Contacts of the helix formed by residues 647 - 667 (chain A) in PDB entry 3H0G
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 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A ASP* 5.5 9.9 - - + +
587A ILE 6.1 0.2 - - - +
588A ILE 5.2 0.2 - - - -
589A PRO* 3.5 46.7 - - + -
590A LYS* 4.9 2.7 - - + +
643A LYS* 6.3 3.4 - - + -
646A GLU* 1.3 69.3 + - - +
648A CYS* 1.3 54.8 + - - +
649A LYS 3.3 0.4 - - - -
650A GLY* 2.6 29.2 + - - +
651A PHE* 3.0 8.9 + - - +
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Residues in contact with CYS 648 (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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517A ILE* 3.6 31.4 - - - -
589A PRO* 5.9 0.2 - - - -
636A VAL 5.1 2.0 - - - -
639A ILE* 2.7 36.3 - - + +
640A TRP* 3.8 3.4 - - - -
643A LYS 5.8 0.2 - - - +
644A GLY 2.8 14.6 + - - +
645A PRO* 2.9 7.4 - - + -
646A GLU* 2.3 40.7 - - - +
647A ILE* 1.3 67.5 - - - +
649A LYS* 1.3 54.6 + - - -
651A PHE* 2.8 32.1 + - - +
652A PHE* 4.0 10.1 - - - -
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Residues in contact with LYS 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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366A SER* 4.0 15.5 + - - -
367A LEU* 4.3 24.4 - - + +
368A ASP* 2.4 51.3 + - + +
465A ARG* 4.3 10.7 - - - +
514A PRO* 4.6 19.3 - - + -
517A ILE* 6.2 1.1 - - - -
645A PRO* 3.6 3.7 - - - +
646A GLU* 2.8 33.9 + - + +
648A CYS* 1.3 73.5 - - - +
650A GLY* 1.3 53.6 + - - +
651A PHE 3.3 0.2 - - - -
652A PHE* 3.9 6.9 + - - +
653A ASN* 2.7 29.5 + - - +
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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
----------------------------------------------------------
559A VAL 4.9 1.8 - - - +
560A PRO* 4.9 11.2 - - - +
646A GLU* 4.5 0.8 - - - +
647A ILE* 2.6 22.5 + - - +
649A LYS* 1.3 74.5 - - - +
651A PHE* 1.3 53.2 + - - -
652A PHE 3.2 0.4 - - - -
653A ASN* 2.8 16.5 + - - +
654A GLY* 2.7 32.7 + - - -
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Residues in contact with PHE 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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529A ILE* 4.2 16.4 - - + -
587A ILE* 3.5 20.8 - - + +
588A ILE* 4.0 24.0 - - + -
589A PRO* 4.4 2.9 - - + -
628A VAL* 4.9 5.6 - - + -
635A LEU* 3.5 34.1 - - + -
636A VAL* 4.5 13.2 - - + -
639A ILE* 3.9 23.3 - - + -
647A ILE 3.0 5.3 + - - +
648A CYS* 2.8 17.2 + - - +
650A GLY* 1.3 78.6 - - - +
652A PHE* 1.3 76.4 + + + +
654A GLY* 3.2 0.5 + - - -
655A ILE* 2.8 62.3 + - + +
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Residues in contact with PHE 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 4.0 30.3 - - + -
477A ASN* 5.0 0.2 - - - +
479A SER* 3.1 30.5 - - - +
517A ILE* 4.8 18.2 - - + -
527A MET* 4.0 10.8 - - + -
528A GLY* 3.8 24.0 - - - -
529A ILE* 4.3 16.8 - - + -
636A VAL* 3.8 29.8 - - + -
648A CYS* 4.0 16.8 - - - -
649A LYS* 3.9 5.6 + - - +
650A GLY 3.2 0.4 - - - -
651A PHE* 1.3 85.9 - + + +
653A ASN* 1.3 55.1 + - - +
655A ILE* 5.2 0.4 - - - -
656A GLN* 2.5 48.7 + - - +
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Residues in contact with ASN 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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365A LEU 3.6 4.2 - - - +
366A SER* 2.8 43.0 - - - -
