Contacts of the helix formed by residues 605 - 619 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582B GLU* 4.5 20.0 - - + +
584B THR* 5.7 0.7 - - - +
601B ILE* 4.2 12.8 - - + -
602B LEU* 2.9 11.9 + - + +
604B GLU* 1.3 75.5 - - + +
606B PHE* 1.3 66.2 + - - +
607B SER 3.1 2.9 - - - -
608B PHE* 4.0 17.3 - - - +
609B ALA* 2.8 27.1 + - - +
1001B 4K7 3.8 44.2 - - + -
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Residues in contact with PHE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ILE* 3.6 15.7 - - + -
602B LEU* 3.0 30.1 - - - -
603B PRO* 3.6 35.7 - - + +
604B GLU 3.4 2.0 - - - -
605B CYS* 1.3 76.2 - - - +
607B SER* 1.3 62.2 + - - +
609B ALA* 3.9 0.5 - - - +
610B ASP* 2.8 34.9 + - - +
633B LYS* 3.3 26.7 - - - -
635B ARG 5.9 1.8 - - - -
636B GLN 4.3 2.0 - - - -
637B PHE* 3.9 15.5 - - - -
638B GLN* 3.3 39.5 - - + +
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Residues in contact with SER 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B PRO 5.4 1.0 + - - -
604B GLU 4.5 6.8 + - - -
605B CYS* 3.1 1.0 - - - +
606B PHE* 1.3 79.7 - - - +
608B PHE* 1.3 63.2 + - - +
610B ASP* 3.3 6.6 + - - +
611B ARG* 3.1 24.4 + - - +
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Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B GLU 5.3 0.2 + - - -
605B CYS* 3.3 21.2 + - - +
607B SER* 1.3 78.9 - - - +
609B ALA* 1.3 62.2 + - - +
611B ARG* 4.0 5.0 - - - +
612B GLU* 3.3 33.7 + - - +
1001B 4K7 4.8 11.9 - - + -
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Residues in contact with ALA 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ILE* 3.7 23.3 - - + -
605B CYS* 2.8 21.8 + - - +
606B PHE 3.9 2.5 - - - +
608B PHE* 1.3 77.5 - - - +
610B ASP* 1.3 63.0 + - - +
613B VAL* 3.1 28.7 + - - +
638B GLN* 4.6 2.7 - - - +
640B ILE* 4.3 7.2 - - + -
1001B 4K7 3.4 33.0 - - - +
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Residues in contact with ASP 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B PHE* 2.8 24.2 + - - +
607B SER* 3.3 4.8 + - - +
609B ALA* 1.3 77.1 - - - +
611B ARG* 1.3 64.0 + - - +
613B VAL* 3.3 10.0 + - - +
614B GLN* 3.1 24.3 + - - +
631B THR* 5.3 5.0 - - - +
638B GLN* 3.4 23.0 + - - +
640B ILE* 6.2 0.2 - - - +
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B SER 3.1 16.5 + - - +
608B PHE* 4.0 7.0 - - - +
609B ALA 3.4 0.2 - - - -
610B ASP* 1.3 77.4 - - - +
612B GLU* 1.3 64.1 + - + +
614B GLN* 3.2 6.2 + - - +
615B LEU* 3.1 35.4 + - + +
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Residues in contact with GLU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B PHE* 3.3 16.6 + - - +
609B ALA 4.2 1.8 - - - +
611B ARG* 1.3 76.3 - - + +
613B VAL* 1.3 66.3 + - - +
615B LEU* 4.1 9.4 - - + +
616B LEU* 3.1 27.4 + - - +
684B ILE* 4.0 18.2 - - + +
687B ARG* 3.4 21.8 + - - -
1001B 4K7 2.8 82.3 + - + +
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Residues in contact with VAL 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B ALA 3.1 23.6 + - - +
