Contacts of the helix formed by residues 609 - 618 (chain B) in PDB entry 4YZD
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 ALA 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B SER 3.8 1.5 + - - +
608B PHE* 1.3 72.1 - - - +
610B ASP* 1.3 63.0 + - - +
611B ARG* 3.4 1.3 - - + +
612B GLU* 4.1 28.9 - - + +
613B VAL* 3.2 28.4 + - - +
687B ARG* 5.3 2.7 - - - +
713B GLY* 3.2 20.8 + - - +
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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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608B PHE* 3.1 37.7 + - - +
609B ALA* 1.3 72.1 - - - +
611B ARG* 1.3 60.0 + - - +
613B VAL* 4.1 1.8 - - - +
614B GLN* 3.0 32.1 + - - +
631B THR* 4.4 9.0 - - - +
638B GLN* 5.3 4.6 + - - -
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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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609B ALA* 3.4 1.2 - - + +
610B ASP* 1.3 78.6 - - - +
612B GLU* 1.3 63.3 + - + +
614B GLN* 3.6 4.3 + - - +
615B LEU* 3.2 23.7 + - - +
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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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609B ALA* 3.9 17.7 + - + +
610B ASP 3.4 0.2 - - - -
611B ARG* 1.3 79.0 - - + +
613B VAL* 1.3 65.9 + - + +
615B LEU* 3.4 7.2 + - + +
616B LEU* 3.1 22.6 + - - +
683B ASN 4.6 2.8 - - - +
684B ILE* 3.7 49.1 - - + +
685B VAL 4.5 0.5 + - - -
687B ARG* 3.6 25.1 + - - -
712B PHE* 6.5 1.3 - - + -
713B GLY* 3.4 25.8 - - - -
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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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608B PHE* 3.6 26.0 - - + -
609B ALA 3.2 19.5 + - - +
610B ASP 3.6 2.2 + - - +
611B ARG 3.4 0.4 - - - -
612B GLU* 1.3 75.3 - - + +
614B GLN* 1.3 60.3 + - - +
616B LEU* 3.0 11.4 + - + +
617B ARG* 2.8 50.6 + - + +
628B TYR* 3.7 36.6 - - + +
712B PHE* 4.8 11.7 - - + +
713B GLY* 5.3 2.7 - - - +
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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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919A ARG* 4.2 15.1 + - - -
610B ASP 3.0 19.3 + - - +
611B ARG* 4.0 4.9 - - - +
613B VAL* 1.3 78.2 - - - +
615B LEU* 1.3 56.6 + - - +
617B ARG* 3.0 37.4 + - - +
618B GLU* 2.8 67.6 + - - +
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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 3.2 17.8 + - - +
612B GLU* 3.7 6.1 - - + +
613B VAL 3.3 0.2 - - - -
614B GLN* 1.3 77.9 - - - +
616B LEU* 1.3 57.5 + - - +
618B GLU* 3.4 16.2 + - + +
619B SER* 2.6 42.1 + - - +
682B LEU* 3.9 42.6 - - + +
684B ILE* 4.6 7.4 - - + -
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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 12.6 + - - +
613B VAL* 3.0 12.7 + - + +
615B LEU* 1.3 78.7 - - - +
617B ARG* 1.3 59.7 + - - +
619B SER* 3.3 19.9 + - - +
620B ASP 4.9 2.6 - - - +
621B GLU* 5.5 4.3 - - - +
625B VAL* 3.9 13.0 - - + -
626B ILE 5.0 1.3 - - - +
678B HIS* 4.0 16.3 - - + -
679B LEU* 3.5 24.7 - - + -
682B LEU* 3.8 21.8 - - + -
684B ILE* 4.1 7.2 - - + -
712B PHE* 3.2 44.4 - - + -
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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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911A TYR* 4.5 10.7 + - - +
924A SER* 4.8 17.3 - - - -
925A LEU 5.0 1.4 + - - -
608B PHE* 6.0 1.4 - - - -
613B VAL* 2.8 35.5 + - + +
614B GLN* 3.0 32.3 + - - +
616B LEU* 1.3 73.4 - - - +
618B GLU* 1.3 59.8 + - - +
619B SER 3.2 6.7 + - - +
621B GLU* 5.8 3.0 - - - +
628B TYR* 3.4 24.5 + - - +
629B PHE 3.6 16.4 + - - -
630B CYS* 5.0 3.2 - - - +
631B THR* 5.7 5.9 - - - +
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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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911A TYR* 3.8 23.4 - - + +
912A ARG* 3.8 35.5 + - + +
919A ARG* 4.3 14.0 + - - +
925A LEU* 3.6 17.2 - - - +
614B GLN* 2.8 47.4 + - - +
615B LEU* 3.9 17.0 + - + +
616B LEU 3.3 0.4 - - - -
617B ARG* 1.3 75.1 - - - +
619B SER* 1.3 59.9 + - - +
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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