Contacts of the helix formed by residues 608 - 618 (chain B) in PDB entry 4OSI
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 GLY 608 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573B ASP 4.6 3.6 + - - -
574B GLY 5.6 0.4 + - - -
606B ASN* 5.7 0.2 - - - -
607B GLY* 1.3 72.6 - - - -
609B GLY* 1.3 53.4 + - - +
610B LYS 3.6 1.6 - - - -
611B GLN* 3.1 8.4 + - - +
612B ALA* 2.8 36.0 + - - +
642B GLY 5.8 0.4 - - - -
12G C 3.9 33.3 + - - +
13G T 3.9 19.9 + - - +
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Residues in contact with GLY 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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574B GLY 5.5 1.4 + - - -
578B ALA* 4.5 6.4 - - - +
603B ILE 4.8 0.4 - - - -
604B ALA* 4.0 18.6 - - - -
606B ASN* 3.0 17.8 + - - -
608B GLY* 1.3 73.6 - - - +
610B LYS* 1.3 68.2 + - - +
612B ALA* 2.7 20.5 + - - +
613B LEU* 2.9 18.6 + - - +
12G C 5.0 0.8 + - - -
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Residues in contact with LYS 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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574B GLY 5.5 0.2 + - - -
577B GLN* 3.4 41.4 + - + +
578B ALA* 4.1 10.9 - - - +
581B THR* 3.2 33.9 - - - +
609B GLY* 1.3 74.0 - - - +
611B GLN* 1.3 82.8 + - - +
613B LEU* 3.2 1.6 + - - +
614B GLU* 2.9 46.4 + - - +
12G C 3.7 15.8 + - - +
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Residues in contact with GLN 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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608B GLY 3.1 9.6 + - - +
610B LYS* 1.3 90.4 - - - +
612B ALA* 1.3 60.4 + - - +
614B GLU* 4.0 10.2 + - - +
615B THR* 2.9 33.7 + - - +
644B LYS* 3.3 43.9 + - + +
12G C 3.3 51.4 + - - +
13G T 4.0 4.7 - - - +
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Residues in contact with ALA 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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603B ILE* 4.1 12.8 - - + +
606B ASN* 4.9 2.9 - - - +
608B GLY 2.8 12.6 + - - +
609B GLY* 2.7 17.1 + - - +
611B GLN* 1.3 70.7 - - - +
613B LEU* 1.3 56.4 + - - +
615B THR* 3.2 5.9 + - - -
616B VAL* 2.9 36.0 + - - +
638B ALA* 3.9 26.5 - - + +
640B HIS 5.7 0.7 - - - +
643B GLY* 4.8 7.4 - - - +
644B LYS 4.4 8.2 - - - +
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Residues in contact with LEU 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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578B ALA 4.4 2.0 - - - +
581B THR* 3.8 20.0 - - + +
582B VAL* 3.4 43.1 - - + +
585B LEU* 4.6 9.4 - - + -
589B LEU* 5.1 12.1 - - + -
600B VAL* 4.3 15.3 - - + -
603B ILE* 4.2 17.0 - - + -
604B ALA* 3.7 24.9 - - + +
609B GLY 2.9 21.4 + - - +
610B LYS 3.8 1.8 - - - +
612B ALA* 1.3 68.9 - - - +
614B GLU* 1.3 69.2 + - - +
615B THR 2.7 2.4 + - - -
616B VAL* 2.9 18.7 + - + -
617B GLN* 2.9 14.9 + - - +
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Residues in contact with GLU 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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581B THR* 3.8 18.4 - - + +
584B ARG* 4.5 10.8 + - - +
585B LEU* 4.4 11.6 - - + +
610B LYS* 2.9 49.4 + - - +
611B GLN* 4.0 11.8 + - - +
613B LEU* 1.3 72.6 - - - +
615B THR* 1.3 60.2 + - + +
617B GLN* 3.6 5.0 - - - +
618B ARG* 2.9 29.6 + - - +
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Residues in contact with THR 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 GLN* 2.9 18.1 + - - +
612B ALA 3.2 2.3 + - - -
613B LEU 2.7 4.0 + - - -
614B GLU* 1.3 73.4 - - + +
616B VAL* 1.3 64.9 + - - +
617B GLN 3.0 1.8 - - - -
618B ARG* 3.7 25.8 - - - +
619B LEU* 2.9 31.5 + - - +
644B LYS* 3.5 36.9 - - + -
647B LEU* 2.9 30.0 - - - +
648B GLU* 3.9 6.7 - - + +
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Residues in contact with VAL 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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589B LEU* 4.8 16.2 - - + -
595B LEU* 6.0 1.6 - - + -
603B ILE* 4.0 22.9 - - + -
612B ALA 2.9 27.4 + - - +
613B LEU* 2.9 10.1 + - + +
615B THR* 1.3 71.6 + - - +
617B GLN* 1.3 56.9 + - - +
619B LEU* 5.2 0.2 - - - -
620B LEU* 2.9 45.2 + - + +
634B VAL* 4.0 25.7 - - + +
638B ALA* 3.3 30.1 - - + -
647B LEU* 3.5 8.0 - - + +
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Residues in contact with GLN 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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585B LEU* 3.0 44.2 - - + +
588B VAL* 5.0 7.2 - - + -
589B LEU* 4.6 11.0 - - + -
593B HIS* 4.0 26.5 + - + +
613B LEU 2.9 15.3 + - - +
614B GLU* 3.6 5.4 + - - +
616B VAL* 1.3 74.1 - - - +
618B ARG* 1.3 81.1 + - - +
619B LEU 2.4 19.9 + - - -
620B LEU* 3.0 11.9 + - - +
621B PRO* 3.2 11.3 - - - +
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Residues in contact with ARG 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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614B GLU 2.9 17.2 + - - +
615B THR* 3.1 26.3 + - - +
617B GLN* 1.3 90.9 - - - +
619B LEU* 1.3 92.5 + - - +
621B PRO* 4.4 7.7 - - - +
648B GLU* 4.1 13.3 + - - +
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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
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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