Contacts of the helix formed by residues 605 - 623 (chain A) in PDB entry 4PK7
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 605 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A GLU* 5.0 8.5 - - + +
568A ALA* 3.9 19.1 - - + -
569A VAL* 4.0 15.3 - - + -
599A ILE* 3.3 32.5 - - + +
600A TYR* 2.9 23.9 + - + +
603A GLY* 3.6 14.4 - - - +
604A ARG* 1.3 76.7 - - - +
606A GLU* 1.3 56.5 + - - +
607A LYS* 3.1 5.8 - - - -
608A HIS* 2.8 61.5 + - + +
609A LEU 3.3 3.8 + - - -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A TYR* 3.5 16.4 + - + +
601A THR* 3.4 32.3 - - + +
604A ARG* 3.5 11.0 - - - +
605A LEU* 1.3 83.2 + - - +
607A LYS* 1.3 62.5 + - + +
608A HIS 3.2 0.2 - - - -
609A LEU* 3.7 14.1 - - + +
610A ASP* 3.2 23.0 + - - +
646A ILE* 5.7 1.3 - - + -
649A ARG* 3.5 45.1 + - - +
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Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ARG 5.7 4.4 + - - +
605A LEU 2.9 1.5 + - - -
606A GLU* 1.3 80.4 - - + +
608A HIS* 1.3 65.2 + - + +
609A LEU 3.4 0.2 - - - -
610A ASP* 3.7 6.3 - - - +
611A ALA* 3.2 22.9 + - - +
614A ARG* 5.1 1.7 + - - -
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Residues in contact with HIS 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ALA 3.4 19.7 - - - +
569A VAL* 3.6 36.5 - - + +
572A PRO* 3.6 7.3 - - + +
600A TYR* 4.8 2.2 - - + -
604A ARG 5.2 1.8 - - - -
605A LEU* 2.8 49.4 + - + +
607A LYS* 1.3 85.1 + - + +
609A LEU* 1.3 58.9 + - - +
611A ALA* 3.1 9.0 + - + +
612A LEU* 2.8 28.1 + - - +
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A TYR* 3.6 45.2 - - + +
605A LEU 3.3 1.8 + - - -
606A GLU* 3.7 12.8 - - + +
608A HIS* 1.3 76.8 - - - +
610A ASP* 1.3 65.4 + - - +
612A LEU* 3.1 8.5 + - + +
613A LEU* 3.1 47.0 + - + +
639A LEU* 4.5 11.4 - - + -
646A ILE* 3.3 36.8 - - + -
649A ARG* 3.6 24.9 - - + +
650A VAL* 4.6 3.8 - - + -
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Residues in contact with ASP 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLU 3.2 14.8 + - - +
607A LYS* 3.7 8.2 - - - +
609A LEU* 1.3 80.6 - - - +
611A ALA* 1.3 62.3 + - - +
613A LEU* 3.5 14.2 + - - +
614A ARG* 3.2 41.5 + - - +
617A ARG* 5.8 1.7 + - - -
649A ARG* 4.7 14.2 + - - +
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PRO* 4.2 14.8 - - + -
607A LYS 3.2 12.7 + - - +
608A HIS* 3.1 15.1 + - + +
610A ASP* 1.3 75.5 - - - +
612A LEU* 1.3 67.8 - - - +
614A ARG* 3.3 25.2 + - - +
615A GLN* 3.3 23.4 + - - +
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Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU* 3.7 22.9 - - + -
572A PRO* 4.0 14.1 - - + +
575A LEU* 3.7 24.7 - - + -
589A LEU* 5.9 0.4 - - + -
592A PRO* 4.4 13.9 - - + -
600A TYR* 3.8 20.0 - - - +
608A HIS 2.8 13.0 + - - +
609A LEU* 3.1 11.6 + - + +
611A ALA* 1.3 72.7 - - - +
613A LEU* 1.3 69.1 + - - +
615A GLN* 2.8 17.4 + - - +
616A ILE* 3.0 28.2 + - + +
639A LEU* 3.7 28.5 - - + -
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 3.1 26.2 + - + +
610A ASP* 3.7 16.2 - - - +
612A LEU* 1.3 79.1 - - + +
614A ARG* 1.3 57.5 + - - +
616A ILE* 3.2 10.7 + - + +
617A ARG* 2.8 37.0 + - - +
636A TYR* 4.2 13.9 + - + +
639A LEU* 4.0 21.8 - - + -
649A ARG* 4.5 8.3 - - + +
650A VAL* 3.9 31.2 - - + -
653A SER* 3.4 35.0 - - - +
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Residues in contact with ARG 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LYS 5.1 1.4 + - - -
610A ASP* 3.2 34.6 + - - +
611A ALA* 3.4 33.8 - - - +
612A LEU 3.0 0.6 - - - -
613A LEU* 1.3 79.2 - - - +
615A GLN* 1.3 66.5 + - - +
617A ARG* 3.6 14.8 + - + +
618A ASN* 3.0 28.2 + - - +
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Residues in contact with GLN 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PRO* 3.8 27.3 + - + +
575A LEU* 3.7 23.1 - - + +
576A ALA* 3.6 25.6 + - - +
579A SER* 5.1 3.8 - - - -
611A ALA* 3.5 13.5 + - - +
612A LEU 2.8 7.9 + - - +
614A ARG* 1.3 84.3 - - - +
