Contacts of the helix formed by residues 601 - 609 (chain F) in PDB entry 6V3O
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 TYR 601 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599F VAL* 4.2 10.8 - - + -
600F GLY* 1.3 75.2 - - - -
602F SER* 1.3 68.9 + - - +
603F ASP* 3.1 0.6 + - - -
604F SER* 3.5 1.4 + - - -
605F GLY* 2.9 23.7 + - - -
610F ARG* 4.0 20.2 + - - +
613F ALA* 4.8 3.6 - - - +
614F ALA* 6.0 4.9 - - + -
617F LEU* 3.3 31.5 - - + +
621F GLN* 4.6 0.5 + - - -
639F HIS* 2.6 42.9 + - + -
640F GLY 3.6 15.9 - - - -
641F ARG 3.5 9.2 + - - +
642F GLY 3.5 13.2 - - - +
643F GLY* 3.4 27.8 - - - -
644F THR* 4.4 10.5 - - + -
645F VAL* 4.1 7.0 - - + +
659F GLN* 4.5 4.5 + - - -
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Residues in contact with SER 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601F TYR* 1.3 76.6 - - - +
603F ASP* 1.3 62.4 + - - +
605F GLY* 3.9 1.0 - - - -
606F LYS* 3.1 24.8 + - - +
610F ARG* 4.9 0.9 - - - +
641F ARG* 3.4 28.8 + - - -
642F GLY* 3.6 10.3 - - - -
774F ALA* 4.1 15.9 - - - +
777F TRP* 5.3 1.9 - - - -
778F ILE* 4.2 11.4 - - - +
970F GLY 2.6 32.4 + - - -
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Residues in contact with ASP 603 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564F LEU* 4.4 6.4 - - - +
566F GLU* 3.1 48.5 - - + +
598F MET* 5.8 2.4 - - - +
600F GLY* 3.7 24.1 - - - -
601F TYR 4.3 0.7 + - - -
602F SER* 1.3 82.5 + - - +
604F SER* 1.3 62.0 + - - +
606F LYS* 3.3 13.9 + - - +
607F ASP* 3.5 5.7 + - - +
640F GLY* 5.8 0.3 - - - -
641F ARG* 4.8 8.0 + - - +
774F ALA* 4.4 3.9 - - - +
1001F SO4 3.8 19.1 + - - -
1002F SO4 3.6 19.8 + - - -
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Residues in contact with SER 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F PHE 4.3 1.0 + - - -
566F GLU* 2.5 29.1 + - - -
567F ARG 5.0 2.7 - - - -
568F LEU* 5.0 3.7 - - - +
571F LEU* 3.7 20.6 - - - +
600F GLY 3.0 19.5 + - - -
601F TYR 3.5 2.4 + - - -
603F ASP* 1.3 72.2 - - - +
605F GLY* 1.3 66.3 + - - +
607F ASP* 2.9 16.3 + - - +
608F ALA* 3.2 11.4 + - - +
613F ALA* 3.6 21.5 - - - +
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Residues in contact with GLY 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601F TYR 2.9 17.9 + - - -
602F SER* 3.9 1.3 - - - -
604F SER* 1.3 76.8 - - - +
606F LYS* 1.3 58.2 + - - +
609F GLY* 2.8 45.8 + - - -
610F ARG* 4.2 8.5 - - - -
613F ALA* 3.6 4.8 - - - +
728F TYR* 3.6 5.6 + - - -
777F TRP* 5.5 0.2 - - - -
789F PRO* 5.0 5.8 - - - +
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Residues in contact with LYS 606 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602F SER 3.1 14.2 + - - +
603F ASP* 3.5 10.5 - - - +
604F SER 3.2 0.2 - - - -
605F GLY* 1.3 76.3 - - - +
607F ASP* 1.3 60.4 - - - +
728F TYR* 2.8 22.4 + - - +
732F VAL* 5.4 0.9 - - - +
769F ILE* 3.0 40.0 + - + +
770F THR* 3.5 12.7 + - - +
772F LEU* 2.8 29.1 + - - +
773F ARG 4.3 8.1 - - - +
774F ALA* 4.4 4.5 - - - +
777F TRP* 3.4 43.5 - - + +
1002F SO4 4.3 11.2 + - - +
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Residues in contact with ASP 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567F ARG* 3.4 29.7 + - + +
568F LEU* 2.9 32.7 + - - +
569F ALA 4.5 0.9 + - - -
603F ASP 3.5 4.0 + - - +
604F SER* 2.9 18.4 + - - +
606F LYS* 1.3 82.3 - - - +
608F ALA* 1.3 59.4 + - + +
728F TYR* 3.8 8.1 - - - -
729F ARG* 4.1 12.6 - - - +
733F VAL* 5.4 2.9 - - - +
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Residues in contact with ALA 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568F LEU* 3.7 28.5 - - + -
604F SER 3.2 4.9 + - - +
607F ASP* 1.3 81.3 - - + +
609F GLY* 1.3 65.2 + - - +
612F SER* 3.3 18.3 + - - -
724F ALA 4.5 0.2 - - - -
725F THR* 3.4 38.7 + - + +
728F TYR* 3.8 10.9 - - - +
729F ARG* 4.9 1.3 - - - -
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Residues in contact with GLY 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605F GLY* 2.8 18.6 + - - -
608F ALA* 1.3 81.2 - - - +
610F ARG* 1.3 65.2 + - - -
611F LEU 3.5 1.8 - - - -
612F SER* 4.3 1.3 - - - -
613F ALA* 3.2 22.2 + - - +
724F ALA* 5.5 1.8 - - - -
728F TYR* 3.5 28.7 - - - -
789F PRO 5.4 0.2 - - - -
792F LEU 4.3 4.5 - - - -
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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