Contacts of the helix formed by residues 215 - 224 (chain A) in PDB entry 4J44
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 ARG 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A HIS* 5.7 3.2 - - - -
179A LEU* 4.2 11.0 - - - +
183A GLU* 2.9 38.6 + - - +
210A TRP* 4.3 1.3 - - - -
213A GLY* 3.5 17.5 + - - +
214A ASP* 1.3 95.0 + - - +
216A ALA* 1.3 66.6 + - - +
217A TRP* 3.4 2.2 - - + +
218A SER* 3.2 23.1 + - - +
219A GLU* 3.0 25.3 + - - +
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Residues in contact with ALA 216 (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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179A LEU* 3.7 3.7 - - + +
183A GLU* 2.9 33.0 + - + +
184A LEU* 4.0 22.4 - - + -
187A ALA* 3.7 20.6 - - + +
189A LEU* 4.2 4.7 - - + +
210A TRP* 4.1 12.2 - - - -
215A ARG* 1.3 71.9 - - - +
217A TRP* 1.3 63.7 + - - +
219A GLU* 3.9 1.4 - - - +
220A HIS* 2.9 24.9 + - - +
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Residues in contact with TRP 217 (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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183A GLU* 4.7 5.3 + - + +
186A SER* 3.5 26.2 + - - -
187A ALA* 3.6 27.9 - - + +
215A ARG* 3.4 2.5 - - + +
216A ALA* 1.3 79.1 - - + +
218A SER* 1.3 59.2 + - - +
220A HIS* 3.3 6.6 + - - +
221A ARG* 2.9 35.3 + - - +
229A PHE* 3.4 37.0 - + - -
230A VAL* 3.9 32.3 - - + -
233A ARG* 3.5 61.9 - - + +
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Residues in contact with SER 218 (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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215A ARG* 3.2 31.0 + - - +
217A TRP* 1.3 79.3 - - - +
219A GLU* 1.3 64.1 + - - +
221A ARG* 3.8 25.8 - - - +
222A ARG* 2.8 32.2 + - - +
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Residues in contact with GLU 219 (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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207A LEU* 4.2 5.5 - - + +
210A TRP* 3.7 28.3 - - + -
214A ASP* 3.8 22.0 - - + +
215A ARG 3.0 21.2 + - - +
218A SER* 1.3 78.7 + - - +
220A HIS* 1.3 64.7 + - - +
222A ARG* 2.9 35.3 + - - -
223A HIS* 3.0 39.0 + - + +
1B ALA* 2.8 27.0 + - + +
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Residues in contact with HIS 220 (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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187A ALA 2.8 28.4 + - - -
189A LEU* 3.9 11.0 - - + +
200A CYS* 3.3 19.7 - - + +
207A LEU* 4.1 11.3 - - + +
216A ALA 2.9 18.8 + - - +
217A TRP* 3.5 10.5 - - + +
219A GLU* 1.3 76.1 - - - +
221A ARG* 1.3 57.9 + - - +
224A PHE* 2.9 43.0 + + + +
227A CYS* 3.6 2.8 - - - -
229A PHE* 4.6 5.8 - + - -
230A VAL* 3.5 19.3 - - + +
501A ZN 2.1 36.9 - - - -
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Residues in contact with ARG 221 (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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217A TRP* 2.9 22.3 + - + +
218A SER* 3.8 24.4 + - - +
220A HIS* 1.3 74.9 - - - +
222A ARG* 1.3 65.9 + - - +
224A PHE 4.5 0.7 - - - -
225A PRO* 3.3 27.8 - - + +
230A VAL* 3.9 30.5 - - + -
233A ARG* 3.8 22.8 - - - +
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Residues in contact with ARG 222 (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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218A SER 2.8 18.9 + - - +
219A GLU* 2.9 39.5 + - - +
221A ARG* 1.3 79.3 - - - +
223A HIS* 1.3 83.4 + - + +
225A PRO* 3.9 6.9 - - - +
1B ALA 3.3 10.7 + - - +
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Residues in contact with HIS 223 (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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207A LEU* 3.5 16.6 - - + -
219A GLU* 3.0 34.3 + - - +
222A ARG* 1.3 106.8 + - - +
224A PHE* 1.3 90.8 + - + +
225A PRO* 3.4 6.8 - - - +
1B ALA 3.0 28.5 + - - -
2B ILE* 4.1 1.6 - - + -
3B ALA* 3.9 22.6 - - + +
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Residues in contact with PHE 224 (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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189A LEU* 6.3 0.4 - - + -
203A CYS* 3.8 21.1 - - + -
205A GLY* 3.5 36.1 - - - -
206A LYS 3.6 15.7 - - - -
207A LEU* 3.7 25.1 - - + -
220A HIS* 2.9 37.2 + + + +
223A HIS* 1.3 91.8 - - + +
225A PRO* 1.3 65.2 - - - +
226A ASN* 3.1 10.3 + - - +
227A CYS* 3.2 16.4 + - + +
230A VAL* 3.9 3.8 - - - +
3B ALA* 3.9 19.3 - - + -
4B VAL 5.9 1.1 - - - -
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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