Contacts of the helix formed by residues 628 - 645 (chain A) in PDB entry 5ID6
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 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A THR* 2.9 10.8 + - - +
626A MSE 4.3 3.8 - - - +
627A PHE* 1.3 78.0 - - - +
629A LEU* 1.3 53.7 + - - +
630A ASN* 3.4 12.6 + - - +
631A ASP* 2.7 63.3 + - + +
632A CYS* 2.7 17.2 + - - +
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Residues in contact with LEU 629 (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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627A PHE* 3.5 26.9 - - + -
628A ASN* 1.3 72.6 + - - +
630A ASN* 1.3 57.4 + - - +
632A CYS* 3.3 3.0 + - + +
633A HIS* 2.9 70.3 + - + +
663A TYR 3.8 3.1 - - - +
664A LYS* 3.3 26.2 - - - +
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Residues in contact with ASN 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASN* 3.1 12.2 + - - +
629A LEU* 1.3 76.4 - - - +
631A ASP* 1.3 61.2 + - - +
633A HIS* 3.4 12.1 + - - +
634A LYS* 3.0 53.3 + - - +
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Residues in contact with ASP 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ASP* 4.9 1.3 - - - +
615A ILE* 3.2 40.0 - - + +
620A THR* 2.5 38.2 + - - +
628A ASN* 2.7 45.8 + - + +
630A ASN* 1.3 75.3 + - - +
632A CYS* 1.3 58.8 + - - +
634A LYS* 3.4 8.9 + - - +
635A LEU* 3.2 16.1 + - - +
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Residues in contact with CYS 632 (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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621A PHE* 4.0 22.2 - - - +
627A PHE* 3.7 19.3 - - + -
628A ASN 2.7 10.2 + - - +
629A LEU* 3.3 9.6 - - - +
631A ASP* 1.3 76.4 - - - +
633A HIS* 1.3 64.4 + - + +
635A LEU* 3.0 19.1 + - - +
636A ILE* 3.0 22.1 + - - +
664A LYS 4.8 0.4 - - - -
665A ASP* 4.0 6.1 - - - -
666A ILE* 3.9 39.9 - - - -
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Residues in contact with HIS 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 2.9 39.0 + - + +
630A ASN* 3.8 15.1 + - - +
631A ASP 3.3 0.2 - - - -
632A CYS* 1.3 79.4 - - + +
634A LYS* 1.3 65.5 + - + +
636A ILE* 3.5 2.9 + - + -
637A ASP* 3.0 23.5 + - - +
660A THR* 3.2 40.9 + - + +
661A GLU* 3.4 27.6 - - + +
663A TYR* 2.7 30.2 + - + -
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Residues in contact with LYS 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ASP* 2.6 45.4 + - - -
612A ILE* 4.4 14.6 - - + +
615A ILE* 4.1 11.9 - - + -
630A ASN* 3.0 42.2 + - - +
631A ASP* 3.6 11.9 + - - +
632A CYS 3.1 0.2 - - - -
633A HIS* 1.3 76.5 - - - +
635A LEU* 1.3 65.2 + - - +
637A ASP* 3.3 5.9 + - - +
638A PHE* 2.9 23.7 + - - +
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Residues in contact with LEU 635 (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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598A PHE* 4.2 20.4 - - + -
612A ILE* 4.3 18.8 - - + +
615A ILE* 4.6 7.1 - - + +
616A TYR* 4.8 5.8 - - + -
621A PHE* 3.4 47.8 - - + -
631A ASP 3.2 9.4 + - - +
632A CYS* 3.0 11.5 + - - +
634A LYS* 1.3 78.6 - - - +
636A ILE* 1.3 57.5 + - + +
638A PHE* 3.2 7.9 + - + +
639A PHE* 2.8 62.6 + - + -
666A ILE* 4.5 5.8 - - + -
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Residues in contact with ILE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A CYS* 3.0 23.3 + - - +
633A HIS* 3.6 11.2 - - + +
635A LEU* 1.3 76.1 - - - +
637A ASP* 1.3 53.9 + - - +
639A PHE* 3.0 9.0 + - + +
640A LYS* 2.6 45.6 + - - +
660A THR* 3.8 17.0 - - + -
663A TYR* 4.0 10.8 - - + -
665A ASP 5.3 0.2 - - - +
666A ILE* 3.5 39.7 - - + -
669A PHE* 3.6 41.7 - - + -
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Residues in contact with ASP 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A HIS* 3.0 20.2 + - - +
634A LYS* 3.8 5.7 - - - +
636A ILE* 1.3 75.3 - - - +
638A PHE* 1.3 63.6 + - - +
640A LYS* 3.6 12.0 - - - +
641A ASP* 3.0 27.7 + - - +
660A THR* 2.5 34.3 + - - +