610B ASP* 3.5 9.2 - - - +
612B GLU* 1.3 76.7 - - - +
614B GLN* 1.3 62.8 + - - +
616B LEU* 4.0 4.9 - - - +
617B ARG* 3.1 70.9 + - - +
628B TYR* 3.9 26.4 - - + +
631B THR* 4.8 3.1 - - - +
640B ILE* 4.9 2.7 - - + -
1001B 4K7 3.9 26.7 - - + -
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Residues in contact with GLN 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ASN* 4.2 12.0 + - - +
610B ASP 3.1 13.4 + - - +
611B ARG* 3.2 9.2 + - - +
613B VAL* 1.3 76.5 - - - +
615B LEU* 1.3 71.1 - - + +
617B ARG* 3.2 45.1 + - - +
618B GLU* 3.5 21.0 + - + +
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Residues in contact with LEU 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611B ARG* 3.1 24.5 + - + +
612B GLU* 4.1 8.1 - - + +
613B VAL 3.5 0.2 - - - -
614B GLN* 1.3 82.5 - - + +
616B LEU* 1.3 62.4 + - - +
617B ARG 3.3 0.3 + - - -
618B GLU* 3.5 23.5 + - - +
619B SER 4.2 0.7 + - - -
682B LEU* 4.1 32.4 - - - +
683B ASN* 4.4 8.7 - - + +
684B ILE* 4.1 21.1 - - + -
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Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B GLU 3.1 18.0 + - - +
613B VAL* 4.0 5.4 - - - +
615B LEU* 1.3 77.1 - - - +
617B ARG* 1.3 63.5 + - + +
618B GLU 3.4 0.3 + - - -
619B SER* 3.1 18.4 + - - +
620B ASP 5.4 1.6 - - - +
621B GLU* 5.9 3.8 - - - -
622B HIS 5.9 0.7 - - - +
625B VAL* 4.7 13.0 - - + -
626B ILE 5.0 3.6 - - - +
628B TYR* 5.1 10.8 - - + +
678B HIS* 3.9 28.5 - - + +
679B LEU* 4.6 8.1 - - + -
682B LEU* 4.0 11.4 - - + -
684B ILE* 4.2 7.1 - - + +
1001B 4K7 4.3 35.2 - - + -
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Residues in contact with ARG 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASP* 2.8 33.9 + - - -
593A ASN* 3.2 27.3 + - - +
594A ARG* 3.4 46.7 + - + +
627A ARG* 5.0 9.0 + - - +
613B VAL* 3.1 50.6 + - + +
614B GLN* 3.2 29.6 + - - +
616B LEU* 1.3 76.5 - - + +
618B GLU* 1.3 66.4 + - + +
619B SER 3.1 8.4 - - - +
628B TYR* 3.3 17.8 + - + -
631B THR* 5.6 0.4 - - - -
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Residues in contact with GLU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A PRO 4.2 13.9 - - - +
700A ASN* 4.7 1.1 - - - -
701A ALA* 4.8 14.1 - - + +
614B GLN* 3.5 21.0 + - + +
615B LEU* 3.9 16.0 - - - +
616B LEU 3.3 1.0 - - - -
617B ARG* 1.3 78.7 - - + +
619B SER* 1.3 61.2 + - - +
620B ASP 4.0 0.3 + - - -
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Residues in contact with SER 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A ARG* 4.9 2.2 + - - -
700A ASN* 2.4 33.3 + - - -
701A ALA* 3.9 4.4 - - - +
702A HIS* 5.5 1.7 + - - -
615B LEU 4.2 1.2 + - - -
616B LEU 3.1 12.2 + - - +
617B ARG 3.1 13.4 - - - +
618B GLU* 1.3 79.6 - - - +
620B ASP* 1.3 72.2 + - - +
621B GLU* 3.8 0.9 + - - +
678B HIS* 3.6 9.9 - - - -
682B LEU* 3.6 37.6 - - - +
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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