Contacts of the helix formed by residues 717 - 724 (chain D) in PDB entry 6PUO
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 CYS 717 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649D ILE* 3.7 31.9 - - - -
650D ALA* 3.9 22.9 - - + -
653D LEU* 3.5 28.3 - - - +
704D LEU 3.6 23.6 - - - +
705D LEU* 4.2 10.5 - - + +
707D ARG* 4.1 4.7 + - + +
716D THR* 1.3 80.2 + - - +
718D LEU* 1.3 57.6 + - - +
719D GLN 3.6 0.2 - - - -
720D LEU* 4.1 6.1 + - - +
721D ALA* 3.9 5.0 + - - +
729D PHE* 5.0 4.8 - - - -
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Residues in contact with LEU 718 (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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705D LEU* 3.6 23.2 + - + +
716D THR* 3.2 8.8 + - + -
717D CYS* 1.3 76.9 - - - +
719D GLN* 1.3 61.1 + - + +
720D LEU 3.2 1.8 - - - -
721D ALA* 3.2 10.2 + - + +
722D LEU* 3.0 48.7 + - + +
729D PHE* 5.2 7.4 - - + -
730D VAL* 5.8 5.2 - - + -
735D ILE* 4.3 22.7 - - + -
738D PHE* 4.5 23.1 - - + -
739D LEU* 5.2 6.3 - - + -
1068D HIS* 4.8 14.4 - - + +
1109D LEU* 5.6 7.0 - - + +
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Residues in contact with GLN 719 (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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572D PHE* 3.7 23.1 - - + +
715D THR* 3.2 24.9 + - - +
716D THR* 3.6 16.7 - - + +
717D CYS 3.6 0.2 - - - -
718D LEU* 1.3 78.1 - - + +
720D LEU* 1.3 58.1 + - - +
722D LEU* 3.7 11.6 - - + -
723D GLU* 2.9 37.7 + - + +
1110D LYS* 5.3 14.0 + - - +
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Residues in contact with LEU 720 (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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569D LEU* 4.8 20.4 - - + +
572D PHE* 4.4 22.0 - - + -
573D THR* 5.6 0.4 - - + -
650D ALA* 4.0 30.5 - - + +
653D LEU* 4.1 17.8 - - + +
654D ALA* 4.2 14.6 - - + +
657D LYS* 4.9 10.3 - - + +
712D TRP* 5.2 5.6 - - + -
715D THR* 4.1 19.3 - - + -
716D THR 3.9 12.2 + - - +
717D CYS* 4.2 6.5 - - - +
718D LEU 3.2 0.8 - - - -
719D GLN* 1.3 77.7 - - - +
721D ALA* 1.3 61.5 + - - +
723D GLU* 4.1 2.4 - - + +
724D ALA* 3.1 27.4 + - - +
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Residues in contact with ALA 721 (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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653D LEU* 4.1 13.8 - - + +
717D CYS 3.9 3.0 + - - +
718D LEU* 3.2 12.9 + - + +
720D LEU* 1.3 80.5 - - - +
722D LEU* 1.3 63.2 + - - +
725D LYS* 3.7 1.2 + - - -
726D ASP* 3.4 33.8 + - + +
729D PHE* 3.6 35.0 - - + -
730D VAL* 4.2 14.8 - - + +
1065D PHE* 4.4 0.9 - - - -
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Residues in contact with LEU 722 (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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718D LEU* 3.0 37.0 + - + +
719D GLN* 3.8 12.1 - - + +
720D LEU 3.3 0.2 - - - -
721D ALA* 1.3 80.5 - - - +
723D GLU* 1.3 73.5 + - - +
725D LYS* 3.8 6.8 + - - -
730D VAL* 4.8 14.6 - - + -
1065D PHE* 3.7 37.4 - - + +
1068D HIS* 3.5 52.7 - - + +
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Residues in contact with GLU 723 (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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572D PHE* 3.6 34.7 - - + -
657D LYS* 4.3 22.3 + - + +
719D GLN* 2.9 24.0 + - + +
720D LEU* 4.2 2.9 - - - +
722D LEU* 1.3 87.5 - - - +
724D ALA* 1.3 57.8 + - - +
725D LYS* 3.1 25.4 + - - +
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Residues in contact with ALA 724 (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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653D LEU 4.9 0.4 - - - +
656D SER* 4.0 4.3 - - - +
657D LYS* 3.8 35.9 - - + +
660D LYS* 3.4 26.0 + - + +
720D LEU 3.1 18.1 + - - +
721D ALA 3.8 0.6 + - - +
722D LEU 3.4 0.2 - - - -
723D GLU* 1.3 75.0 - - - +
725D LYS* 1.3 69.7 + - - +
726D ASP* 3.2 18.7 + - - +
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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