Contacts of the helix formed by residues 666 - 670 (chain B) in PDB entry 2PZ5
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 PRO 666 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A ASP* 3.6 19.7 - - + +
523A ALA 3.7 8.5 - - - +
524A THR* 4.3 5.2 - - + -
625B ARG 5.1 1.3 - - - +
626B ASP* 3.5 19.1 - - - +
630B ARG* 3.2 24.9 - - - +
647B LEU* 4.8 1.8 - - + -
664B ARG 3.9 6.7 - - - +
665B LEU* 1.3 81.5 - - + +
667B VAL* 1.3 66.7 + - - +
668B LYS 3.4 1.3 - - - -
669B TRP* 3.2 36.2 + - + +
670B MET* 3.3 10.4 + - - +
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Residues in contact with VAL 667 (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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522A ASP 5.1 0.2 - - - -
523A ALA 3.1 19.3 + - - +
524A THR 4.0 1.8 - - - +
525A GLU* 3.9 25.8 - - + +
665B LEU 3.0 4.4 + - - +
666B PRO* 1.3 71.2 - - - +
668B LYS* 1.3 58.4 + - - +
669B TRP 3.1 5.2 + - - -
670B MET* 3.1 26.2 + - - +
675B LEU* 5.9 0.4 - - + -
709B VAL* 4.4 26.2 - - + +
712B LEU* 3.9 18.5 - - + +
713B PHE* 3.5 34.6 - - + -
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Residues in contact with LYS 668 (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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521A ASP* 2.6 45.9 + - - +
522A ASP* 6.0 0.2 - - - +
523A ALA 5.0 0.2 + - - -
666B PRO 3.4 1.2 + - - -
667B VAL* 1.3 75.4 - - - +
669B TRP* 1.3 74.6 + - + +
670B MET 5.4 0.2 - - - -
687B TRP* 5.2 1.1 + - - -
691B VAL* 3.6 13.5 - - - +
703B PRO* 3.2 26.2 + - + +
704B TYR* 2.9 44.4 + - + -
705B PRO* 4.9 1.2 - - - +
706B GLY 5.0 1.4 - - - +
707B ILE* 2.8 28.7 + - - +
709B VAL* 4.1 17.9 - - + +
712B LEU* 3.9 21.3 - - + -
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Residues in contact with TRP 669 (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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521A ASP* 4.5 6.5 - - + -
522A ASP* 4.0 25.8 - - + -
573B ARG* 4.9 7.2 - - - -
626B ASP* 6.1 0.7 - - - +
627B LEU 3.4 25.8 - - - +
628B ALA* 3.4 4.9 - - + +
630B ARG* 3.6 31.4 - - + +
666B PRO* 3.2 19.5 + - + +
667B VAL 3.1 0.6 - - - -
668B LYS* 1.3 95.9 - - + +
670B MET* 1.3 58.8 + - - +
687B TRP* 3.9 5.2 - - - -
688B SER* 2.8 36.4 + - - +
691B VAL* 3.5 26.4 - - + +
692B LEU 4.6 2.7 - - - -
695B GLU* 2.8 43.2 + - - -
703B PRO* 3.7 22.7 - - + -
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Residues in contact with MET 670 (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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525A GLU* 6.0 0.2 - - - -
662B ASN* 2.9 39.3 - - + +
665B LEU* 3.2 43.5 - - + +
666B PRO 3.3 13.4 + - - +
667B VAL* 3.1 18.7 + - - +
668B LYS 3.5 0.6 - - - -
669B TRP* 1.3 78.0 - - - +
671B ALA* 1.3 67.2 + - - +
672B PRO* 3.7 2.9 - - - +
674B ALA* 3.6 17.3 - - + -
675B LEU* 3.8 22.4 - - + -
680B TYR* 5.8 1.3 - - + -
687B TRP* 3.5 12.9 + - - -
688B SER* 4.8 1.1 - - - -
713B PHE* 4.0 20.8 - - + -
716B LEU* 5.1 1.2 - - - +
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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