Contacts of the helix formed by residues 600 - 609 (chain H) 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 GLY 600 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564H LEU* 4.0 4.7 - - - +
565H PHE 3.9 9.9 + - - -
598H MET* 5.7 0.9 - - - -
599H VAL* 1.3 73.6 - - - +
601H TYR* 1.3 61.8 + - - -
603H ASP* 4.1 23.8 - - - -
604H SER* 2.6 28.1 + - - -
617H LEU* 3.9 8.2 - - - +
640H GLY* 4.9 4.0 - - - -
641H ARG 4.8 2.7 - - - -
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Residues in contact with TYR 601 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599H VAL* 4.2 14.8 - - + +
600H GLY* 1.3 73.3 - - - -
602H SER* 1.3 62.5 + - - +
603H ASP 3.2 0.9 - - - -
604H SER* 3.4 1.6 + - - -
605H GLY* 2.9 27.5 + - - -
610H ARG* 3.8 17.6 + - - +
613H ALA* 4.6 2.6 - - - +
614H ALA* 6.0 3.1 - - + -
617H LEU* 3.9 26.1 - - + +
621H GLN* 4.6 2.6 + - - -
639H HIS* 2.7 48.0 + - + -
640H GLY 3.7 8.3 - - - -
641H ARG 3.3 9.8 + - - +
642H GLY 3.5 13.2 - - - +
643H GLY* 3.4 31.4 - - - -
644H THR* 4.3 11.1 + - + -
645H VAL* 4.4 4.3 - - + +
659H GLN* 4.6 6.6 + - - -
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Residues in contact with SER 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H TYR* 1.3 74.3 - - - +
603H ASP* 1.3 65.5 + - - +
605H GLY* 3.9 1.5 - - - +
606H LYS* 3.0 24.9 + - - +
610H ARG* 4.8 1.3 - - - +
641H ARG* 3.4 16.4 + - - +
642H GLY* 3.5 9.9 + - - -
774H ALA* 4.2 14.7 - - - +
777H TRP* 5.3 2.3 - - - -
778H ILE* 3.0 24.8 - - - +
970H GLY 2.4 32.1 + - - -
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Residues in contact with ASP 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564H LEU* 4.0 10.0 - - - +
566H GLU* 3.4 44.9 - - + +
598H MET* 5.9 0.7 - - - +
600H GLY* 4.1 19.9 - - - -
601H TYR 4.1 0.2 - - - +
602H SER* 1.3 80.6 - - - +
604H SER* 1.3 63.5 + - - +
606H LYS* 3.2 11.1 + - - +
607H ASP* 3.5 8.8 + - - +
774H ALA* 3.8 3.5 - - - +
1003H SO4 3.3 20.5 + - - -
1004H SO4 3.1 33.7 + - - +
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Residues in contact with SER 604 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H PHE 4.3 0.7 + - - -
566H GLU* 2.8 24.3 + - - -
567H ARG* 5.0 0.2 - - - +
568H LEU* 5.2 6.6 + - - +
571H LEU* 3.6 23.1 - - - +
600H GLY 2.6 24.8 + - - -
601H TYR 3.4 2.7 + - - -
603H ASP* 1.3 76.7 - - - +
605H GLY* 1.3 57.3 + - - +
607H ASP* 3.0 20.2 + - - +
608H ALA* 3.3 11.3 + - - +
613H ALA* 3.6 23.3 - - - +
617H LEU* 4.9 1.1 - - - -
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Residues in contact with GLY 605 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H TYR 2.9 17.8 + - - -
602H SER* 3.9 1.8 - - - -
603H ASP 3.2 0.2 - - - -
604H SER* 1.3 77.8 - - - +
606H LYS* 1.3 58.1 + - - +
609H GLY* 2.9 43.9 + - - -
610H ARG* 4.2 7.6 - - - -
613H ALA* 3.7 4.6 - - - +
728H TYR* 3.5 6.8 + - - -
777H TRP* 5.2 0.8 + - - -
789H PRO* 4.8 6.4 - - - +
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Residues in contact with LYS 606 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602H SER 3.0 14.9 + - - +
603H ASP 3.2 4.8 + - - +
605H GLY* 1.3 76.6 - - - +
607H ASP* 1.3 60.4 + - - +
728H TYR* 2.8 22.0 + - - -
732H VAL* 5.1 0.9 - - - +
763H ARG* 5.1 0.4 - - - +
769H ILE* 3.6 33.1 + - + +
770H THR* 4.6 5.3 + - - +
772H LEU* 3.0 26.2 + - + +
773H ARG 4.2 1.3 - - - +
774H ALA* 3.8 24.0 - - - +
777H TRP* 3.3 44.8 - - + +
1004H SO4 3.5 20.0 + - - -
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Residues in contact with ASP 607 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H ARG* 3.3 32.7 - - + +
568H LEU* 2.8 31.9 + - - +
569H ALA 4.4 1.4 + - - -
603H ASP 3.5 5.4 + - - +
604H SER 3.0 13.5 + - - +
606H LYS* 1.3 81.0 - - - +
608H ALA* 1.3 59.3 + - + +
609H GLY 3.9 0.2 - - - -
728H TYR* 4.0 7.1 - - - -
729H ARG* 3.6 32.2 + - - +
733H VAL* 5.9 1.0 - - - +
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Residues in contact with ALA 608 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568H LEU* 4.4 20.0 - - + -
604H SER 3.3 5.1 + - - +
607H ASP* 1.3 79.5 - - - +
609H GLY* 1.3 67.3 + - - +
612H SER* 3.3 13.5 + - - -
613H ALA* 5.5 0.7 - - - +
725H THR* 3.2 38.1 + - + +
728H TYR* 3.8 11.7 - - - -
729H ARG* 3.8 17.3 - - - +
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Residues in contact with GLY 609 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605H GLY* 2.9 17.8 + - - -
608H ALA* 1.3 80.3 - - - +
610H ARG* 1.3 66.4 + - - -
611H LEU 3.5 2.2 - - - -
612H SER 4.2 0.7 - - - -
613H ALA* 3.1 22.9 + - - +
724H ALA* 5.4 1.8 - - - -
728H TYR* 3.5 27.8 - - - -
789H PRO 5.3 0.4 - - - -
792H LEU 4.3 5.2 - - - -
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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