367A LEU* 2.9 9.3 + - - +
477A ASN* 4.8 1.0 - - - +
560A PRO* 4.5 11.5 - - + +
649A LYS* 2.7 30.9 + - - +
650A GLY* 2.8 14.3 + - - +
652A PHE* 1.3 77.6 - - - +
654A GLY* 1.3 53.0 + - - +
656A GLN* 4.8 0.7 - - - +
657A ARG* 2.6 59.7 - - - +
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Residues in contact with GLY 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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559A VAL* 4.4 14.5 + - - -
587A ILE* 4.0 19.5 - - - -
650A GLY 2.7 17.2 + - - -
651A PHE 3.8 1.1 - - - -
653A ASN* 1.3 71.3 - - - +
655A ILE* 1.3 54.7 + - - +
657A ARG* 2.8 3.9 + - - +
658A VAL* 2.4 44.9 + - - +
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Residues in contact with ILE 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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529A ILE* 4.7 17.9 - - + -
533A THR* 4.9 2.0 - - - +
537A VAL* 4.0 16.4 - - + -
584A LEU* 4.4 11.4 - - + -
587A ILE* 3.1 25.6 - - + +
588A ILE* 5.2 0.2 - - + -
628A VAL* 5.2 7.0 - - + -
651A PHE* 2.8 59.9 + - + +
652A PHE 5.4 0.2 - - - -
654A GLY* 1.3 67.2 - - - +
656A GLN* 1.3 58.7 + - - +
657A ARG 2.8 10.5 + - - -
658A VAL* 4.4 3.6 - - + +
659A VAL* 3.0 46.7 + - + +
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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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363A PRO* 3.9 17.5 - - - +
365A LEU 5.7 0.7 - - - -
477A ASN* 2.5 42.2 + - - +
478A LEU* 3.9 13.9 - - - +
479A SER* 3.6 25.0 - - - -
529A ILE* 5.5 4.2 - - + +
533A THR* 3.6 30.5 - - + +
652A PHE* 2.5 31.8 + - - +
653A ASN* 4.0 0.6 + - - -
655A ILE* 1.3 76.3 - - - +
657A ARG* 1.3 62.0 + - + +
660A ASN* 3.3 25.2 + - - +
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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
----------------------------------------------------------
363A PRO 4.0 10.4 + - - +
364A ASN* 3.4 33.6 + - - +
365A LEU 3.7 2.2 + - - -
366A SER* 3.6 27.9 - - - +
369A GLU* 5.5 1.2 + - - -
558A TRP* 3.3 42.7 - - + +
559A VAL 6.0 0.2 - - - +
560A PRO* 4.0 24.6 - - - +
653A ASN* 2.6 37.0 + - - +
654A GLY* 2.8 2.2 + - - +
655A ILE 2.8 0.2 + - - -
656A GLN* 1.3 84.0 - - - +
658A VAL* 1.3 68.0 + - - +
659A VAL 3.4 0.9 - - - -
660A ASN* 4.2 3.5 - - - +
661A TYR* 3.2 21.2 + - - +
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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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540A PHE* 4.8 12.1 - - + -
555A ILE* 3.7 34.1 - - + +
558A TRP* 4.4 20.0 - - + +
559A VAL* 5.5 0.2 - - + -
583A ILE 5.0 8.3 - - - +
584A LEU* 5.7 2.9 - - + -
587A ILE* 3.6 24.9 - - + -
654A GLY* 2.4 37.0 + - - +
655A ILE* 4.2 3.8 - - + +
657A ARG* 1.3 72.7 - - - +
659A VAL* 1.3 61.6 + - + +
661A TYR* 2.9 10.8 + - - +
662A TRP* 2.8 24.0 + - + +
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Residues in contact with VAL 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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533A THR* 3.6 24.9 - - - +
536A GLY* 3.8 24.5 - - - +
537A VAL* 3.9 11.0 - - + -
540A PHE* 4.5 19.7 - - + -
584A LEU* 4.9 2.5 - - + -
655A ILE* 3.0 34.3 + - + +
658A VAL* 1.3 78.7 - - + +
660A ASN* 1.3 71.0 + - - +
661A TYR 2.8 1.3 - - - -
662A TRP* 2.7 13.0 + - + +
663A LEU* 2.7 26.8 + - + +
