Contacts of the helix formed by residues 607 - 622 (chain B) 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 ILE 607 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B GLU* 4.2 25.8 - - + +
571B GLU* 5.0 3.4 - - - +
605B SER* 3.1 10.4 + - - +
606B PRO* 1.3 84.6 - - + +
608B GLU* 1.3 65.9 + - - +
609B ASN* 3.8 26.0 - - + +
610B ILE* 3.0 37.6 + - + +
611B GLN* 3.3 13.7 + - - +
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B PRO 3.8 5.1 + - - +
607B ILE* 1.3 71.8 - - - +
609B ASN* 1.3 68.8 + - - +
611B GLN* 2.9 35.4 + - - +
612B ARG* 3.2 10.6 + - - +
646B SER* 5.3 4.0 + - - +
648B ASN* 3.0 35.6 + - + +
651B VAL* 3.8 7.5 - - + +
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Residues in contact with ASN 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B GLU* 3.4 34.1 + - - +
607B ILE* 3.2 12.7 + - + +
608B GLU* 1.3 79.5 + - - +
610B ILE* 1.3 59.9 + - - +
612B ARG* 3.3 17.7 + - - +
613B VAL* 3.0 21.5 + - - +
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Residues in contact with ILE 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B GLU* 4.2 18.2 - - + +
570B VAL* 4.6 13.7 - - + -
571B GLU* 3.7 23.8 - - + -
574B THR* 5.4 2.4 - - - +
602B LEU* 4.1 34.1 - - + +
605B SER* 3.8 24.9 - - - +
607B ILE* 3.0 32.3 + - + +
609B ASN* 1.3 74.8 - - - +
611B GLN* 1.3 58.3 + - - +
613B VAL* 3.5 9.5 - - + +
614B ALA* 3.1 26.0 + - - +
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Residues in contact with GLN 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU 4.7 6.3 - - - +
603B LEU* 4.6 15.4 - - - +
605B SER* 2.7 26.8 - - - +
606B PRO* 4.4 2.6 - - - +
607B ILE 3.4 11.7 - - - +
608B GLU* 2.9 32.7 + - - +
610B ILE* 1.3 76.1 - - - +
612B ARG* 1.3 65.9 + - - +
614B ALA* 4.0 3.3 - - - +
615B ALA* 3.0 27.5 + - - +
643B LEU* 3.7 20.4 - - + +
646B SER* 5.1 2.6 + - - -
651B VAL* 3.5 27.8 - - + +
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Residues in contact with ARG 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ARG* 4.9 9.5 - - - +
571B GLU* 5.9 0.6 + - - -
578B HIS* 4.5 15.4 + - - -
608B GLU 3.2 4.5 + - - +
609B ASN* 3.3 13.0 + - - +
611B GLN* 1.3 80.1 - - - +
613B VAL* 1.3 78.8 + - - +
615B ALA* 3.8 2.0 - - - +
616B GLY* 2.9 25.6 + - - -
648B ASN* 4.7 5.2 - - - +
650B GLY* 3.9 33.4 - - - +
651B VAL* 3.9 19.0 - - + +
654B TYR* 3.9 16.5 - - + -
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Residues in contact with VAL 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ARG* 4.8 8.5 - - - +
571B GLU* 4.5 14.8 - - + +
574B THR* 3.9 18.7 - - + +
575B GLY* 3.5 27.4 - - - +
578B HIS* 3.9 20.9 - - - +
609B ASN 3.0 20.9 - - - +
610B ILE* 3.5 16.6 - - - +
612B ARG* 1.3 88.6 - - - +
614B ALA* 1.3 62.6 + - - +
616B GLY* 3.7 0.2 - - - -
617B VAL* 3.0 25.1 + - - +
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Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B THR* 4.1 8.7 - - - -
599B PHE* 4.0 10.2 - - - +
602B LEU* 3.8 32.3 - - + -
603B LEU* 4.4 8.1 - - + -
610B ILE 3.1 21.6 + - - +
611B GLN* 4.0 2.9 - - - +
613B VAL* 1.3 76.5 - - - +
615B ALA* 1.3 63.3 + - - +
617B VAL* 3.2 20.7 - - - +
618B LEU* 3.2 16.2 - - - +
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Residues in contact with ALA 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B LEU* 4.3 15.4 - - + +
611B GLN 3.0 19.1 + - - +
612B ARG* 3.9 3.8 - - - +
614B ALA* 1.3 77.7 - - - +
