Contacts of the helix formed by residues 607 - 622 (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 ILE 607 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A GLU* 4.2 26.0 - - + +
571A GLU* 5.0 3.1 - - - +
605A SER* 3.1 10.9 + - - +
606A PRO* 1.3 84.7 - - + +
608A GLU* 1.3 66.8 + - - +
609A ASN* 3.9 25.4 - - + +
610A ILE* 3.1 36.7 + - + +
611A GLN* 3.3 13.1 + - - +
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Residues in contact with GLU 608 (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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606A PRO 3.8 4.3 + - - +
607A ILE* 1.3 71.6 - - - +
609A ASN* 1.3 67.6 + - - +
611A GLN* 3.0 35.5 + - - +
612A ARG* 3.1 11.1 + - - +
646A SER* 5.2 4.4 + - - +
648A ASN* 3.1 36.0 + - + +
651A VAL* 3.7 7.4 - - + +
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Residues in contact with ASN 609 (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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571A GLU* 3.4 37.2 + - + +
607A ILE* 3.2 12.8 - - + +
608A GLU* 1.3 79.2 - - - +
610A ILE* 1.3 61.9 + - - +
611A GLN 3.3 0.2 + - - -
612A ARG* 3.3 18.8 + - - +
613A VAL* 3.4 16.1 + - - +
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Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A GLU* 4.1 18.6 - - + +
570A VAL* 4.6 11.0 - - + -
571A GLU* 3.6 26.7 - - + +
574A THR* 5.5 2.0 - - - +
602A LEU* 4.1 34.1 - - + +
605A SER* 4.0 24.7 - - - +
607A ILE* 3.1 31.2 + - + +
609A ASN* 1.3 75.9 - - - +
611A GLN* 1.3 59.3 + - - +
613A VAL* 3.6 8.3 - - + +
614A ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 611 (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 4.7 7.4 - - - +
603A LEU* 4.5 14.5 - - - +
605A SER* 2.7 26.6 - - - +
606A PRO* 4.4 2.3 - - - +
607A ILE 3.4 12.4 + - - +
608A GLU* 3.0 32.5 + - - +
610A ILE* 1.3 75.9 - - - +
612A ARG* 1.3 64.8 + - - +
614A ALA* 3.8 3.8 - - - +
615A ALA* 3.0 27.4 + - - +
643A LEU* 3.7 21.1 - - + +
646A SER* 5.0 2.4 + - - -
651A VAL* 3.6 27.9 - - + +
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Residues in contact with ARG 612 (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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515A ARG* 4.8 9.5 - - - +
571A GLU* 5.9 0.8 + - - -
578A HIS* 4.4 14.3 - - - -
608A GLU 3.1 5.2 + - - +
609A ASN* 3.3 13.4 + - - +
611A GLN* 1.3 79.9 - - - +
613A VAL* 1.3 82.7 + - - +
615A ALA* 3.7 2.5 - - - +
616A GLY* 2.8 25.8 + - - -
648A ASN* 4.7 5.8 - - - +
650A GLY* 4.0 31.4 - - - -
651A VAL* 3.9 18.3 - - + +
654A TYR* 3.9 17.5 - - + -
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Residues in contact with VAL 613 (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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515A ARG* 4.6 9.4 - - - +
571A GLU* 4.4 13.2 - - + +
574A THR* 3.8 18.9 - - + +
575A GLY* 3.8 24.0 - - - +
578A HIS* 3.8 25.9 - - - +
609A ASN 3.4 16.4 - - - +
610A ILE* 3.6 11.7 - - - +
612A ARG* 1.3 96.7 - - - +
614A ALA* 1.3 62.5 + - - +
616A GLY 3.5 0.9 - - - +
617A VAL* 3.0 28.9 + - - +
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Residues in contact with ALA 614 (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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574A THR* 4.2 8.1 - - - -
599A PHE* 4.2 9.4 - - - +
602A LEU* 3.8 31.2 - - + -
603A LEU* 4.4 6.7 - - + -
610A ILE 3.0 22.4 + - - +
611A GLN* 3.8 4.9 - - - +
613A VAL* 1.3 75.7 - - - +
615A ALA* 1.3 62.7 + - - +
617A VAL* 3.1 22.7 - - - +
618A LEU* 3.3 14.9 - - - +
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Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU* 4.3 15.7 - - + +
611A GLN 3.0 17.8 + - - +
612A ARG* 3.9 2.9 - - - +
614A ALA* 1.3 76.3 - - - +
616A GLY* 1.3 58.6 + - - +
