Contacts of the helix formed by residues 658 - 669 (chain A) in PDB entry 1IJB
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 ASN 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A THR* 5.7 0.4 - - + -
622A MET* 3.6 16.0 - - + +
624A SER 3.0 18.8 + - - +
625A GLN* 3.6 29.9 - - + +
626A GLU* 4.2 8.1 + - - +
631A SER* 5.6 0.2 + - - -
657A ALA* 1.3 67.9 - - - +
659A LEU* 1.3 61.7 + - - +
660A LYS* 3.4 11.1 + - - +
661A GLN* 3.0 47.6 + - - +
662A ILE* 3.1 25.4 + - - +
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Residues in contact with LEU 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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625A GLN* 5.1 1.0 + - - -
652A GLY* 5.5 0.7 - - - -
654A GLY 4.8 4.9 - - - +
655A PRO* 5.6 2.5 - - + +
657A ALA* 2.8 34.8 + - + +
658A ASN* 1.3 72.3 + - - +
660A LYS* 1.3 63.7 + - - +
662A ILE* 3.2 13.1 + - + +
663A ARG* 3.0 54.7 + - - +
676A VAL* 4.2 24.9 - - + -
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Residues in contact with LYS 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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658A ASN* 3.2 8.6 + - - +
659A LEU* 1.3 77.2 - - - +
661A GLN* 1.3 64.3 + - + +
663A ARG* 3.4 9.1 + - + +
664A LEU* 3.1 53.5 + - + +
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Residues in contact with GLN 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A THR* 2.5 30.2 + - - +
622A MET* 4.3 5.0 - - + +
626A GLU* 3.1 25.1 + - - -
631A SER* 3.7 10.9 + - - -
634A PHE* 3.5 41.6 - - + +
658A ASN* 3.0 42.0 + - + +
660A LYS* 1.3 74.2 - - + +
662A ILE* 1.3 66.6 + - - +
664A LEU* 3.1 7.2 + - + +
665A ILE* 2.9 30.6 + - - +
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Residues in contact with ILE 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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622A MET* 3.7 24.0 - - + -
650A PRO* 3.9 13.6 - - + +
651A VAL 4.7 0.4 - - - -
652A GLY* 3.5 35.0 - - - +
657A ALA* 4.6 1.6 - - + -
658A ASN 3.1 16.2 + - - +
659A LEU* 3.2 26.0 + - + +
661A GLN* 1.3 76.9 - - - +
663A ARG* 1.3 84.7 - - - +
665A ILE* 3.2 6.4 + - - +
666A GLU* 3.1 22.7 + - - +
674A ALA* 3.5 18.4 - - + -
676A VAL* 4.8 3.6 - - + -
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Residues in contact with ARG 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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659A LEU* 3.0 32.3 + - - +
660A LYS* 3.6 10.8 - - + +
662A ILE* 1.3 97.3 - - - +
664A LEU* 1.3 60.8 + - - +
666A GLU* 3.0 30.3 + - - +
667A LYS* 3.2 22.0 + - - +
674A ALA* 3.7 4.2 - - - +
676A VAL* 3.6 22.4 - - - +
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Residues in contact with LEU 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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634A PHE* 4.2 19.1 - - + -
635A VAL* 4.0 27.8 - - + -
638A VAL* 5.4 0.4 - - - -
660A LYS* 3.1 42.2 + - + +
661A GLN* 3.1 11.4 + - + +
663A ARG* 1.3 75.3 - - - +
665A ILE* 1.3 63.2 + - - +
667A LYS* 3.3 19.5 + - + +
668A GLN* 3.0 38.3 + - - +
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Residues in contact with ILE 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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598A LEU* 4.7 2.0 - - + -
620A LEU* 3.9 26.5 - - + -
622A MET* 4.9 2.7 - - - -
634A PHE* 3.8 23.8 - - + -
638A VAL* 4.1 12.1 - - + -
648A VAL* 3.7 31.4 - - + +
650A PRO* 3.8 21.1 - - + -
661A GLN 2.9 19.8 + - - +
662A ILE* 3.5 7.0 - - - +
664A LEU* 1.3 77.6 - - - +
666A GLU* 1.3 62.1 + - - +
668A GLN* 3.2 14.0 + - - +
672A ASN* 2.9 36.9 + - + +
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Residues in contact with GLU 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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650A PRO* 4.8 2.2 - - + -
662A ILE 3.1 12.0 + - - +
663A ARG* 3.0 40.6 + - - +
664A LEU 3.4 0.2 - - - -
665A ILE* 1.3 76.9 - - - +
667A LYS* 1.3 62.5 + - - +
669A ALA 3.1 19.6 - - - +
670A PRO* 5.1 1.0 - - - +
672A ASN* 3.4 21.3 - - - +
673A LYS* 4.2 4.0 - - - +
674A ALA* 3.2 41.2 + - + +
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Residues in contact with LYS 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 ARG 3.2 9.9 + - - +
664A LEU* 3.5 21.3 - - + +
665A ILE 3.2 0.2 - - - -
666A GLU* 1.3 79.5 - - - +
668A GLN* 1.3 75.8 + - - +
669A ALA* 3.5 1.4 + - - -
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Residues in contact with GLN 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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635A VAL* 5.0 9.1 - - - +
638A VAL* 3.3 31.4 - - + -
639A GLN* 3.4 32.1 + - + +
642A LYS* 3.8 27.8 - - + +
664A LEU* 3.0 33.8 + - - +
665A ILE 3.2 7.5 + - - +
667A LYS* 1.3 96.4 - - - +
669A ALA* 1.3 60.7 + - + +
672A ASN* 4.0 4.0 - - - +
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Residues in contact with ALA 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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642A LYS* 4.0 20.0 - - + +
647A ILE* 6.4 0.4 - - + -
666A GLU 3.1 15.9 + - - +
667A LYS 3.4 1.3 - - - -
668A GLN* 1.3 80.8 - - - +
670A PRO* 1.3 76.6 - - + +
671A GLU* 3.9 9.9 - - + +
672A ASN* 3.0 34.0 + - - +
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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