616A ILE* 1.3 55.7 + - - +
618A ASN* 3.1 12.8 + - - +
619A ILE* 2.7 40.9 + - - +
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Residues in contact with ILE 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU* 4.2 1.8 - - + +
589A LEU* 4.1 13.7 - - + -
612A LEU* 3.0 40.5 + - + +
613A LEU* 3.5 18.2 - - + +
615A GLN* 1.3 74.8 - - - +
617A ARG* 1.3 53.1 + - - +
619A ILE* 3.0 10.3 + - - +
620A VAL* 2.7 39.9 + - + +
632A CYS* 4.2 23.6 - - + -
635A THR* 4.1 24.9 - - + -
636A TYR* 3.7 29.4 - - + -
639A LEU* 4.7 1.8 - - + -
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Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ASP* 5.8 2.0 + - - -
613A LEU* 2.8 24.5 + - - +
614A ARG* 3.8 14.1 - - - +
616A ILE* 1.3 72.3 - - - +
618A ASN* 1.3 64.1 + - - +
620A VAL* 3.3 6.7 + - - +
621A GLU* 3.1 33.9 + - + +
636A TYR* 3.6 12.6 - - - +
653A SER* 2.9 48.7 + - - +
656A GLN* 3.5 25.3 + - - +
657A LEU* 4.0 31.0 - - + +
660A GLU* 4.9 10.5 + - - -
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Residues in contact with ASN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A SER* 4.9 1.2 + - - -
614A ARG 3.0 19.1 + - - +
615A GLN* 3.6 14.1 - - - +
617A ARG* 1.3 75.7 - - - +
619A ILE* 1.3 62.2 + - - +
621A GLU* 3.5 7.4 + - - +
622A LYS* 3.3 50.8 + - - +
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Residues in contact with ILE 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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575A LEU* 3.6 40.8 - - + -
579A SER* 4.2 21.8 - - - +
585A VAL* 3.7 19.1 - - + -
589A LEU* 4.7 2.9 - - + -
615A GLN* 2.7 22.1 + - - +
616A ILE* 3.3 9.0 - - - +
618A ASN* 1.3 69.6 - - - +
620A VAL* 1.3 67.3 + - - +
621A GLU 2.9 3.5 + - - -
622A LYS* 3.2 7.4 + - - +
623A HIS* 3.2 38.0 + - + +
628A VAL* 3.7 19.5 - - + -
632A CYS* 3.8 10.5 - - - -
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Residues in contact with VAL 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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616A ILE* 2.7 29.4 + - + +
617A ARG 3.3 5.8 + - - +
619A ILE* 1.3 73.8 - - - +
621A GLU* 1.3 61.0 + - + +
623A HIS 3.5 6.9 - - - +
629A LEU* 3.8 13.3 - - + +
632A CYS* 3.5 20.9 - - + -
657A LEU* 4.2 20.2 - - + -
661A LEU* 4.5 3.1 - - + -
693A ARG* 3.1 37.7 + - + -
697A PHE* 3.8 35.9 - - + -
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Residues in contact with GLU 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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617A ARG* 3.1 20.7 + - - +
618A ASN* 4.0 6.1 - - - +
619A ILE 2.9 1.2 - - - -
620A VAL* 1.3 83.2 - - + +
622A LYS* 1.3 58.3 + - - +
623A HIS 3.4 0.4 - - - -
657A LEU* 3.8 22.3 - - + +
660A GLU* 3.1 31.8 - - - +
661A LEU* 5.0 6.9 - - + +
664A LYS* 6.0 0.2 + - - -
693A ARG* 3.3 28.5 + - - +
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Residues in contact with LYS 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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579A SER* 2.6 50.4 + - - +
580A VAL* 4.3 12.4 - - + +
618A ASN* 3.3 42.1 + - - +
619A ILE* 3.9 6.1 - - - +
621A GLU* 1.3 75.1 - - - +
623A HIS* 1.3 75.1 + - + +
624A THR* 5.4 1.2 - - - +
693A ARG* 4.8 1.8 - - - -
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Residues in contact with HIS 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A SER 3.0 27.5 + - - -
580A VAL* 4.0 18.9 - - + -
581A ASP 4.6 2.4 + - - -
582A ALA* 4.2 24.0 - - + +
585A VAL* 5.2 2.0 - - + +
619A ILE* 3.2 34.1 + - + +
620A VAL 3.5 4.0 - - - +
621A GLU 3.4 0.4 - - - -
622A LYS* 1.3 91.1 + - + +
624A THR* 1.3 65.2 + - - +
625A ASP* 4.6 3.2 - - - +
628A VAL* 3.8 29.3 - - + +
629A LEU* 3.7 9.8 - - + +
693A ARG* 3.2 22.3 + - - -
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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
------------------------------------------------------------
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