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Residues in contact with PHE 638 (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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597A PHE* 3.7 24.0 - - + -
598A PHE* 3.7 28.7 - + - -
602A TRP* 4.4 1.6 - + - -
606A TYR* 3.3 41.5 + + - -
608A PRO* 3.8 13.5 - - + -
609A SER 5.8 0.2 - - - -
612A ILE* 3.8 32.1 - - + -
634A LYS 2.9 14.0 + - - +
635A LEU* 3.3 10.5 - - + +
637A ASP* 1.3 77.1 - - - +
639A PHE* 1.3 74.9 + + - +
641A ASP* 3.8 1.8 - - - +
642A SER* 2.8 50.3 + - - -
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Residues in contact with PHE 639 (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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593A LEU* 4.0 28.0 - - + -
594A PRO* 4.2 15.9 - - + -
597A PHE* 3.8 16.5 - + + -
598A PHE* 4.3 10.8 - + - -
616A TYR* 5.9 0.7 - + - -
635A LEU* 2.8 51.8 + - + -
636A ILE* 3.3 6.7 - - - +
638A PHE* 1.3 93.9 - + - +
640A LYS* 1.3 57.1 + - - +
642A SER* 3.1 5.6 + - - -
643A ILE* 2.8 35.2 + - - +
666A ILE* 4.9 1.3 - - + -
669A PHE* 3.8 26.2 - + + -
670A TYR* 3.6 25.8 - + - -
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Residues in contact with LYS 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 2.6 22.8 + - + +
637A ASP* 3.6 12.1 - - - +
639A PHE* 1.3 71.3 - - - +
641A ASP* 1.3 61.3 + - - +
643A ILE* 3.2 23.0 + - - +
644A SER* 3.3 9.9 + - - -
657A PHE* 3.7 36.0 + - + +
658A SER 2.6 30.0 + - - -
659A GLU* 4.0 1.2 - - - +
660A THR* 2.8 35.8 + - - +
663A TYR* 3.9 13.5 - - - -
669A PHE* 3.8 10.0 - - + -
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Residues in contact with ASP 641 (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 TYR* 2.3 44.1 + - - +
637A ASP 3.0 17.8 + - - +
638A PHE* 3.9 1.6 - - - +
640A LYS* 1.3 73.0 - - - +
642A SER* 1.3 64.6 + - - +
643A ILE 3.0 1.6 - - - -
644A SER* 3.0 20.9 + - - -
645A ARG* 3.3 28.1 + - - -
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Residues in contact with SER 642 (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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597A PHE* 3.6 24.2 - - - -
602A TRP* 3.0 39.9 + - - -
606A TYR* 4.2 5.1 - - - -
638A PHE* 2.8 35.7 + - - -
639A PHE* 3.4 6.5 - - - -
641A ASP* 1.3 77.3 - - - +
643A ILE* 1.3 61.3 + - - +
645A ARG 3.3 1.6 + - - +
646A TYR* 3.3 20.4 + - - +
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Residues in contact with ILE 643 (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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593A LEU* 4.4 13.7 - - + -
597A PHE* 4.1 17.5 - - + -
639A PHE 2.8 16.0 + - - +
640A LYS 3.2 12.1 - - - +
641A ASP 3.0 0.4 - - - -
642A SER* 1.3 74.2 - - - +
644A SER* 1.3 65.2 + - - +
645A ARG 3.1 2.3 + - - -
646A TYR* 3.3 12.3 + - - +
649A TRP* 4.7 10.7 - - + +
650A SER* 3.4 16.1 + - - -
655A PHE* 3.7 36.1 - - + -
657A PHE* 3.6 34.5 - - + -
669A PHE* 4.4 9.9 - - + -
673A VAL* 4.7 3.6 - - + -
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Residues in contact with SER 644 (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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640A LYS 3.3 10.0 + - - -
641A ASP* 3.0 16.8 + - - -
643A ILE* 1.3 79.3 - - - +
645A ARG* 1.3 66.7 + - - +
646A TYR 3.7 1.0 + - - -
650A SER* 3.8 13.0 + - - -
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Residues in contact with ARG 645 (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 TRP* 3.0 25.6 - - + -
605A TYR* 4.5 19.3 + - + -
606A TYR* 3.4 35.0 - - - +
641A ASP* 3.3 36.6 + - - +
642A SER 3.3 1.0 + - - -
643A ILE 3.1 1.0 - - - -
644A SER* 1.3 85.8 - - - +
646A TYR* 1.3 57.5 - - - +
647A PRO* 3.4 10.4 - - - +
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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
------------------------------------------------------------
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