Contacts of the helix formed by residues 602 - 616 (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 VAL 602 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B SER* 4.3 9.6 - - - +
570B LEU* 4.8 1.3 - - + -
574B LEU* 3.7 25.8 - - + -
595B VAL* 3.7 27.4 - - + -
596B TRP* 3.3 8.8 - - - -
599B ASN* 3.1 36.3 + - + +
601B GLY* 1.3 77.3 - - - +
603B ILE* 1.3 57.9 + - - +
604B SER* 3.3 2.0 - - - +
605B ALA* 2.9 27.0 + - + +
754B GOL 3.9 27.4 - - - +
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Residues in contact with ILE 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN* 6.2 1.1 - - - +
481A ASP* 4.1 10.3 - - + +
421B THR* 4.1 10.9 - - + +
424B VAL* 3.9 11.4 - - + -
596B TRP* 4.0 17.5 - - + -
600B ASP 4.6 1.1 - - - +
601B GLY* 3.2 19.8 + - - +
602B VAL* 1.3 68.9 - - - +
604B SER* 1.3 67.0 + - - +
605B ALA 3.0 2.0 - - - -
606B ALA* 3.0 12.2 + - - +
607B PHE* 3.3 39.3 + - + -
629B VAL* 4.4 13.7 - - + -
630B PRO* 4.8 4.7 - - + -
633B SER* 3.3 35.2 - - - +
635B HIS* 4.0 13.5 - - + -
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Residues in contact with SER 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B SER 4.2 2.4 + - - -
421B THR* 3.3 13.5 - - - +
422B PHE* 2.9 70.7 + - - +
424B VAL* 4.9 2.2 - - - -
574B LEU* 4.5 11.0 - - - +
592B TYR* 4.1 4.0 - - - -
602B VAL* 3.3 1.3 - - - -
603B ILE* 1.3 77.9 - - - +
605B ALA* 1.3 57.1 + - - +
607B PHE* 3.8 2.4 + - - +
608B GLY* 3.0 23.9 + - - -
611B ARG* 4.9 0.9 + - - -
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Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 4.1 8.6 - - + +
592B TYR* 3.7 25.6 - - + +
595B VAL* 3.7 28.3 - - + -
596B TRP* 3.9 8.4 - - + +
602B VAL 2.9 14.9 + - - +
604B SER* 1.3 78.9 - - - +
606B ALA* 1.3 58.9 + - - +
609B LEU* 2.8 33.8 + - - +
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Residues in contact with ALA 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B TRP* 3.7 42.4 - - + +
602B VAL 3.7 2.6 + - - -
603B ILE 3.0 9.5 + - - +
605B ALA* 1.3 77.5 - - - +
607B PHE* 1.3 62.6 + - + +
610B ALA* 3.0 21.8 + - - +
625B THR* 3.4 19.2 - - + +
626B LEU* 4.7 2.8 - - + +
629B VAL* 3.7 19.1 - - + -
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 3.6 20.2 - - - +
424B VAL* 3.5 40.6 - - + -
603B ILE* 3.3 39.9 + - + +
604B SER 4.2 3.4 - - - +
606B ALA* 1.3 80.8 - - + +
608B GLY* 1.3 56.4 + - - +
610B ALA* 3.4 5.2 + - + +
611B ARG* 3.0 37.9 + - - +
626B LEU* 3.7 18.4 - - + -
629B VAL* 4.5 5.2 - - + -
635B HIS* 4.2 4.7 - - + -
638B THR 4.1 0.4 - - - -
639B ALA* 3.5 33.0 - - + -
642B THR* 3.5 28.3 - - + -
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Residues in contact with GLY 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B GLU* 4.7 1.7 - - - +
592B TYR* 3.4 29.2 - - - -
604B SER 3.0 18.0 + - - -
605B ALA 3.9 0.2 - - - -
607B PHE* 1.3 77.6 - - - +
609B LEU* 1.3 60.0 + - - +
611B ARG* 3.5 25.4 + - - +
612B ALA* 3.2 18.0 + - - +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B TYR* 3.8 13.8 - - + -
