Contacts of the helix formed by residues 673 - 681 (chain B) in PDB entry 4PBZ
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 SER 673 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ASN* 5.0 0.4 - - - -
670B LYS* 4.7 11.3 - - - +
671B LEU 4.3 0.4 - - - -
672B LEU* 1.3 73.9 - - - +
674B SER* 1.3 60.0 + - - +
675B SER* 3.7 10.8 + - - -
676B GLU* 2.8 41.8 + - - +
677B THR* 2.9 31.0 + - - -
691B ARG* 4.8 8.9 - - - +
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Residues in contact with SER 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 3.7 33.7 + - - +
411A ASP* 5.4 2.9 + - - -
672B LEU 4.0 0.2 + - - -
673B SER* 1.3 72.2 - - - +
675B SER* 1.3 57.4 + - - +
677B THR* 3.0 2.8 + - - -
678B LYS* 2.7 53.6 + - - +
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Residues in contact with SER 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B SER* 3.2 10.2 - - - -
674B SER* 1.3 83.1 + - - +
676B GLU* 1.3 57.6 + - - +
678B LYS* 3.3 12.6 + - - +
679B ARG* 3.1 45.2 + - - +
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Residues in contact with GLU 676 (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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671B LEU 4.1 2.4 - - - +
672B LEU* 3.5 16.3 - - + +
673B SER* 2.8 37.3 + - - +
675B SER* 1.3 74.1 - - - +
677B THR* 1.3 59.6 + - - +
679B ARG* 3.8 18.3 - - - +
680B ALA* 3.0 27.7 + - - +
688B ILE* 5.9 1.5 - - + +
689B ALA 5.2 8.0 - - - +
691B ARG* 3.4 34.4 + - - +
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Residues in contact with THR 677 (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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30A PHE* 3.7 24.0 - - + +
31A LEU* 4.1 4.3 - - + +
407A ASN* 3.8 23.4 + - - +
408A ILE* 3.8 21.5 - - + -
672B LEU* 2.3 38.6 - - + +
673B SER 2.9 10.8 + - - -
674B SER 3.0 8.9 + - - -
676B GLU* 1.3 74.1 - - - +
678B LYS* 1.3 62.7 + - - +
680B ALA* 3.3 6.2 + - - +
681B ALA* 3.0 26.5 + - - +
688B ILE* 6.3 0.2 - - + -
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Residues in contact with LYS 678 (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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349A LYS* 5.1 11.7 - - - +
367A LEU* 4.8 1.0 - - + +
407A ASN* 2.5 32.1 + - - +
408A ILE* 3.8 24.1 + - + +
409A TYR 6.0 0.2 - - - -
410A ASN 4.8 0.2 + - - -
411A ASP* 3.7 30.8 - - - +
674B SER* 2.7 36.7 + - - +
675B SER* 3.3 9.6 + - - +
677B THR* 1.3 73.6 - - - +
679B ARG* 1.3 61.1 + - - +
681B ALA* 3.3 20.6 - - - +
682B ARG* 3.5 16.9 - - - -
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Residues in contact with ARG 679 (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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355A SER* 4.7 5.5 + - - -
357A GLU* 4.9 9.6 - - - +
358A ASP* 3.0 38.7 + - - +
361A ASP* 4.1 2.0 - - - +
675B SER* 3.1 39.2 + - - +
676B GLU* 3.8 15.8 - - - +
678B LYS* 1.3 77.8 - - - +
680B ALA* 1.3 62.0 + - - +
682B ARG* 3.2 21.8 + - - +
683B ARG* 3.3 51.2 + - - +
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Residues in contact with ALA 680 (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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31A LEU* 4.0 13.7 - - + +
676B GLU 3.0 19.8 + - - +
677B THR* 3.3 6.3 + - - +
679B ARG* 1.3 73.2 - - - +
681B ALA* 1.3 63.8 + - - +
682B ARG 3.0 2.5 - - - -
683B ARG* 3.1 30.0 + - - +
684B PRO 3.8 1.0 - - - -
688B ILE* 3.7 38.6 - - + -
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Residues in contact with ALA 681 (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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31A LEU* 4.0 9.5 - - - +
367A LEU 3.5 18.2 - - - +
368A PHE* 3.7 18.3 - - + -
369A ILE* 3.1 31.9 + - - +
408A ILE* 4.0 14.4 - - + -
677B THR 3.0 13.8 + - - +
678B LYS* 3.3 15.0 - - - +
679B ARG 3.2 0.4 - - - -
680B ALA* 1.3 76.5 - - - +
682B ARG* 1.3 57.2 + - - +
683B ARG 3.4 0.8 + - - -
684B PRO* 4.6 1.0 - - - +
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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