Contacts of the helix formed by residues 192 - 200 (chain A) in PDB entry 1PD0
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 ASN 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A PRO* 3.0 4.8 + - - +
191A LYS* 1.3 85.9 - - - +
193A SER* 1.3 63.3 + - - +
194A SER* 2.9 27.0 + - - -
195A LEU* 3.0 18.8 + - - +
196A LEU* 3.1 18.9 + - - +
600A VAL* 4.2 11.7 - - - -
603A SER* 3.7 21.8 - - - +
637A GLU* 4.0 21.0 + - - +
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Residues in contact with SER 193 (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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192A ASN* 1.3 69.3 - - - +
194A SER* 1.3 60.5 + - - +
196A LEU* 2.7 30.4 + - - +
197A LYS* 2.7 16.0 + - - +
600A VAL* 2.6 32.0 + - - +
601A ASP* 3.0 16.9 + - - -
603A SER* 5.1 1.6 + - - +
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Residues in contact with SER 194 (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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192A ASN* 2.9 17.4 + - - +
193A SER* 1.3 78.0 - - - +
195A LEU* 1.3 56.9 + - - +
197A LYS* 3.6 9.2 + - - +
198A LYS* 3.0 29.4 + - - +
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Residues in contact with LEU 195 (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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190A PRO* 4.2 13.2 - - + -
191A LYS 4.3 1.8 - - - +
192A ASN* 3.0 23.1 + - - +
194A SER* 1.3 80.0 + - - +
196A LEU* 1.3 66.9 + - - +
198A LYS* 3.3 13.8 + - + +
199A SER* 3.0 22.0 + - - -
636A THR 3.7 9.6 - - - +
637A GLU* 3.4 42.2 - - + +
638A SER 4.4 0.2 - - - +
639A LEU* 4.0 29.4 - - + +
642A VAL* 4.4 10.3 - - + -
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Residues in contact with LEU 196 (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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186A LEU* 4.0 15.9 - - + -
190A PRO* 3.8 25.3 - - + +
192A ASN 3.1 12.4 + - - +
193A SER* 2.7 16.7 + - - +
195A LEU* 1.3 72.5 - - - +
197A LYS* 1.3 61.6 - - - +
199A SER* 2.6 24.9 + - - +
200A LYS* 3.4 3.6 + - - -
201A LEU 3.8 20.7 - - - +
203A PHE* 4.3 16.8 - - + +
598A VAL 5.0 2.7 - - - +
599A ASN* 5.2 0.9 - - - -
600A VAL* 3.9 37.9 - - + +
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Residues in contact with LYS 197 (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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193A SER 2.7 14.2 + - - +
194A SER* 3.8 9.9 - - - +
196A LEU* 1.3 78.7 - - - +
198A LYS* 1.3 61.3 + - - +
200A LYS* 3.6 25.6 + - - +
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Residues in contact with LYS 198 (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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194A SER 3.0 19.3 + - - +
195A LEU* 3.7 14.8 - - + +
196A LEU 3.1 0.4 - - - -
197A LYS* 1.3 75.1 - - - +
199A SER* 1.3 64.5 + - - +
200A LYS* 3.2 6.6 + - - +
639A LEU* 3.8 18.1 - - + +
685A THR* 3.3 16.3 + - - +
689A GLU* 3.7 29.7 + - - +
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Residues in contact with SER 199 (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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186A LEU* 5.6 0.2 - - - +
190A PRO* 5.3 0.2 - - - -
195A LEU 3.0 11.4 + - - -
196A LEU* 2.6 25.8 + - - +
198A LYS* 1.3 75.5 - - - +
200A LYS* 1.3 62.4 + - - +
201A LEU* 3.0 25.8 + - - +
639A LEU* 3.5 27.3 - - - +
642A VAL* 4.3 13.0 - - - +
643A TYR* 2.6 34.3 + - - -
685A THR* 3.5 1.2 - - - +
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Residues in contact with LYS 200 (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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196A LEU 3.4 4.8 + - - -
197A LYS* 3.6 17.4 + - - +
198A LYS 3.2 8.2 - - - +
199A SER* 1.3 82.4 + - - +
201A LEU* 1.3 63.2 + - - +
643A TYR* 4.5 0.7 - - - +
655A TYR* 3.7 14.2 + - - -
677A LYS* 5.0 7.9 - - - +
681A ASP* 4.3 38.8 + - + +
682A ILE* 4.1 9.8 - - - +
685A THR* 3.1 23.6 - - - +
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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