MET* 2.8 38.0 + - + +
690A ILE* 4.2 7.5 - - + +
757A ASP* 3.5 1.2 + - - -
758A PHE* 2.8 48.2 + - + +
759A GLY* 4.6 3.0 - - - -
762A ARG* 3.5 15.2 + - - -
1001A L66 2.5 41.9 + - - -
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Residues in contact with ALA 664 (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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602A LEU* 4.5 5.2 - - + -
605A THR* 3.9 2.4 + - - -
660A PHE 3.7 2.4 + - - -
661A LEU* 3.1 11.7 + - - +
663A GLU* 1.3 76.3 - - - +
665A GLY* 1.3 60.5 + - - +
667A MET* 4.3 5.8 - - - -
668A GLY* 2.8 28.1 + - - -
678A LEU* 3.6 18.1 - - + +
681A VAL* 3.4 32.5 - - + -
690A ILE* 4.2 15.0 - - + +
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Residues in contact with GLY 665 (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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601A VAL* 3.7 46.0 - - - +
602A LEU* 4.3 5.1 - - - +
605A THR* 4.6 0.7 - - - -
661A LEU 2.9 13.9 + - - -
662A GLY 3.2 4.0 + - - -
664A ALA* 1.3 76.9 - - - +
666A ILE* 1.3 61.2 + - - +
668A GLY* 3.7 4.0 + - - -
669A GLN* 3.4 19.2 + - - +
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Residues in contact with ILE 666 (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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601A VAL* 6.0 1.6 - - + -
662A GLY 3.0 19.3 + - - +
663A GLU 3.6 5.2 - - - +
664A ALA 3.2 0.2 - - - -
665A GLY* 1.3 76.1 - - - +
667A MET* 1.3 66.3 + - - +
669A GLN* 3.0 24.0 + - - +
670A PHE* 3.5 33.4 - - + -
735A TYR* 3.8 21.8 - - + -
758A PHE* 4.0 8.5 - - + -
759A GLY* 3.6 33.4 - - - +
760A LEU* 4.6 13.9 - - + +
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Residues in contact with MET 667 (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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663A GLU* 2.8 33.3 + - + +
664A ALA* 3.8 4.3 - - - +
666A ILE* 1.3 72.6 - - - +
668A GLY* 1.3 61.3 + - - +
670A PHE* 3.1 31.1 + - + +
676A ILE* 3.5 34.8 - - + +
677A ARG* 6.1 0.2 - - - -
678A LEU* 3.7 29.7 + - + +
690A ILE* 4.6 5.4 - - + -
692A THR* 3.8 15.9 - - + -
758A PHE* 4.1 18.6 - - + -
1001A L66 3.6 32.5 - - + -
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Residues in contact with GLY 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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604A PHE* 3.9 25.5 - - - +
605A THR* 4.8 2.2 - - - -
664A ALA 2.8 16.3 + - - -
665A GLY 4.2 3.1 - - - -
666A ILE 3.2 0.4 - - - -
667A MET* 1.3 75.3 - - - +
669A GLN* 1.3 62.2 + - - +
670A PHE 3.3 3.9 + - - +
678A LEU* 3.9 17.0 - - - +
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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