593B GLN* 3.9 39.5 - - + +
596B TRP* 4.0 16.6 - - + -
605B ALA 2.8 21.3 + - - +
606B ALA 3.9 2.7 - - - +
608B GLY* 1.3 69.6 - - - +
610B ALA* 1.3 61.9 + - - +
612B ALA* 3.2 9.8 + - + +
613B ARG* 2.8 58.9 + - + +
625B THR* 3.7 26.5 - - + +
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Residues in contact with ALA 610 (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 3.0 18.1 + - - +
607B PHE* 3.8 4.5 - - - +
609B LEU* 1.3 73.1 - - - +
611B ARG* 1.3 61.7 + - - +
613B ARG* 3.2 1.0 + - - +
614B SER* 2.8 28.9 + - - -
622B ALA* 3.4 42.0 - - + +
625B THR* 4.5 3.4 - - - -
626B LEU* 3.9 19.5 - - + -
642B THR* 6.1 1.1 - - + -
646B THR* 5.7 0.9 - - - +
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 4.8 3.6 - - - -
423B GLY* 2.9 29.7 + - - -
426B LEU* 3.4 30.9 - - - +
427B LEU* 5.2 16.2 - - + -
444B LEU* 4.1 8.5 - - - +
581B GLU* 2.7 45.5 + - - +
592B TYR* 4.2 2.0 + - - -
604B SER 4.9 0.6 + - - -
607B PHE* 3.0 27.5 + - - +
608B GLY* 3.5 18.8 - - - +
610B ALA* 1.3 76.5 - - + +
612B ALA* 1.3 58.0 + - - +
614B SER* 3.2 7.5 + - - -
615B ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B TYR* 5.1 6.3 - - + -
608B GLY 3.2 11.4 + - - +
609B LEU* 3.2 16.7 + - + +
611B ARG* 1.3 80.9 - - - +
613B ARG* 1.3 63.7 + - + +
615B ALA* 3.5 6.1 + - - +
616B GLU* 3.0 37.2 + - - +
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B GLN* 3.1 27.1 + - - +
609B LEU* 2.8 42.3 + - + +
610B ALA 3.7 3.8 - - - +
612B ALA* 1.3 70.5 - - + +
614B SER* 1.3 63.6 + - - +
616B GLU* 3.2 10.8 + - - +
617B GLY 3.2 0.3 + - - -
618B ASP* 2.9 52.4 + - + +
621B GLY* 2.9 32.1 + - - -
622B ALA* 3.8 4.5 - - + +
624B ARG* 4.1 15.1 - - - +
625B THR* 2.9 25.4 + - - +
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Residues in contact with SER 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 5.8 2.6 - - - +
610B ALA 2.8 20.2 + - - -
611B ARG* 3.4 8.1 - - - -
613B ARG* 1.3 71.3 - - - +
615B ALA* 1.3 62.9 + - - +
616B GLU 3.0 1.6 + - - -
617B GLY* 3.1 12.9 + - - +
618B ASP 4.7 4.7 - - - +
619B ARG* 4.8 7.7 - - - +
622B ALA* 4.0 3.7 - - - +
646B THR* 3.3 32.7 + - - +
649B SER* 5.4 5.7 - - - -
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Residues in contact with ALA 615 (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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611B ARG 2.8 20.4 + - - +
612B ALA* 3.5 10.8 - - - +
613B ARG 3.3 0.4 - - - -
614B SER* 1.3 72.7 - - - +
616B GLU* 1.3 67.0 + - + +
617B GLY 3.6 0.2 - - - -
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Residues in contact with GLU 616 (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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586B THR* 4.3 27.7 + - - +
612B ALA* 3.0 28.7 + - - +
613B ARG* 3.2 5.2 + - - +
614B SER 3.0 0.6 - - - -
615B ALA* 1.3 86.5 - - + +
617B GLY* 1.3 56.5 + - - +
618B ASP* 3.5 4.3 + - + +
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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