Contacts of the helix formed by residues 648 - 662 (chain A) in PDB entry 1JPP
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 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A GLU* 3.1 34.9 + - - +
612A ARG* 4.7 5.6 - - - +
646A SER* 3.1 13.3 + - - +
647A ARG* 1.3 76.0 - - - +
649A GLU* 1.3 55.1 + - - +
650A GLY* 2.6 42.8 + - - -
651A VAL* 3.2 26.6 + - + +
652A ALA* 2.9 22.5 + - - +
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Residues in contact with GLU 649 (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 SER 5.4 0.2 - - - -
647A ARG 3.3 8.8 + - - +
648A ASN* 1.3 69.3 + - - +
650A GLY* 1.3 56.1 + - - +
652A ALA* 4.3 6.7 - - - -
653A THR* 2.7 35.4 + - - +
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Residues in contact with GLY 650 (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 ARG* 4.0 19.1 - - - -
648A ASN* 2.6 15.1 + - - -
649A GLU* 1.3 74.3 - - - +
651A VAL* 1.3 63.1 + - - -
652A ALA 3.0 2.4 + - - -
653A THR* 4.2 2.1 - - - -
654A TYR* 3.3 31.5 + - - +
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Residues in contact with VAL 651 (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 GLU* 3.7 20.9 - - + +
611A GLN* 3.6 33.7 - - + +
612A ARG* 3.9 17.9 - - + +
615A ALA* 5.0 2.9 - - + +
643A LEU* 3.7 23.5 - - + +
646A SER* 4.1 7.6 - - - +
648A ASN* 2.9 35.7 + - + +
650A GLY* 1.3 74.5 - - - +
652A ALA* 1.3 60.7 + - - +
654A TYR* 4.4 2.9 - - - +
655A ALA* 3.5 20.3 + - - +
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Residues in contact with ALA 652 (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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643A LEU 3.7 9.2 - - - +
644A LEU* 4.0 16.3 - - - +
646A SER* 3.8 18.8 - - - +
648A ASN 2.9 14.5 + - - +
649A GLU* 4.3 6.3 - - - +
651A VAL* 1.3 75.6 - - - +
653A THR* 1.3 67.4 + - - +
654A TYR 3.0 1.6 - - - -
655A ALA* 2.8 16.1 + - - +
656A ALA* 3.2 11.5 + - - +
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Residues in contact with THR 653 (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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649A GLU* 2.7 24.0 + - - +
650A GLY* 3.6 3.3 + - - -
652A ALA* 1.3 78.6 - - - +
654A TYR* 1.3 67.5 + - + +
656A ALA* 3.7 7.8 + - - +
657A ALA* 3.5 18.3 + - + +
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Residues in contact with TYR 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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578A HIS* 3.6 31.8 + + - -
612A ARG* 3.9 29.4 - - + +
615A ALA* 4.1 18.4 - - + +
616A GLY* 4.1 7.9 - - - -
619A CYS* 4.0 33.2 - - + -
650A GLY* 3.3 20.9 + - - +
651A VAL* 4.4 1.8 - - - +
652A ALA 2.8 1.4 + - - -
653A THR* 1.3 85.1 - - + +
655A ALA* 1.3 63.0 + - - +
656A ALA 3.2 2.0 - - - -
657A ALA* 3.4 3.9 + - + +
658A VAL* 3.3 28.8 + - - +
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Residues in contact with ALA 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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615A ALA* 4.8 2.9 - - + +
640A LEU* 3.7 34.3 - - + +
643A LEU* 3.9 20.9 - - + +
644A LEU* 3.9 4.5 - - + -
651A VAL 3.5 13.6 + - - +
652A ALA 2.8 12.9 + - - +
654A TYR* 1.3 74.5 - - - +
656A ALA* 1.3 60.6 + - - +
657A ALA 3.3 0.2 - - - -
658A VAL* 4.2 1.4 - - - +
659A LEU* 3.3 30.1 + - - +
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Residues in contact with ALA 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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644A LEU* 3.8 18.6 - - + +
652A ALA 3.2 8.1 + - - +
653A THR* 3.9 11.0 - - - +
655A ALA* 1.3 78.4 - - - +
657A ALA* 1.3 61.6 + - - +
659A LEU* 3.8 3.3 + - - +
660A PHE* 3.2 23.9 + - - +
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Residues in contact with ALA 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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619A CYS* 3.6 26.9 - - - -
653A THR* 3.5 11.5 + - + +
654A TYR* 3.4 9.8 + - + +
655A ALA 3.3 0.2 - - - -
656A ALA* 1.3 78.2 - - - +
658A VAL* 1.3 64.1 + - - +
660A PHE* 3.2 8.6 + - - +
661A ARG* 3.0 28.9 + - - +
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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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615A ALA* 3.5 21.1 - - - +
618A LEU* 4.1 13.5 - - + -
619A CYS* 3.5 21.3 - - - +
622A ALA* 4.5 14.4 - - + +
631A ILE* 5.0 5.2 - - + -
640A LEU* 3.6 31.2 - - + -
654A TYR 3.3 17.4 + - - +
655A ALA 4.5 1.1 - - - +
656A ALA 3.6 0.2 - - - -
657A ALA* 1.3 76.4 - - - +
659A LEU* 1.3 61.9 + - - +
661A ARG* 3.6 5.0 + - - +
662A MET* 3.2 33.7 + - + +
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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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637A THR* 4.5 18.6 - - + +
640A LEU* 3.6 45.5 - - + +
641A THR* 4.5 5.8 - - - +
644A LEU* 4.2 21.3 - - + -
655A ALA 3.3 19.6 + - - +
656A ALA* 4.1 4.3 - - - +
657A ALA 3.2 0.6 - - - -
658A VAL* 1.3 74.7 - - - +
660A PHE* 1.3 67.6 + - - +
661A ARG 3.5 0.2 + - - -
662A MET* 3.6 18.3 + - + +
663A SER* 3.4 20.3 - - - -
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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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656A ALA 3.2 17.0 + - - +
657A ALA* 3.2 9.4 + - - +
659A LEU* 1.3 79.5 - - - +
661A ARG* 1.3 74.2 + - + +
663A SER* 3.1 28.8 + - - +
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Residues in contact with ARG 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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619A CYS* 2.5 54.7 + - - +
620A GLU* 4.3 6.7 + - - +
622A ALA* 3.8 20.1 - - + +
623A GLN* 3.7 40.4 + - - +
628A ALA* 4.7 4.0 - - - +
657A ALA* 3.0 19.2 + - - +
658A VAL 4.0 3.8 - - - +
659A LEU 3.3 0.2 - - - -
660A PHE* 1.3 85.3 - - + +
662A MET* 1.3 56.0 + - - +
663A SER 2.9 12.8 + - - -
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Residues in contact with MET 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 ALA* 5.5 1.8 - - + -
628A ALA* 4.0 28.5 - - + +
631A ILE* 4.3 14.4 - - + -
632A GLU* 3.6 50.4 - - - +
636A ALA* 4.6 5.2 - - + -
637A THR* 4.3 9.2 - - - +
640A LEU* 3.4 32.8 - - + -
658A VAL* 3.2 27.8 + - + +
659A LEU* 3.8 15.7 - - + +
660A PHE 3.4 0.2 - - - -
661A ARG* 1.3 74.3 - - - +
663A SER* 1.3 61.1 + - - +
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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