618A LEU* 3.7 6.5 + - - -
619A CYS* 3.1 25.6 + - - +
640A LEU* 4.9 10.1 - - + -
643A LEU* 5.2 4.5 - - + -
651A VAL 5.0 5.6 - - - +
654A TYR* 4.1 23.1 - - + +
655A ALA* 4.8 2.0 - - - +
658A VAL* 3.5 8.2 - - + +
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Residues in contact with GLY 616 (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* 4.0 20.2 + - - -
612A ARG 2.8 16.9 + - - -
613A VAL 3.4 2.2 + - - -
614A ALA 3.1 0.2 - - - -
615A ALA* 1.3 75.2 - - - +
617A VAL* 1.3 63.7 + - - +
618A LEU 3.1 1.3 - - - -
619A CYS* 2.9 14.2 + - - +
620A GLU* 3.1 15.1 + - - +
654A TYR* 4.1 17.3 - - - -
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Residues in contact with VAL 617 (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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574A THR* 4.6 2.9 - - + -
577A LEU* 4.4 10.5 - - + +
578A HIS* 4.1 25.6 - - + +
581A ALA* 4.8 5.6 - - + -
590A ILE* 5.4 3.6 - - + -
599A PHE* 3.7 50.5 - - + -
613A VAL 3.0 14.9 + - - +
614A ALA* 3.1 15.3 - - - +
616A GLY* 1.3 74.6 - - - +
618A LEU* 1.3 66.3 + - + +
620A GLU* 3.3 7.9 + - - +
621A LEU* 3.2 32.5 + - + +
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Residues in contact with LEU 618 (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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596A ILE* 5.0 6.3 - - + -
599A PHE* 3.9 35.2 - - + +
600A VAL* 4.7 11.0 - - + -
603A LEU* 4.3 29.4 - - + -
614A ALA 3.3 16.8 + - - +
615A ALA* 3.8 7.0 - - - +
616A GLY 3.1 0.4 - - - -
617A VAL* 1.3 80.6 - - + +
619A CYS* 1.3 60.4 + - - +
621A LEU* 3.9 5.6 - - + +
622A ALA* 2.9 34.5 + - - +
631A ILE* 4.1 32.7 - - + +
636A ALA* 5.3 2.2 - - + -
640A LEU* 5.5 2.7 - - + -
658A VAL* 4.1 15.9 - - + -
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Residues in contact with CYS 619 (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 3.1 15.2 + - - +
616A GLY 2.9 10.4 + - - +
618A LEU* 1.3 77.3 - - - +
620A GLU* 1.3 60.9 + - - +
622A ALA* 3.8 4.0 + - - -
654A TYR* 4.0 22.2 - - + -
657A ALA* 3.6 26.5 - - - -
658A VAL* 3.5 17.7 - - + +
661A ARG* 2.5 48.9 + - - -
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Residues in contact with GLU 620 (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* 4.2 19.1 + - + +
581A ALA* 3.4 38.2 - - + +
582A ARG* 4.4 11.0 - - - +
587A ARG* 3.8 3.4 + - - -
616A GLY 3.1 13.3 + - - +
617A VAL* 3.5 9.2 - - - +
618A LEU 3.1 0.4 - - - -
619A CYS* 1.3 79.4 - - + +
621A LEU* 1.3 64.3 + - - +
622A ALA 3.3 0.3 + - - -
623A GLN* 3.1 49.9 + - - +
654A TYR* 6.2 0.2 - - - -
661A ARG* 4.3 4.5 + - - +
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Residues in contact with LEU 621 (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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581A ALA* 5.0 4.5 - - + -
587A ARG* 3.7 48.0 - - + +
590A ILE* 4.6 20.2 - - + -
591A ARG* 4.7 15.5 - - + -
595A THR* 5.0 0.4 - - - +
596A ILE* 4.9 12.8 - - + -
599A PHE* 4.7 12.1 - - + -
617A VAL* 3.2 26.6 + - + +
618A LEU* 4.2 7.0 - - + +
620A GLU* 1.3 80.5 - - + +
622A ALA* 1.3 56.6 + - - +
623A GLN 3.1 5.3 + - - -
624A ASP* 3.5 8.3 + - - +
627A ALA* 3.0 29.3 - - + +
631A ILE* 4.9 5.8 - - + -
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Residues in contact with ALA 622 (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 LEU 2.9 20.2 + - - +
619A CYS* 4.1 6.5 - - - +
620A GLU 3.2 0.6 - - - -
621A LEU* 1.3 72.9 - - - +
623A GLN* 1.3 55.3 + - - +
624A ASP 2.9 12.4 + - - -
628A ALA* 3.6 25.3 - - + +
631A ILE* 4.0 18.3 - - + +
658A VAL* 4.5 14.6 - - + +
661A ARG* 3.8 24.4 - - + +
662A MET* 5.4 1.3 - - + +
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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