Contacts of the helix formed by residues 199 - 203 (chain D) in PDB entry 4KEU
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 HIS 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D HIS* 3.6 22.4 - + - -
137D KCX 3.1 7.1 + - - -
170D HIS* 2.8 50.6 + + - +
171D SER* 3.4 20.6 - - - +
173D ALA* 3.3 15.2 - - - +
198D GLY* 1.3 70.4 - - - +
200D LEU* 1.3 64.4 + - - +
201D GLY 3.0 2.5 - - - +
202D ASP* 3.1 27.5 + - - +
220D GLY 3.3 0.4 + - - -
222D ASP* 2.8 44.0 + - - -
223D ARG* 3.4 27.8 + - - -
256D ASP* 3.6 13.0 + - - -
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Residues in contact with LEU 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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171D SER* 4.2 10.1 - - - +
173D ALA* 4.3 6.7 - - - -
197D ILE* 3.6 30.5 - - + +
198D GLY 4.3 0.2 - - - +
199D HIS* 1.3 79.3 - - - +
201D GLY* 1.3 56.8 + - - +
202D ASP 3.0 4.5 + - - -
203D THR* 3.2 22.2 - - - +
208D TYR* 3.7 33.0 - - + +
209D ILE* 3.4 25.9 - - + +
212D ILE* 3.7 22.0 - - + -
219D ILE* 3.5 33.9 - - + -
220D GLY 3.0 9.6 + - - +
221D LEU* 4.3 1.6 - - + -
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Residues in contact with GLY 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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199D HIS* 3.0 2.2 - - - +
200D LEU* 1.3 74.9 - - - +
202D ASP* 1.3 58.3 + - - +
203D THR 3.2 7.5 - - - +
209D ILE* 5.2 0.2 - - - -
220D GLY 3.0 9.1 + - - -
221D LEU* 3.8 24.4 - - - +
222D ASP* 4.8 0.4 - - - -
230D LEU* 3.3 17.8 - - - +
235D ARG* 3.1 29.7 + - - +
238D THR* 6.0 2.0 - - - -
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Residues in contact with ASP 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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171D SER 5.0 0.5 - - - +
172D ASN* 5.9 0.3 - - - -
173D ALA* 3.8 11.9 + - + +
174D HIS* 3.7 15.8 + - + +
199D HIS* 3.3 19.8 - - - +
200D LEU 3.0 1.4 - - - -
201D GLY* 1.3 78.0 - - - +
203D THR* 1.3 57.4 + - - +
223D ARG* 2.8 43.1 + - - +
229D PHE* 3.4 35.5 - - + +
230D LEU* 3.6 9.7 - - - +
235D ARG* 2.8 26.9 + - - +
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Residues in contact with THR 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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173D ALA* 3.8 25.6 + - + +
174D HIS* 3.9 18.0 + - - -
200D LEU* 3.2 22.3 - - - +
201D GLY 4.0 2.3 - - - +
202D ASP* 1.3 80.3 - - - +
204D ASP* 1.3 63.2 + - - +
205D ASN* 3.0 26.1 + - + +
208D TYR* 4.7 5.6 - - + -
209D ILE* 3.8 22.4 - - + +
230D LEU* 3.9 11.5 - - - +
238D THR* 4.1 6.1 - - - +
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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