Contacts of the helix formed by residues 618 - 628 (chain B) in PDB entry 2PZI
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 ASP 618 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B ARG* 2.9 37.5 + - + +
616B GLU* 3.5 3.9 - - + +
617B GLY* 1.3 74.7 - - - +
619B ARG* 1.3 59.2 + - - +
620B VAL* 3.3 8.0 + - - +
621B GLY* 3.2 26.8 + - - -
622B ALA* 2.9 23.4 + - - +
624B ARG* 4.5 6.1 + - - -
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Residues in contact with ARG 619 (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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614B SER* 4.8 8.9 - - - +
617B GLY* 3.2 16.5 + - - +
618B ASP* 1.3 72.3 - - - +
620B VAL* 1.3 62.5 + - + +
622B ALA* 3.2 7.7 + - - +
623B VAL* 2.9 36.0 + - - +
646B THR* 3.4 25.2 + - + +
647B LEU* 4.2 16.8 - - + +
649B SER 3.4 36.1 + - - -
655B GLU 4.0 28.3 + - - +
656B VAL* 3.6 21.6 - - - +
660B GLN* 4.5 21.5 + - - +
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Residues in contact with VAL 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ASP* 3.3 5.6 - - - +
619B ARG* 1.3 77.4 - - + +
621B GLY* 1.3 57.3 + - - +
623B VAL* 3.6 7.0 + - - +
624B ARG* 3.0 41.0 + - - +
647B LEU* 6.1 1.8 - - + -
660B GLN* 4.9 14.6 - - - +
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Residues in contact with GLY 621 (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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613B ARG* 2.9 13.0 + - - -
618B ASP* 3.2 22.7 + - - -
620B VAL* 1.3 78.2 - - - +
622B ALA* 1.3 61.7 + - - +
624B ARG* 3.4 25.4 + - - +
625B THR* 2.9 27.9 + - - -
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Residues in contact with ALA 622 (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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610B ALA* 3.4 37.7 - - + +
613B ARG* 3.8 5.2 - - + +
614B SER* 4.0 3.8 - - - +
618B ASP 2.9 13.6 + - - +
619B ARG 3.2 8.0 + - - +
621B GLY* 1.3 71.7 - - - +
623B VAL* 1.3 66.5 + - - +
625B THR* 3.3 4.4 + - - -
626B LEU* 3.1 28.5 + - - +
646B THR* 4.0 18.2 - - + -
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Residues in contact with VAL 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ARG 2.9 20.5 + - - +
620B VAL* 3.7 6.7 - - - +
622B ALA* 1.3 75.5 - - - +
624B ARG* 1.3 57.3 - - - +
626B LEU* 3.1 5.2 + - - +
627B ASP* 2.9 33.2 + - - +
643B SER* 3.9 20.4 - - - +
646B THR* 4.4 7.9 - - + -
647B LEU* 3.9 33.2 - - + -
663B ASP* 5.3 1.3 - - - +
667B ARG* 3.3 35.4 - - - +
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Residues in contact with ARG 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ARG* 4.1 13.7 - - - +
618B ASP* 4.5 6.3 + - - -
620B VAL* 3.0 36.9 + - - +
621B GLY* 3.5 23.5 - - - +
622B ALA 3.3 0.2 - - - -
623B VAL* 1.3 78.1 - - - +
625B THR* 1.3 60.6 + - - +
627B ASP* 3.4 9.3 + - - +
628B GLU* 3.3 34.7 + - + +
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Residues in contact with THR 625 (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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596B TRP* 3.8 18.2 + - + +
606B ALA* 3.4 27.6 - - - +
609B LEU* 3.7 22.6 - - + +
610B ALA* 4.3 2.0 - - - +
613B ARG* 2.9 23.4 + - - +
621B GLY 2.9 18.0 + - - -
622B ALA* 3.4 11.2 - - - -
624B ARG* 1.3 75.6 - - - +
626B LEU* 1.3 63.5 + - - +
628B GLU* 3.2 27.9 + - - +
629B VAL* 3.9 3.5 + - - +
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Residues in contact with LEU 626 (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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606B ALA 4.7 2.2 - - - +
607B PHE* 3.7 42.6 - - + +
610B ALA* 3.9 19.7 - - + -
622B ALA 3.1 18.3 + - - +
623B VAL* 3.1 4.1 + - - +
625B THR* 1.3 75.2 - - - +
627B ASP* 1.3 67.1 + - - +
628B GLU 3.1 1.8 - - - -
629B VAL* 3.3 24.0 + - + +
639B ALA* 3.9 19.0 - - + +
640B ARG* 4.7 4.2 + - - -
642B THR* 4.0 11.0 - - + -
643B SER* 3.4 39.7 - - - +
646B THR* 4.1 7.9 - - - +
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Residues in contact with ASP 627 (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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623B VAL* 2.9 20.3 + - - +
624B ARG* 3.7 9.4 - - - +
625B THR 3.3 0.2 - - - -
626B LEU* 1.3 76.9 - - - +
628B GLU* 1.3 61.0 + - - +
629B VAL 3.5 4.2 + - - +
640B ARG* 3.0 41.8 + - - +
643B SER* 3.7 6.1 + - - -
667B ARG* 3.0 42.2 + - - -
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Residues in contact with GLU 628 (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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596B TRP* 2.9 44.1 + - + +
600B ASP* 4.6 7.0 - - + +
609B LEU* 5.6 0.2 - - - +
624B ARG* 3.3 25.4 + - + +
625B THR* 3.2 16.2 + - - +
626B LEU 3.1 1.0 - - - -
627B ASP* 1.3 77.2 - - - +
629B VAL* 1.3 61.7 + - - +
630B PRO* 3.3 10.4 - - - +
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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