Contacts of the helix formed by residues 198 - 203 (chain D) in PDB entry 1SJB
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 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D PRO* 5.0 4.2 - - - +
193D ALA 4.4 1.7 - - - +
194D TYR* 3.4 31.1 - - + +
195D THR* 2.4 61.7 + - - +
197D GLY* 1.4 66.2 - - - -
199D ALA* 1.3 51.5 + - - +
200D PRO* 3.1 4.9 - - - -
201D GLN* 2.7 38.8 + - + +
202D LEU* 3.1 6.6 + - + +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D THR 3.6 1.8 + - - -
196D LEU* 3.0 18.5 + - + +
198D ASP* 1.3 76.6 - - - +
200D PRO* 1.3 59.1 - - + +
202D LEU* 3.1 4.3 + - - +
203D ALA* 2.5 37.5 + - - +
228D LEU* 3.7 26.9 - - + -
231D ARG* 4.2 27.8 - - + +
232D ILE* 3.6 3.3 - - - +
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Residues in contact with PRO 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D LEU 4.3 0.2 - - - +
197D GLY 3.5 14.1 - - - +
198D ASP 3.1 4.7 - - - -
199D ALA* 1.3 100.7 - - + +
201D GLN* 1.3 60.4 + - - +
203D ALA* 3.3 10.2 + - + +
204D ARG* 3.2 22.4 + - - +
231D ARG* 5.4 3.1 - - - +
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Residues in contact with GLN 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PRO* 6.3 0.9 - - + -
169D ASP* 3.0 30.6 + - - +
170D VAL* 3.6 28.1 - - - +
194D TYR* 4.8 8.7 - - + -
198D ASP* 2.7 21.6 + - + +
200D PRO* 1.3 78.5 - - - +
202D LEU* 1.3 60.0 + - + +
204D ARG* 2.9 56.9 + - - +
205D LEU* 4.7 0.5 - - - +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 4.7 4.3 - - + -
169D ASP* 4.8 3.4 - - - +
194D TYR* 3.6 59.9 - - + +
195D THR 5.0 1.6 - - - +
198D ASP 3.1 16.0 + - - +
199D ALA* 3.7 7.2 - - - +
201D GLN* 1.3 75.9 - - + +
203D ALA* 1.3 62.3 + - - +
204D ARG 2.9 5.7 + - - -
205D LEU* 3.2 28.2 + - + +
206D ASP* 4.2 3.1 + - - +
213D ILE* 4.5 15.3 - - + -
216D PRO* 4.1 19.5 - - + -
228D LEU* 4.5 12.8 - - + -
232D ILE* 3.9 21.2 - - + +
234D THR* 5.2 1.2 + - - -
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ALA 2.5 21.0 + - - +
200D PRO* 3.4 13.0 - - + +
201D GLN 3.1 0.2 - - - -
202D LEU* 1.3 74.1 - - - +
204D ARG* 1.3 56.1 + - - +
205D LEU 3.2 0.9 - - - -
206D ASP* 3.0 37.0 - - - +
207D PRO* 4.0 1.0 - - - +
231D ARG 4.0 9.0 - - - +
232D ILE* 3.5 17.2 - - + +
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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