Contacts of the helix formed by residues 605 - 618 (chain A) in PDB entry 4YZ9
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 CYS 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A GLU* 4.0 25.8 - - + +
584A THR* 4.6 1.8 - - - +
601A ILE* 3.6 20.4 - - + -
602A LEU 2.9 9.1 + - - +
604A GLU* 1.3 76.9 - - - +
606A PHE* 1.3 63.6 + - - +
607A SER 3.3 2.7 - - - -
608A PHE* 3.2 18.7 + - - -
609A ALA* 2.9 22.6 + - - +
1001A 4K7 3.7 42.4 - - - -
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Residues in contact with PHE 606 (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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601A ILE* 3.3 23.8 - - + -
602A LEU 3.1 22.4 - - - -
603A PRO* 3.3 30.9 + - + +
604A GLU 3.5 0.2 - - - -
605A CYS* 1.3 77.8 - - - +
607A SER* 1.3 66.5 + - - +
609A ALA* 3.2 0.9 + - - +
610A ASP* 3.0 33.6 + - - +
635A ARG 4.5 9.6 - - - -
636A GLN 3.9 6.1 - - - -
637A PHE* 3.8 24.0 - - - -
638A GLN* 3.7 32.8 - - + +
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Residues in contact with SER 607 (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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603A PRO 5.0 0.2 + - - -
604A GLU 4.8 3.2 + - - -
605A CYS 3.3 0.4 - - - -
606A PHE* 1.3 78.4 - - - +
608A PHE* 1.3 73.1 + - - +
610A ASP* 3.6 6.3 + - - +
611A ARG* 3.3 24.3 + - - +
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Residues in contact with PHE 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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582A GLU* 4.0 22.9 - - + -
604A GLU 4.1 13.0 - - - -
605A CYS* 3.2 25.5 + - - +
607A SER* 1.3 85.9 - - - +
609A ALA* 1.3 64.8 + - - +
611A ARG* 3.5 7.0 + - - +
612A GLU* 3.2 28.1 + - - +
1001A 4K7 3.9 26.0 - - + -
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Residues in contact with ALA 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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601A ILE* 4.0 15.9 - - + -
605A CYS 2.9 13.1 + - - +
606A PHE 3.5 8.1 - - - +
608A PHE* 1.3 75.0 - - - +
610A ASP* 1.3 64.7 + - - +
612A GLU* 2.9 4.9 + - - +
613A VAL* 2.8 25.9 + - - +
638A GLN* 3.7 20.0 - - - +
640A ILE* 4.6 2.7 - - + -
1001A 4K7 3.6 27.7 + - - +
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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
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606A PHE* 3.0 21.4 + - - +
607A SER* 4.1 5.9 - - - +
609A ALA* 1.3 70.8 - - - +
611A ARG* 1.3 63.7 + - - +
613A VAL* 4.0 6.1 - - - +
614A GLN* 3.0 29.1 + - - +
633A LYS* 4.2 14.1 + - - -
638A GLN* 2.8 32.2 + - - +
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Residues in contact with ARG 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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607A SER 3.3 14.9 + - - +
608A PHE* 3.9 6.4 + - - +
609A ALA 3.2 0.4 - - - -
610A ASP* 1.3 79.2 - - - +
612A GLU* 1.3 80.6 + - - +
614A GLN* 4.0 6.6 - - - +
615A LEU* 3.1 41.9 + - + +
683A ASN* 2.6 36.6 + - - +
684A ILE* 4.7 5.3 - - - +
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Residues in contact with GLU 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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608A PHE* 3.2 16.4 + - - +
609A ALA 2.9 4.2 + - - +
611A ARG* 1.3 95.4 + - - +
613A VAL* 1.3 60.0 + - - +
615A LEU* 3.2 5.5 + - - +
616A LEU* 2.8 33.8 + - - +
684A ILE* 3.9 21.2 - - + +
685A VAL 4.8 0.9 - - - +
1001A 4K7 2.7 88.2 + - + -
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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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609A ALA 2.8 20.2 + - - +
610A ASP* 4.0 5.4 - - - +
612A GLU* 1.3 71.6 - - - +
614A GLN* 1.3 57.5 + - - +
616A LEU* 3.3 5.6 + - - +
617A ARG* 2.7 57.9 + - - +
628A TYR* 3.5 29.8 - - + +
631A THR* 5.1 4.9 - - + -
638A GLN* 6.0 0.2 - - - +
640A ILE* 3.9 14.6 - - + -
1001A 4K7 3.5 36.3 - - + -
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Residues in contact with GLN 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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610A ASP 3.0 20.0 + - - +
611A ARG* 4.0 5.4 - - - +
613A VAL* 1.3 76.6 - - - +
615A LEU* 1.3 60.2 + - + +
617A ARG* 3.3 23.5 + - - +
618A GLU* 3.0 61.3 + - + +
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Residues in contact with LEU 615 (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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611A ARG* 3.1 40.3 + - + +
612A GLU 3.2 3.6 + - - +
614A GLN* 1.3 78.0 - - + +
616A LEU* 1.3 62.5 + - - +
618A GLU* 3.4 23.8 + - + +
619A SER* 3.7 9.7 + - - -
682A LEU* 3.0 49.2 - - + +
683A ASN* 5.2 0.7 - - + -
684A ILE* 4.0 19.7 - - + -
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Residues in contact with LEU 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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612A GLU 2.8 15.5 + - - +
613A VAL* 3.7 4.7 - - - +
615A LEU* 1.3 74.6 - - - +
617A ARG* 1.3 65.7 + - - +
618A GLU 3.3 0.3 + - - -
619A SER* 3.4 18.4 + - - +
620A ASP 4.9 2.4 - - - +
621A GLU* 6.1 0.7 - - - +
625A VAL* 4.6 11.2 - - + -
626A ILE 5.0 1.8 - - - +
628A TYR* 5.0 11.4 - - + -
678A HIS* 4.4 10.9 - - + -
679A LEU* 4.1 20.0 - - + -
682A LEU* 3.7 23.1 - - + -
684A ILE* 4.4 5.6 - - + -
1001A 4K7 3.9 49.4 - - + -
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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
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613A VAL* 2.7 46.0 + - - +
614A GLN* 3.3 35.8 + - - +
616A LEU* 1.3 73.3 - - - +
618A GLU* 1.3 64.5 + - - +
619A SER 3.4 6.1 + - - +
628A TYR* 3.9 5.6 + - + -
631A THR* 5.1 2.4 - - - +
592B ASP* 3.3 32.9 + - - -
593B ASN* 3.7 34.3 + - - +
594B ARG* 3.4 58.3 + - + +
627B ARG* 5.2 1.9 + - - -
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Residues in contact with GLU 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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614A GLN* 3.0 51.2 + - + +
615A LEU* 3.4 18.3 + - + +
616A LEU 3.2 1.0 - - - -
617A ARG* 1.3 82.1 - - + +
619A SER* 1.3 60.2 + - - +
701B ALA* 5.1 7.4 + - - +
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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
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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