Contacts of the helix formed by residues 657 - 670 (chain A) 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 THR 657 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A VAL* 1.3 78.2 - - - +
658A GLU* 1.3 63.9 + - - +
659A GLU* 3.4 13.7 + - - +
660A GLN* 3.0 42.6 + - - +
661A ILE* 3.2 25.8 + - - +
692A TRP* 3.9 6.1 - - - +
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Residues in contact with GLU 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A THR* 1.3 74.4 - - - +
659A GLU* 1.3 54.1 + - - +
661A ILE* 3.0 8.1 + - + +
662A ARG* 2.8 44.1 + - - +
692A TRP* 3.3 40.1 - - + -
697A LYS 3.7 3.1 - - - +
698A ALA* 4.1 0.4 - - - -
699A SER* 3.3 39.9 + - - -
700A THR* 3.4 24.3 + - - -
708A PHE* 3.5 20.8 - - + -
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Residues in contact with GLU 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A THR* 3.3 11.2 + - - +
658A GLU* 1.3 79.7 - - - +
660A GLN* 1.3 57.0 + - - +
662A ARG* 3.6 33.8 + - - +
663A ASP* 2.9 41.7 + - - +
666A ARG* 4.8 3.6 - - - +
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Residues in contact with GLN 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A ARG* 2.8 39.1 + - - +
620A VAL* 5.2 14.1 - - + +
647A LEU* 3.9 22.6 - - + +
648A LEU* 5.3 1.1 - - - -
656A VAL* 3.5 16.0 - - + +
657A THR* 3.0 42.3 + - - +
658A GLU 3.2 0.2 - - - -
659A GLU* 1.3 77.3 - - - +
661A ILE* 1.3 59.5 + - - +
663A ASP* 3.2 12.1 + - - +
664A ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A LEU* 4.1 16.6 - - + -
656A VAL* 3.6 21.1 - - + -
657A THR 3.2 23.0 + - - +
658A GLU* 3.0 10.1 + - - +
660A GLN* 1.3 76.9 - - - +
662A ARG* 1.3 59.2 + - - +
664A ALA* 3.4 8.1 + - - +
665A ALA* 2.9 26.7 + - - +
685A VAL* 4.6 4.6 - - + +
688A GLY 4.7 2.5 - - - +
689A ALA* 3.9 30.3 - - + +
692A TRP* 3.7 29.6 - - + -
703A ILE* 3.9 24.0 - - + -
708A PHE* 4.7 6.7 - - + -
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Residues in contact with ARG 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A GLU* 2.8 32.1 + - + +
659A GLU* 3.6 30.7 + - - +
660A GLN 3.2 0.2 - - - -
661A ILE* 1.3 75.2 - - - +
663A ASP* 1.3 59.8 + - - +
665A ALA* 3.2 6.8 + - - +
666A ARG* 2.8 69.9 + - - +
699A SER* 5.4 3.4 + - - -
700A THR* 3.7 29.2 + - + +
703A ILE* 4.3 17.0 - - + -
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Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A VAL* 6.1 0.7 - - + -
647A LEU* 3.7 14.0 - - + +
659A GLU* 2.9 30.9 + - - +
660A GLN* 3.3 14.5 - - - +
662A ARG* 1.3 74.1 - - - +
664A ALA* 1.3 64.3 + - - +
666A ARG* 3.2 30.9 + - - +
667A ARG* 3.0 43.6 + - - +
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Residues in contact with ALA 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ALA* 3.7 25.8 - - - +
647A LEU* 3.6 18.8 - - + +
648A LEU* 4.1 15.7 - - + -
660A GLN 2.9 15.7 + - - +
661A ILE* 3.6 7.2 - - - +
663A ASP* 1.3 77.0 - - - +
665A ALA* 1.3 58.1 + - - +
667A ARG* 3.5 2.3 + - - +
668A VAL* 3.0 29.9 + - - +
685A VAL* 4.2 6.7 - - + -
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Residues in contact with ALA 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A ILE 2.9 17.4 + - - +
662A ARG* 3.2 6.9 + - - +
664A ALA* 1.3 74.0 - - - +
666A ARG* 1.3 60.7 + - + +
668A VAL* 3.2 2.2 + - - -
669A GLU* 2.8 36.3 + - - +
685A VAL* 4.0 9.4 - - + +
703A ILE* 3.9 30.5 - - + -
704A LEU* 3.4 16.5 - - + +
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Residues in contact with ARG 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A GLU* 4.1 4.8 + - - +
662A ARG* 2.8 64.6 + - - +
663A ASP* 3.2 30.0 + - - +
665A ALA* 1.3 78.6 - - - +
667A ARG* 1.3 66.6 + - - +
669A GLU* 3.5 26.2 + - - +
670A ALA* 3.9 9.4 + - - +
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Residues in contact with ARG 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A VAL* 3.6 19.7 - - - +
627A ASP* 3.0 38.7 + - - -
640A ARG* 3.6 45.7 - - - +
643A SER* 3.4 22.5 - - - -
644A ALA* 4.6 3.4 - - + +
647A LEU* 4.8 2.5 - - - -
663A ASP* 3.0 49.0 + - - +
664A ALA 3.9 6.5 - - - +
665A ALA 3.2 0.2 - - - -
666A ARG* 1.3 84.0 - - + +
668A VAL* 1.3 59.3 + - - +
670A ALA* 4.3 3.6 + - - +
671A LEU* 3.4 21.4 - - - +
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Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LEU* 4.5 8.5 - - + -
644A ALA* 3.7 13.7 - - + -
664A ALA 3.0 18.6 - - - +
665A ALA* 3.2 4.9 + - - +
667A ARG* 1.3 76.3 - - - +
669A GLU* 1.3 64.7 + - - +
670A ALA 3.3 0.9 - - - -
671A LEU* 3.2 27.5 + - - +
678A VAL* 4.3 7.8 - - + +
681A ILE* 3.8 8.5 - - + -
682A ARG* 3.6 42.7 + - + +
685A VAL* 3.7 22.4 - - + -
704A LEU* 4.3 6.3 - - + -
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Residues in contact with GLU 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A ALA* 2.8 18.5 + - - +
666A ARG* 3.6 23.4 - - - +
667A ARG 3.4 0.2 - - - -
668A VAL* 1.3 78.9 - - - +
670A ALA* 1.3 62.7 + - + +
671A LEU 3.3 5.7 + - - +
682A ARG* 4.8 7.9 + - - +
702A HIS* 3.8 22.2 + - - -
704A LEU* 3.8 33.4 + - + +
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Residues in contact with ALA 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A ARG 3.9 9.3 + - - +
667A ARG* 4.8 2.5 - - - +
668A VAL 3.3 1.0 - - - -
669A GLU* 1.3 79.8 - - - +
671A LEU* 1.3 70.1 - - + +
672A PRO* 3.9 3.8 - - - +
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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