Contacts of the helix formed by residues 652 - 669 (chain W) in PDB entry 5IY6
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 LEU 652 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626W VAL* 3.9 27.4 - - + +
627W TYR* 3.7 14.4 - - - +
628W THR* 3.2 29.4 - - - +
637W LEU* 5.1 5.4 - - + -
648W GLU* 3.0 29.2 + - + +
650W ASP 3.4 0.2 - - - -
651W PHE* 1.4 103.7 - - + +
653W THR* 1.3 68.9 + - + +
654W PHE 3.5 1.8 - - - -
655W ASP* 3.6 3.0 + - - +
656W ALA* 3.0 24.5 + - - +
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Residues in contact with THR 653 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625W TYR* 5.2 12.1 - - + -
648W GLU* 3.3 15.2 + - + +
649W ASN* 3.1 27.1 + - + +
652W LEU* 1.3 76.1 - - + +
654W PHE* 1.4 55.2 + - - +
656W ALA* 3.1 8.1 + - - +
657W MET* 2.9 47.4 + - - +
686W ARG* 6.0 4.3 - - - +
692W LYS* 3.9 11.8 - - - -
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Residues in contact with PHE 654 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463W PRO* 4.6 17.9 - - + -
465W ASP* 6.3 0.9 - - + -
466W ILE* 3.3 50.7 - - + -
649W ASN 3.0 17.7 + - - +
650W ASP* 4.1 18.2 - - - +
653W THR* 1.4 73.9 + - - +
655W ASP* 1.3 56.3 + - - +
657W MET* 3.2 4.8 + - - +
658W ARG* 3.0 37.8 + - + +
690W ARG* 5.5 7.4 - - + -
691W GLY 4.8 0.9 - - - -
692W LYS* 3.5 58.1 - - + -
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Residues in contact with ASP 655 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W HIS* 4.6 17.2 - - - +
626W VAL* 5.7 3.4 - - + +
650W ASP 4.4 4.9 + - - +
651W PHE 3.7 24.0 - - - +
652W LEU* 3.6 3.7 + - - +
653W THR 3.3 0.2 - - - -
654W PHE* 1.3 78.3 - - - +
656W ALA* 1.4 58.2 + - - +
658W ARG* 3.6 8.0 + - - +
659W HIS* 3.1 49.4 + - - -
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Residues in contact with ALA 656 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624W PRO* 3.0 27.6 - - - +
625W TYR* 3.7 19.1 - - + -
626W VAL* 4.1 9.8 - - + +
652W LEU 3.0 18.3 + - - +
653W THR* 3.5 5.2 - - - +
655W ASP* 1.4 71.2 - - - +
657W MET* 1.3 58.8 + - - +
659W HIS* 2.9 35.2 + - - +
660W ALA* 2.9 9.9 + - - +
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Residues in contact with MET 657 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623W VAL* 4.3 15.5 - - + -
624W PRO 4.7 0.7 - - - +
625W TYR* 4.0 28.0 - - + +
653W THR* 2.9 28.1 + - - +
654W PHE* 3.6 8.5 - - - +
656W ALA* 1.3 69.1 - - - +
658W ARG* 1.3 56.8 + - - +
660W ALA* 2.8 23.9 + - + +
661W ALA* 2.8 14.0 + - - +
684W PHE* 6.1 0.2 - - + -
686W ARG* 5.0 1.1 - - + -
687W GLY* 3.6 39.9 - - - +
692W LYS* 3.7 32.8 - - - +
693W LEU* 3.6 26.8 - - + +
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Residues in contact with ARG 658 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W HIS* 3.3 47.9 + - + +
458W SER* 3.1 23.9 + - - -
460W THR* 2.8 40.8 + - - -
461W LEU* 4.6 3.8 - - - +
467W TYR* 5.5 1.8 + - - -
654W PHE* 3.0 22.8 + - + +
655W ASP* 3.7 13.0 - - - +
656W ALA 3.3 0.2 - - - -
657W MET* 1.3 70.9 - - - +
659W HIS* 1.3 68.6 + - + +
661W ALA* 4.0 15.0 - - - +
662W GLN* 2.9 44.8 + - + +
692W LYS 4.4 3.5 + - - +
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Residues in contact with HIS 659 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W HIS* 6.1 1.1 - - - -
600W ALA* 5.1 6.6 - - + +
601W ARG* 3.2 51.5 + - - +
624W PRO* 4.8 9.5 - - + +
626W VAL* 4.0 22.8 - - + +
655W ASP* 3.1 41.2 + - - -
656W ALA* 2.9 19.7 + - - +
658W ARG* 1.3 80.7 - - + +
660W ALA* 1.4 63.7 + - - +
662W GLN* 3.6 11.8 + - - +
663W CYS* 3.7 14.9 + - - +
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Residues in contact with ALA 660 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620W MET* 3.6 17.5 - - - +
623W VAL* 5.8 0.4 - - + -
624W PRO* 3.9 31.1 - - + +
656W ALA 2.9 6.5 + - - +
657W MET* 2.8 21.3 + - + +
659W HIS* 1.4 76.0 - - - +
661W ALA* 1.3 58.6 + - - +
663W CYS 3.2 12.3 + - - -
664W VAL* 3.2 17.7 + - - +
679W PHE* 4.0 14.4 - - + -
693W LEU* 4.4 1.6 - - + -
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Residues in contact with ALA 661 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460W THR* 5.6 0.4 - - - +
