Contacts of the helix formed by residues 607 - 617 (chain D) in PDB entry 6UZA
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 PHE 607 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A MET* 4.6 6.1 - - - -
646A VAL* 4.1 11.9 - - + -
647A ALA* 3.7 36.6 - - + -
650A ILE* 4.3 19.1 - - + -
450D PHE* 4.7 4.3 - - - -
454D LEU* 3.9 28.3 - - + -
457D LEU* 4.9 6.5 - - + -
458D VAL* 5.0 2.9 - - + -
603D VAL* 3.2 34.8 - - + -
604D VAL 3.4 5.7 + - - +
605D LEU 3.2 1.4 - - - -
606D SER* 1.3 79.1 + - - +
608D SER* 1.3 55.3 + - - +
609D ARG 3.2 4.3 - - - -
610D ILE* 3.3 33.9 - - + +
1003D S9Y 3.5 12.8 - - + +
1004D Y01 3.8 31.6 - - + -
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Residues in contact with SER 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D TRP* 3.4 32.0 + - - -
529D LEU* 3.4 27.5 - - - +
533D MET* 5.7 0.7 - - - +
604D VAL 4.5 0.4 + - - -
605D LEU* 2.5 24.3 + - - -
606D SER 3.2 0.4 - - - -
607D PHE* 1.3 75.4 - - - +
609D ARG* 1.3 58.9 + - - +
610D ILE 3.2 6.9 + - - +
611D ALA* 3.7 5.5 + - - +
1003D S9Y 4.1 30.9 - - - +
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Residues in contact with ARG 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D PHE* 3.7 34.8 - - + +
453D PHE* 6.3 1.3 - - - -
505D MET* 3.5 39.0 + - - +
509D GLU* 4.3 4.9 + - - -
526D TRP* 5.8 0.4 - - - +
530D ASP* 2.6 44.4 + - - +
533D MET* 3.7 23.1 - - + +
606D SER 4.0 2.2 - - - +
607D PHE 3.2 2.0 - - - -
608D SER* 1.3 77.6 - - - +
610D ILE* 1.3 63.8 + - - +
611D ALA 3.1 1.3 - - - -
612D TYR* 3.5 28.6 + - + +
613D ILE* 4.3 1.9 + - - +
762D VAL* 5.6 3.8 - - - +
1002D R0G 3.5 51.1 + - + +
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Residues in contact with ILE 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A MET* 3.7 36.1 - - + -
450D PHE* 3.7 20.0 - - + -
454D LEU* 4.8 3.1 - - + -
607D PHE* 3.3 35.4 - - + +
608D SER 3.2 0.8 - - - -
609D ARG* 1.3 73.4 - - - +
611D ALA* 1.3 56.5 + - - +
612D TYR 3.1 5.8 + - - -
613D ILE* 3.3 14.6 + - + -
614D LEU* 2.9 45.4 + - + +
1003D S9Y 4.7 7.0 - - + -
1004D Y01 3.7 34.3 - - + -
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Residues in contact with ALA 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D TRP* 3.7 30.7 - - + +
608D SER 3.7 5.9 + - - +
609D ARG 3.1 0.2 - - - -
610D ILE* 1.3 78.5 - - - +
612D TYR* 1.3 56.3 + - - +
614D LEU* 4.4 0.4 - - - -
615D PRO* 3.3 19.8 - - - +
624D GLN* 3.3 24.9 + - - +
1003D S9Y 3.4 38.4 - - + +
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Residues in contact with TYR 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D PHE* 4.6 2.4 - - - -
526D TRP* 3.5 43.2 + + - +
527D ASN* 3.8 14.5 + - - -
530D ASP* 3.8 17.1 + - - -
609D ARG* 3.5 19.4 + - + +
610D ILE 3.1 1.4 - - - -
611D ALA* 1.3 79.9 - - - +
613D ILE* 1.3 61.0 + - - +
614D LEU 3.7 0.2 - - - -
615D PRO* 4.3 0.2 - - - -
749D LEU* 3.3 23.6 - - - +
753D TYR* 4.9 4.5 + - - -
1002D R0G 3.7 69.4 + + + +
1003D S9Y 3.7 25.4 - - - -
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Residues in contact with ILE 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D PHE* 3.8 35.3 - - + -
447D ALA* 4.2 12.8 - - + -
450D PHE* 4.5 14.4 - - + -
609D ARG 4.6 0.7 - - - +
610D ILE* 3.6 22.4 - - + +
612D TYR* 1.3 79.6 - - - +
614D LEU* 1.3 64.2 + - - +
615D PRO* 3.6 1.8 - - - -
616D ALA* 3.7 10.5 + - - +
749D LEU* 4.9 0.4 - - - -
1002D R0G 3.6 32.8 - - + -
1004D Y01 3.9 57.1 - - + +
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Residues in contact with LEU 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A ILE* 4.8 13.0 - - + -
643A MET* 4.0 29.2 - - + -
610D ILE* 2.9 28.1 + - + +
611D ALA* 5.2 0.2 - - - -
613D ILE* 1.3 74.4 - - - +
615D PRO* 1.3 57.2 - - - +
616D ALA 3.1 9.7 + - - -
617D ASN* 3.4 13.9 + - - +
620D PHE* 3.8 34.3 - - + +
621D GLY* 3.8 10.3 + - - -
624D GLN* 3.2 28.0 - - + +
1003D S9Y 5.0 13.5 - - + +
1004D Y01 4.2 18.2 - - + -
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Residues in contact with PRO 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D ALA 3.3 16.2 - - - +
612D TYR 4.3 0.9 - - - -
613D ILE 3.8 2.0 - - - -
614D LEU* 1.3 86.6 - - - +
616D ALA* 1.3 58.2 + - - -
617D ASN 3.2 2.4 + - - -
621D GLY* 4.0 15.9 - - - +
624D GLN* 3.3 22.2 - - - +
625D ILE* 6.1 3.1 - - + -
742D TRP* 3.9 9.0 + - + -
745D ALA* 4.9 20.9 - - + +
746D ARG* 3.6 22.3 - - - +
749D LEU* 3.7 22.2 - - + -
1003D S9Y 4.7 8.5 - - - -
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Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D TRP* 5.4 0.4 - - + -
443D PHE* 3.7 30.1 - - + -
613D ILE 3.7 5.5 + - - +
614D LEU 3.1 2.0 - - - -
615D PRO* 1.3 78.3 - - - +
617D ASN* 1.3 58.3 + - - +
746D ARG* 4.2 15.8 + - + -
749D LEU* 3.7 26.6 - - + +
1004D Y01 3.7 35.4 - - + +
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Residues in contact with ASN 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D MET* 4.8 17.0 - - - +
613D ILE 4.8 0.2 + - - -
614D LEU 3.4 11.4 + - - +
615D PRO 3.2 1.0 - - - -
616D ALA* 1.3 80.7 - - - +
618D GLU* 1.3 69.8 + - - +
619D SER* 3.3 12.0 + - - +
620D PHE* 3.3 36.4 - - + +
621D GLY 3.5 9.9 + - - -
742D TRP* 3.3 21.9 + - - -
746D ARG* 5.5 0.7 - - - -
1004D Y01 3.2 36.4 - - + +
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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