Contacts of the helix formed by residues 198 - 206 (chain B) in PDB entry 4PIM
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B LYS* 1.3 75.2 - - - +
199B THR* 1.3 67.3 + - - +
200B GLY* 3.0 23.9 + - - -
201B ARG* 3.0 35.7 + - + +
202B LEU* 3.2 18.5 + - - +
204B ARG* 4.5 2.3 + - - -
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Residues in contact with THR 199 (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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196B VAL* 6.4 0.2 - - + -
197B LYS 4.0 7.2 - - - +
198B ASP* 1.3 72.5 + - - +
200B GLY* 1.3 66.5 + - - +
202B LEU* 3.3 7.7 + - - +
203B VAL* 3.0 29.6 + - - +
243B TRP* 3.5 43.9 - - + +
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Residues in contact with GLY 200 (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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198B ASP* 3.0 9.5 + - - -
199B THR* 1.3 82.4 + - - +
201B ARG* 1.3 55.4 + - - +
203B VAL* 4.0 4.2 - - - +
204B ARG* 3.0 53.2 + - - +
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Residues in contact with ARG 201 (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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55B GLU 4.6 2.3 - - - +
57B TYR* 4.0 29.4 - - + +
197B LYS* 3.9 21.6 - - + +
198B ASP* 3.0 33.9 + - - +
200B GLY* 1.3 75.8 - - - +
202B LEU* 1.3 62.6 + - - +
204B ARG* 3.5 22.6 + - - +
205B ALA* 3.0 24.1 + - - +
311B ALA* 5.7 0.6 - - - +
313B ASP* 2.8 43.4 + - - -
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Residues in contact with LEU 202 (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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57B TYR* 3.3 25.6 - - + +
195B LEU 4.6 0.2 - - - +
197B LYS* 3.5 39.5 - - + +
198B ASP 3.2 7.2 + - - +
199B THR* 3.6 9.6 - - - +
200B GLY 3.3 0.2 - - - -
201B ARG* 1.3 77.8 - - - +
203B VAL* 1.3 61.4 + - - +
205B ALA* 3.1 7.9 + - - +
206B TYR* 3.1 27.4 - - + -
243B TRP* 3.6 32.8 - - + -
250B ILE* 3.8 14.6 - - + -
286B LYS* 3.9 30.1 - - + -
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Residues in contact with VAL 203 (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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199B THR* 3.0 20.7 + - - +
200B GLY* 4.0 4.9 - - - +
202B LEU* 1.3 74.6 - - - +
204B ARG* 1.3 66.0 + - + +
206B TYR* 3.0 15.4 + - - +
207B ASP* 3.0 22.6 + - + +
241B ALA* 3.8 20.5 - - - +
242B LYS* 4.6 1.8 - - - -
243B TRP* 4.1 29.6 - - + +
250B ILE* 3.9 10.8 - - + -
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Residues in contact with ARG 204 (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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55B GLU* 3.3 29.9 - - + +
198B ASP* 4.5 2.2 + - - -
200B GLY* 3.0 35.0 + - - +
201B ARG* 3.7 32.8 - - - +
203B VAL* 1.3 78.3 - - + +
205B ALA* 1.3 63.2 + - - +
206B TYR 3.1 0.5 + - - -
207B ASP 3.2 26.2 + - - +
208B ASP 3.4 1.2 + - - -
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Residues in contact with ALA 205 (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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50B ILE* 5.1 0.5 - - - +
55B GLU* 3.4 27.4 + - - +
56B TYR* 3.4 30.2 - - + +
57B TYR* 4.1 15.5 - - + -
58B PRO* 5.1 0.4 - - + -
201B ARG 3.0 12.7 + - - +
202B LEU* 3.1 11.2 + - - +
204B ARG* 1.3 75.8 - - - +
206B TYR* 1.3 72.1 + - + +
207B ASP 3.5 0.2 - - - -
208B ASP* 5.0 1.6 - - - +
213B THR* 4.3 8.0 + - - +
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Residues in contact with TYR 206 (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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56B TYR* 4.0 14.6 - + - -
57B TYR* 5.6 0.7 - - - -
58B PRO* 4.6 2.5 - - + +
194B ASP* 5.5 0.4 - - - -
202B LEU* 3.1 20.2 - - + -
203B VAL 3.0 8.0 + - - +
205B ALA* 1.3 88.1 - - + +
207B ASP* 1.3 59.7 + - - +
213B THR* 3.3 15.8 - - + +
239B HIS* 2.8 24.1 + - - -
241B ALA* 3.5 8.9 - - + +
250B ILE* 3.7 35.9 - - + -
252B MSE 4.1 20.4 - - - -
282B GLU* 4.2 5.4 - - - -
284B SER* 2.9 13.2 + - - -
286B LYS* 2.8 28.3 + - - -
401B ACT 2.6 36.8 + - - -
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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