657W MET 2.8 16.4 + - - +
658W ARG* 3.2 24.8 + - - +
660W ALA* 1.3 73.3 - - - +
662W GLN* 1.3 53.4 + - - +
664W VAL* 3.6 9.8 - - - +
665W GLY* 2.7 34.8 + - - -
679W PHE* 6.1 0.2 - - - -
692W LYS 5.3 1.3 - - - +
693W LEU* 4.8 1.7 - - + +
694W PRO* 3.6 33.0 - - + +
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Residues in contact with GLN 662 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235W GLU* 2.8 38.2 + - - +
237W HIS* 3.7 19.9 + - + -
458W SER 4.7 0.2 - - - +
605W SER* 5.3 5.6 - - - +
658W ARG* 2.9 48.5 + - + +
659W HIS* 4.0 7.9 - - - +
660W ALA 3.3 0.4 - - - -
661W ALA* 1.3 77.5 - - - +
663W CYS* 1.3 59.6 + - - +
665W GLY* 3.8 1.4 - - - -
666W ARG* 2.9 39.8 + - + +
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Residues in contact with CYS 663 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538W PHE* 3.5 41.9 - - + -
600W ALA* 3.3 28.5 - - + -
605W SER* 3.5 26.2 - - - +
620W MET* 3.9 8.1 - - + -
659W HIS 3.7 8.2 + - - +
660W ALA 3.2 9.2 + - - +
662W GLN* 1.3 79.1 - - - +
664W VAL* 1.3 60.2 - - - +
666W ARG* 3.3 7.0 + - - +
667W ALA* 3.1 20.1 + - - +
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Residues in contact with VAL 664 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W VAL* 3.9 16.2 - - + -
620W MET* 3.7 18.2 - - + -
660W ALA 3.2 15.1 + - - +
661W ALA* 3.6 16.4 - - - +
663W CYS* 1.3 74.4 - - - +
665W GLY* 1.4 65.7 + - - +
667W ALA* 3.1 18.5 + - - +
668W ILE* 3.1 17.4 + - + +
677W MET* 3.5 41.3 - - + +
679W PHE* 4.4 13.7 - - + -
694W PRO* 4.2 13.7 - - + -
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Residues in contact with GLY 665 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W SER* 4.3 21.0 - - - +
661W ALA 2.7 23.4 + - - -
662W GLN* 3.8 1.6 - - - -
664W VAL* 1.4 72.9 - - - +
666W ARG* 1.4 52.6 + - - +
668W ILE* 3.5 8.4 + - - +
669W ARG* 2.7 36.4 + - - -
694W PRO* 6.1 1.3 - - - -
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Residues in contact with ARG 666 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W SER 4.4 15.0 + - - -
45W GLY* 5.1 5.9 - - - -
46W THR 5.9 1.0 - - - +
79W GLU* 4.8 11.6 + - - -
82W LYS* 3.7 23.7 - - - +
235W GLU* 5.9 1.2 + - - -
604W VAL 5.5 0.7 - - - +
605W SER* 3.2 27.6 - - - +
606W GLU* 3.5 20.3 + - - +
607W GLY* 4.2 9.2 - - - +
608W ILE 5.5 3.0 + - - +
609W ASP* 5.7 1.0 + - - +
614W TYR* 4.2 15.0 + - - -
662W GLN* 2.9 27.0 + - + +
663W CYS* 3.5 6.7 - - - +
665W GLY* 1.4 73.2 + - - +
667W ALA* 1.3 62.4 + - - +
669W ARG* 3.3 32.6 + - - +
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Residues in contact with ALA 667 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536W VAL* 5.9 1.1 - - + -
538W PHE* 6.0 0.2 - - + -
613W HIS* 3.6 10.0 + - - -
614W TYR* 5.3 5.8 - - - -
615W GLY* 4.9 17.4 + - - +
616W ARG 5.9 2.0 - - - +
618W VAL* 3.7 31.2 - - + -
663W CYS 3.1 9.3 + - - +
664W VAL* 3.1 11.0 + - - +
666W ARG* 1.3 78.1 - - - +
668W ILE* 1.3 57.6 + - - +
669W ARG* 3.1 18.0 - - - -
676W LEU 5.7 2.0 - - - +
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Residues in contact with ILE 668 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W SER* 4.9 8.1 - - - +
488W VAL* 4.8 1.8 - - + +
489W CYS* 3.8 26.7 - - + -
613W HIS* 4.4 4.3 - - - -
664W VAL* 3.1 17.0 + - + +
665W GLY* 3.7 9.6 - - - +
667W ALA* 1.3 75.4 - - + +
669W ARG* 1.3 65.1 + - - +
670W GLY 2.9 18.8 + - - +
673W ASP* 3.3 16.1 - - - +
674W TYR* 3.8 17.9 - - - +
675W GLY* 3.6 28.9 - - - +
677W MET* 4.0 17.9 - - + -
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Residues in contact with ARG 669 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W SER* 3.3 4.1 - - - -
45W GLY* 2.8 31.0 + - - -
46W THR* 2.9 22.3 + - - +
610W PHE 3.1 15.0 + - - -
611W VAL* 2.8 22.0 + - - +
612W HIS 3.1 22.4 + - - -
613W HIS* 3.4 17.9 + - - +
614W TYR* 3.5 21.3 + - - +
615W GLY 6.3 0.4 - - - +
665W GLY 2.7 22.2 + - - -
666W ARG* 3.3 30.7 + - - +
667W ALA 3.1 22.9 - - - -
668W ILE* 1.3 69.9 - - - +
670W GLY* 1.3 49.3 + - - +
673W ASP* 2.9 38.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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