616B GLY* 1.3 57.9 + - - +
618B LEU* 3.6 5.1 + - - +
619B CYS* 3.1 26.9 + - - +
640B LEU* 5.1 8.5 - - + -
643B LEU* 5.3 4.5 - - + -
651B VAL 5.0 5.2 - - - +
654B TYR* 4.0 23.1 - - + +
655B ALA* 4.8 2.2 - - - +
658B VAL* 3.5 8.2 - - - +
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Residues in contact with GLY 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B HIS* 4.0 19.6 + - - -
612B ARG 2.9 17.8 + - - -
613B VAL 3.3 2.4 + - - -
614B ALA 3.1 0.4 - - - -
615B ALA* 1.3 75.5 - - - +
617B VAL* 1.3 64.7 + - - +
619B CYS* 3.0 14.2 + - - +
620B GLU* 3.1 15.4 + - - +
654B TYR* 4.1 17.8 - - - -
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Residues in contact with VAL 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B THR* 4.7 2.9 - - + +
577B LEU* 4.5 8.3 - - + +
578B HIS* 4.1 29.1 - - - +
581B ALA* 4.8 5.6 - - + -
590B ILE* 5.3 3.1 - - + -
599B PHE* 3.7 50.5 - - + -
613B VAL 3.0 14.9 + - - +
614B ALA* 3.2 15.3 - - - +
616B GLY* 1.3 74.0 - - - +
618B LEU* 1.3 67.6 + - + +
620B GLU* 3.2 7.8 + - - +
621B LEU* 3.1 32.3 + - + +
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Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B ILE* 4.8 7.2 - - + -
599B PHE* 3.8 37.9 - - + +
600B VAL* 4.6 11.0 - - + -
603B LEU* 4.3 28.3 - - + -
614B ALA 3.2 18.3 + - - +
615B ALA* 3.7 6.3 - - - +
616B GLY 3.1 0.4 - - - -
617B VAL* 1.3 81.1 - - - +
619B CYS* 1.3 58.4 + - - +
621B LEU* 3.9 4.9 - - + +
622B ALA* 3.0 32.9 + - - +
631B ILE* 4.0 31.6 - - + +
636B ALA* 5.4 1.8 - - + -
640B LEU* 5.6 2.7 - - + -
658B VAL* 4.0 16.1 - - + +
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Residues in contact with CYS 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B ALA 3.1 14.4 + - - +
616B GLY 3.0 11.1 + - - +
618B LEU* 1.3 77.2 - - - +
620B GLU* 1.3 61.2 + - + +
622B ALA* 3.7 6.1 + - - +
654B TYR* 4.0 21.1 - - + -
657B ALA* 3.4 31.6 - - - -
658B VAL* 3.5 15.5 - - + +
661B ARG* 2.5 45.4 + - - -
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Residues in contact with GLU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B HIS* 4.2 25.9 + - + +
581B ALA* 3.7 28.8 - - + +
582B ARG* 4.4 13.0 + - - +
587B ARG* 3.8 3.9 + - - -
616B GLY 3.1 14.2 + - - +
617B VAL* 3.4 9.2 - - - +
618B LEU 3.2 0.2 - - - -
619B CYS* 1.3 80.1 - - + +
621B LEU* 1.3 58.5 + - - +
622B ALA 3.3 0.3 + - - -
623B GLN* 3.0 53.2 + - - +
654B TYR* 6.1 0.5 - - - -
661B ARG* 4.3 4.6 + - - +
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B ALA* 4.8 4.7 - - + -
587B ARG* 3.7 48.9 - - + +
590B ILE* 4.4 22.4 - - + -
591B ARG* 4.8 11.7 - - + -
595B THR* 5.1 0.2 - - - +
596B ILE* 4.9 16.6 - - + -
599B PHE* 4.7 11.9 - - + -
617B VAL* 3.1 27.5 + - + +
618B LEU* 4.3 7.6 - - + +
620B GLU* 1.3 80.3 - - + +
622B ALA* 1.3 58.9 + - - +
623B GLN* 3.1 1.9 + - - -
624B ASP* 3.6 7.8 + - - +
627B ALA* 2.9 30.7 - - + +
631B ILE* 4.8 4.7 - - + -
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Residues in contact with ALA 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU 3.0 21.4 + - - +
619B CYS* 4.0 7.9 - - - +
620B GLU 3.2 0.6 - - - -
621B LEU* 1.3 72.8 - - - +
623B GLN* 1.3 55.6 + - - +
624B ASP 3.0 11.5 + - - -
628B ALA* 3.6 25.0 - - + +
631B ILE* 3.9 17.4 - - + +
658B VAL* 4.5 13.5 - - + +
661B ARG* 3.9 23.7 - - + +
662B MET* 5.4 1.6 - - + +
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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