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Residues in contact with ASN 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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363A PRO* 3.3 33.3 - - + +
478A LEU* 4.9 2.6 - - - +
532A ASP* 4.5 11.9 + - - -
533A THR* 2.9 40.6 - - - +
655A ILE 4.0 1.0 + - - -
656A GLN* 3.3 20.4 + - - +
657A ARG* 4.0 4.0 + - - +
658A VAL 3.5 0.4 - - - -
659A VAL* 1.3 73.8 - - - +
661A TYR* 1.3 57.8 + - - +
663A LEU* 3.4 8.2 + - - +
664A LEU* 2.9 27.9 + - - +
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Residues in contact with TYR 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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554A ASN* 2.9 38.9 + - + -
555A ILE* 3.5 34.5 - - + -
558A TRP* 3.1 41.1 - + + -
657A ARG 3.2 13.1 + - - +
658A VAL* 2.9 12.8 + - - +
659A VAL 2.8 0.8 - - - -
660A ASN* 1.3 74.9 - - - +
662A TRP* 1.3 68.8 + - - +
664A LEU* 3.5 20.2 + - + +
665A HIS* 3.6 34.4 + + + -
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Residues in contact with TRP 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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536A GLY 4.8 2.9 - - - -
539A LYS 3.3 7.5 + - - -
540A PHE* 3.0 47.5 - + + +
545A ASN* 3.0 35.2 - - - -
546A PHE 4.9 0.2 - - - -
547A LEU* 3.5 26.7 - - + -
555A ILE* 5.4 10.7 - - + +
658A VAL* 2.8 11.6 + - + +
659A VAL* 2.7 16.8 + - + +
661A TYR* 1.3 77.4 - - - +
663A LEU* 1.3 68.8 + - + +
665A HIS* 2.9 19.9 + - + +
666A ASN* 2.8 50.3 + - + +
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Residues in contact with LEU 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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532A ASP* 3.4 38.1 - - + +
533A THR* 5.2 0.2 - - - -
535A ALA* 5.0 2.0 - - + -
536A GLY* 3.6 21.5 - - - +
659A VAL* 2.7 20.0 + - + +
660A ASN* 3.7 8.5 - - - +
662A TRP* 1.3 77.8 - - + +
664A LEU* 1.3 63.6 + - - +
666A ASN* 3.9 10.3 - - + +
667A GLY* 2.9 29.1 + - - +
668A PHE* 3.9 32.1 - - + +
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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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660A ASN 2.9 14.6 + - - +
661A TYR* 3.5 16.6 - - + +
663A LEU* 1.3 77.3 - - - +
665A HIS* 1.3 87.3 + - + +
667A GLY* 4.1 5.2 + - - -
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Residues in contact with HIS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 3.6 37.9 + + + +
662A TRP* 2.9 14.8 + - + +
664A LEU* 1.3 110.4 - - + +
666A ASN* 1.3 59.8 + - - +
667A GLY 3.5 0.4 - - - -
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Residues in contact with ASN 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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539A LYS* 3.3 30.3 + - - +
545A ASN* 5.6 0.2 - - - -
662A TRP* 2.8 55.3 + - + +
663A LEU* 2.9 13.3 + - + +
665A HIS* 1.3 81.5 - - - +
667A GLY* 1.3 70.5 + - - +
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Residues in contact with GLY 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LYS* 4.5 9.5 + - - +
663A LEU* 2.9 16.2 + - - +
664A LEU 4.1 4.8 + - - -
665A HIS 3.5 1.6 - - - -
666A ASN* 1.3 93.4 - - - +
668A PHE* 1.3 63.6 - - - +
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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